Starting phenix.real_space_refine on Sun Mar 10 17:03:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/03_2024/7xq2_33389_neut_updated.pdb" } resolution = 3.3 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= 0.004 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 4 5.49 5 S 10 5.16 5 C 2222 2.51 5 N 565 2.21 5 O 576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 26": "NH1" <-> "NH2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A ARG 133": "NH1" <-> "NH2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A TYR 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 330": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3377 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3377 Unusual residues: {'1SY': 2} Classifications: {'peptide': 409, 'undetermined': 2} Link IDs: {'PTRANS': 14, 'TRANS': 394, None: 2} Not linked: pdbres="HIS A 457 " pdbres="1SY A 601 " Not linked: pdbres="1SY A 601 " pdbres="1SY A 602 " Chain breaks: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.68 Number of scatterers: 3377 At special positions: 0 Unit cell: (80, 75, 67, 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 10 16.00 P 4 15.00 O 576 8.00 N 565 7.00 C 2222 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: 1.35 Conformation dependent library (CDL) restraints added in 717.1 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 0 sheets defined 72.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 3.727A pdb=" N TRP A 25 " --> pdb=" O GLU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 39 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 61 through 64 No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 69 through 89 removed outlier: 3.686A pdb=" N SER A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 76 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix removed outlier: 3.751A pdb=" N ASP A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 112 Processing helix chain 'A' and resid 116 through 131 removed outlier: 3.630A pdb=" N GLN A 120 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 removed outlier: 3.605A pdb=" N ILE A 140 " --> pdb=" O TYR A 136 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N PHE A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 152 through 175 removed outlier: 3.502A pdb=" N SER A 168 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 254 through 257 No H-bonds generated for 'chain 'A' and resid 254 through 257' Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.601A pdb=" N TRP A 270 " --> pdb=" O GLN A 266 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 278 " --> pdb=" O TRP A 274 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR A 282 " --> pdb=" O SER A 278 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 330 removed outlier: 3.940A pdb=" N SER A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 353 removed outlier: 3.729A pdb=" N ALA A 344 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N THR A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 351 " --> pdb=" O ALA A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 387 removed outlier: 3.633A pdb=" N ILE A 362 " --> pdb=" O PRO A 359 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N TRP A 363 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 364 " --> pdb=" O SER A 361 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 366 " --> pdb=" O TRP A 363 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 368 " --> pdb=" O CYS A 365 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N LEU A 371 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 373 " --> pdb=" O VAL A 370 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY A 374 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR A 376 " --> pdb=" O ARG A 373 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 377 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL A 380 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.862A pdb=" N THR A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N PHE A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 386 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE A 387 " --> pdb=" O THR A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 417 removed outlier: 3.778A pdb=" N LEU A 398 " --> pdb=" O GLU A 394 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 414 " --> pdb=" O VAL A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 454 removed outlier: 3.691A pdb=" N GLN A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU A 434 " --> pdb=" O LYS A 430 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) 168 hydrogen bonds defined for protein. 483 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: 0.86 Time building geometry restraints manager: 1.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 470 1.31 - 1.44: 1079 1.44 - 1.56: 1905 1.56 - 1.68: 1 1.68 - 1.80: 24 Bond restraints: 3479 Sorted by residual: bond pdb=" O28 1SY A 601 " pdb=" P27 1SY A 601 " ideal model delta sigma weight residual 1.636 1.754 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O28 1SY A 602 " pdb=" P27 1SY A 602 " ideal model delta sigma weight residual 1.636 1.752 -0.116 2.00e-02 2.50e+03 3.35e+01 bond pdb=" C25 1SY A 601 " pdb=" O26 1SY A 601 " ideal model delta sigma weight residual 1.396 1.483 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C25 1SY A 602 " pdb=" O26 1SY A 602 " ideal model delta sigma weight residual 1.396 1.482 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" O17 1SY A 602 " pdb=" P18 1SY A 602 " ideal model delta sigma weight residual 1.650 1.729 -0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 3474 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.59: 73 105.59 - 112.69: 1829 112.69 - 119.78: 1181 119.78 - 126.88: 1616 126.88 - 133.98: 62 Bond angle restraints: 4761 Sorted by residual: angle pdb=" N ARG A 330 " pdb=" CA ARG A 330 " pdb=" C ARG A 330 " ideal model delta sigma weight residual 111.69 118.11 -6.42 1.23e+00 6.61e-01 2.73e+01 angle pdb=" N SER A 321 " pdb=" CA SER A 321 " pdb=" C SER A 321 " ideal model delta sigma weight residual 111.69 105.57 6.12 1.23e+00 6.61e-01 2.47e+01 angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.36 106.73 4.63 1.09e+00 8.42e-01 1.80e+01 angle pdb=" CA LYS A 328 " pdb=" CB LYS A 328 " pdb=" CG LYS A 328 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" C ARG A 330 " pdb=" N TRP A 331 " pdb=" CA TRP A 331 " ideal model delta sigma weight residual 121.54 128.47 -6.93 1.91e+00 2.74e-01 1.32e+01 ... (remaining 4756 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 1932 34.96 - 69.92: 37 69.92 - 104.89: 3 104.89 - 139.85: 1 139.85 - 174.81: 4 Dihedral angle restraints: 1977 sinusoidal: 773 harmonic: 1204 Sorted by residual: dihedral pdb=" C3' 1SY A 602 " pdb=" C16 1SY A 602 " pdb=" C4' 1SY A 602 " pdb=" O17 1SY A 602 " ideal model delta sinusoidal sigma weight residual 116.11 -58.70 174.81 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C3' 1SY A 601 " pdb=" O28 1SY A 601 " pdb=" P27 1SY A 601 " pdb=" O26 1SY A 601 " ideal model delta sinusoidal sigma weight residual -70.28 98.77 -169.05 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3' 1SY A 602 " pdb=" O28 1SY A 602 " pdb=" P27 1SY A 602 " pdb=" O26 1SY A 602 " ideal model delta sinusoidal sigma weight residual -70.28 92.88 -163.16 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 1974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 495 0.070 - 0.139: 52 0.139 - 0.209: 2 0.209 - 0.279: 1 0.279 - 0.348: 1 Chirality restraints: 551 Sorted by residual: chirality pdb=" CA LYS A 328 " pdb=" N LYS A 328 " pdb=" C LYS A 328 " pdb=" CB LYS A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CB ILE A 41 " pdb=" CA ILE A 41 " pdb=" CG1 ILE A 41 " pdb=" CG2 ILE A 41 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA ARG A 330 " pdb=" N ARG A 330 " pdb=" C ARG A 330 " pdb=" CB ARG A 330 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.57e-01 ... (remaining 548 not shown) Planarity restraints: 562 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 325 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.80e+00 pdb=" C GLY A 325 " 0.045 2.00e-02 2.50e+03 pdb=" O GLY A 325 " -0.017 2.00e-02 2.50e+03 pdb=" N PHE A 326 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 69 " 0.043 5.00e-02 4.00e+02 6.38e-02 6.52e+00 pdb=" N PRO A 70 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 49 " 0.038 5.00e-02 4.00e+02 5.68e-02 5.17e+00 pdb=" N PRO A 50 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " 0.032 5.00e-02 4.00e+02 ... (remaining 559 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 866 2.77 - 3.31: 2967 3.31 - 3.84: 5796 3.84 - 4.37: 7069 4.37 - 4.90: 11993 Nonbonded interactions: 28691 Sorted by model distance: nonbonded pdb=" OH TYR A 149 " pdb=" O30 1SY A 601 " model vdw 2.244 2.440 nonbonded pdb=" O VAL A 64 " pdb=" OG1 THR A 69 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.280 2.440 nonbonded pdb=" O VAL A 304 " pdb=" OH TYR A 366 " model vdw 2.294 2.440 nonbonded pdb=" O LYS A 411 " pdb=" OG1 THR A 415 " model vdw 2.300 2.440 ... (remaining 28686 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: 1.280 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: 6.960 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 14.210 Find NCS groups from input model: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 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 0.118 3479 Z= 0.447 Angle : 0.787 7.792 4761 Z= 0.446 Chirality : 0.048 0.348 551 Planarity : 0.006 0.064 562 Dihedral : 16.920 174.810 1203 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.85 % Allowed : 9.92 % Favored : 89.24 % Cbeta Deviations : 0.26 % 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: -6.96 (0.20), residues: 405 helix: -4.57 (0.10), residues: 319 sheet: None (None), residues: 0 loop : -3.38 (0.50), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.000 HIS A 358 PHE 0.009 0.001 PHE A 37 TYR 0.013 0.002 TYR A 92 ARG 0.002 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.367 Fit side-chains REVERT: A 40 GLN cc_start: 0.7697 (mp10) cc_final: 0.7447 (mp10) REVERT: A 105 SER cc_start: 0.8887 (t) cc_final: 0.8685 (t) REVERT: A 282 TYR cc_start: 0.8284 (m-80) cc_final: 0.7812 (m-80) REVERT: A 364 LEU cc_start: 0.8774 (tp) cc_final: 0.8563 (tt) REVERT: A 371 LEU cc_start: 0.8649 (mm) cc_final: 0.8371 (mt) REVERT: A 430 LYS cc_start: 0.8303 (ttpt) cc_final: 0.8012 (tptt) outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.2949 time to fit residues: 16.7942 Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 ARG Chi-restraints excluded: chain A residue 321 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN A 289 HIS A 431 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3479 Z= 0.245 Angle : 0.570 7.787 4761 Z= 0.293 Chirality : 0.039 0.124 551 Planarity : 0.005 0.043 562 Dihedral : 16.609 173.910 493 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.57 % Allowed : 11.33 % Favored : 88.10 % 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: -3.91 (0.32), residues: 405 helix: -2.41 (0.21), residues: 320 sheet: None (None), residues: 0 loop : -2.29 (0.60), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.008 0.001 PHE A 192 TYR 0.018 0.001 TYR A 35 ARG 0.005 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.358 Fit side-chains REVERT: A 84 PHE cc_start: 0.8569 (t80) cc_final: 0.8344 (t80) REVERT: A 207 LYS cc_start: 0.9118 (mmtp) cc_final: 0.8836 (mmtt) REVERT: A 303 ARG cc_start: 0.7027 (ttt-90) cc_final: 0.6640 (mtp85) REVERT: A 430 LYS cc_start: 0.8319 (ttpt) cc_final: 0.7955 (tptt) REVERT: A 456 ARG cc_start: 0.6919 (ttt180) cc_final: 0.6505 (tpm170) outliers start: 2 outliers final: 1 residues processed: 47 average time/residue: 0.2331 time to fit residues: 12.8741 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 37 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3479 Z= 0.246 Angle : 0.522 5.988 4761 Z= 0.267 Chirality : 0.038 0.111 551 Planarity : 0.003 0.035 562 Dihedral : 16.155 177.009 488 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.85 % Allowed : 12.18 % Favored : 86.97 % 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: -2.35 (0.37), residues: 405 helix: -1.16 (0.26), residues: 320 sheet: None (None), residues: 0 loop : -2.46 (0.64), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.006 0.001 PHE A 416 TYR 0.016 0.001 TYR A 35 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 41 time to evaluate : 0.345 Fit side-chains REVERT: A 207 LYS cc_start: 0.9126 (mmtp) cc_final: 0.8869 (mmtt) REVERT: A 303 ARG cc_start: 0.7125 (ttt-90) cc_final: 0.6735 (mtp85) REVERT: A 430 LYS cc_start: 0.8329 (ttpt) cc_final: 0.7994 (tptt) REVERT: A 456 ARG cc_start: 0.6910 (ttt180) cc_final: 0.6501 (tpm170) outliers start: 3 outliers final: 2 residues processed: 43 average time/residue: 0.2413 time to fit residues: 12.1555 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3479 Z= 0.205 Angle : 0.486 5.412 4761 Z= 0.249 Chirality : 0.037 0.109 551 Planarity : 0.003 0.028 562 Dihedral : 16.026 178.221 488 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.57 % Allowed : 13.31 % Favored : 86.12 % 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: -1.25 (0.41), residues: 405 helix: -0.37 (0.28), residues: 320 sheet: None (None), residues: 0 loop : -2.14 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.007 0.001 PHE A 211 TYR 0.014 0.001 TYR A 35 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.366 Fit side-chains REVERT: A 38 MET cc_start: 0.8463 (mmm) cc_final: 0.8122 (mmm) REVERT: A 207 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8869 (mmtt) REVERT: A 303 ARG cc_start: 0.7108 (ttt-90) cc_final: 0.6721 (mtp85) REVERT: A 430 LYS cc_start: 0.8275 (ttpt) cc_final: 0.7904 (tptt) REVERT: A 456 ARG cc_start: 0.6822 (ttt180) cc_final: 0.6400 (tpm170) outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.2517 time to fit residues: 12.0583 Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 7 optimal weight: 0.3980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3479 Z= 0.206 Angle : 0.487 5.392 4761 Z= 0.249 Chirality : 0.037 0.112 551 Planarity : 0.003 0.026 562 Dihedral : 15.898 177.372 488 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.85 % Allowed : 13.31 % Favored : 85.84 % 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: -0.62 (0.42), residues: 405 helix: 0.11 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.08 (0.67), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.005 0.001 PHE A 276 TYR 0.014 0.001 TYR A 35 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.324 Fit side-chains REVERT: A 207 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8871 (mmtt) REVERT: A 303 ARG cc_start: 0.7117 (ttt-90) cc_final: 0.6749 (mtp85) REVERT: A 430 LYS cc_start: 0.8273 (ttpt) cc_final: 0.7910 (tptt) REVERT: A 456 ARG cc_start: 0.6806 (ttt180) cc_final: 0.6380 (tpm170) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.2503 time to fit residues: 11.9691 Evaluate side-chains 39 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.3980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 4 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3479 Z= 0.204 Angle : 0.483 5.370 4761 Z= 0.246 Chirality : 0.037 0.110 551 Planarity : 0.003 0.025 562 Dihedral : 15.849 177.525 488 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.13 % Allowed : 13.03 % Favored : 85.84 % 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: -0.33 (0.42), residues: 405 helix: 0.35 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.18 (0.65), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.005 0.001 PHE A 276 TYR 0.014 0.001 TYR A 35 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 38 time to evaluate : 0.325 Fit side-chains REVERT: A 207 LYS cc_start: 0.9100 (mmtp) cc_final: 0.8870 (mmtt) REVERT: A 303 ARG cc_start: 0.7133 (ttt-90) cc_final: 0.6768 (mtp85) REVERT: A 430 LYS cc_start: 0.8297 (ttpt) cc_final: 0.7910 (tptt) REVERT: A 456 ARG cc_start: 0.6814 (ttt180) cc_final: 0.6351 (tpm170) outliers start: 4 outliers final: 1 residues processed: 40 average time/residue: 0.2469 time to fit residues: 11.4933 Evaluate side-chains 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.1980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.0870 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 overall best weight: 0.2956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3479 Z= 0.152 Angle : 0.459 5.324 4761 Z= 0.233 Chirality : 0.036 0.101 551 Planarity : 0.003 0.024 562 Dihedral : 15.708 176.673 488 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.28 % Allowed : 14.16 % Favored : 85.55 % 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: -0.00 (0.43), residues: 405 helix: 0.61 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.18 (0.63), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 107 HIS 0.001 0.000 HIS A 289 PHE 0.004 0.001 PHE A 276 TYR 0.010 0.001 TYR A 35 ARG 0.002 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.377 Fit side-chains REVERT: A 303 ARG cc_start: 0.7084 (ttt-90) cc_final: 0.6769 (mtp85) REVERT: A 430 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7870 (tptt) REVERT: A 456 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6396 (tpm170) outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.2460 time to fit residues: 11.3307 Evaluate side-chains 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3479 Z= 0.335 Angle : 0.551 5.471 4761 Z= 0.279 Chirality : 0.041 0.129 551 Planarity : 0.003 0.026 562 Dihedral : 15.980 179.221 488 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 0.57 % Allowed : 14.73 % Favored : 84.70 % 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: -0.35 (0.42), residues: 405 helix: 0.38 (0.29), residues: 322 sheet: None (None), residues: 0 loop : -2.43 (0.64), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 331 HIS 0.002 0.000 HIS A 289 PHE 0.007 0.001 PHE A 416 TYR 0.016 0.001 TYR A 35 ARG 0.003 0.000 ARG A 179 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.326 Fit side-chains REVERT: A 207 LYS cc_start: 0.9189 (mmtp) cc_final: 0.8935 (mmtt) REVERT: A 303 ARG cc_start: 0.7378 (ttt-90) cc_final: 0.6925 (mtp85) REVERT: A 430 LYS cc_start: 0.8399 (ttpt) cc_final: 0.7953 (tptt) REVERT: A 456 ARG cc_start: 0.6820 (ttt180) cc_final: 0.6357 (tpm170) outliers start: 2 outliers final: 1 residues processed: 45 average time/residue: 0.2365 time to fit residues: 12.6417 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.4980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 0.2980 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3479 Z= 0.185 Angle : 0.480 5.361 4761 Z= 0.246 Chirality : 0.037 0.105 551 Planarity : 0.003 0.025 562 Dihedral : 15.795 177.548 488 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.85 % Allowed : 13.88 % Favored : 85.27 % 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: 0.17 (0.43), residues: 405 helix: 0.73 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.11 (0.66), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.005 0.001 PHE A 326 TYR 0.014 0.001 TYR A 35 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.404 Fit side-chains REVERT: A 207 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8891 (mmtt) REVERT: A 303 ARG cc_start: 0.7262 (ttt-90) cc_final: 0.6887 (mtp85) REVERT: A 430 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7877 (tptt) REVERT: A 456 ARG cc_start: 0.6854 (ttt180) cc_final: 0.6349 (tpm170) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2319 time to fit residues: 11.3925 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9990 chunk 3 optimal weight: 0.1980 chunk 25 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3479 Z= 0.219 Angle : 0.493 5.368 4761 Z= 0.251 Chirality : 0.038 0.111 551 Planarity : 0.003 0.025 562 Dihedral : 15.772 177.396 488 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.85 % Allowed : 13.88 % Favored : 85.27 % 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: 0.26 (0.43), residues: 405 helix: 0.80 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.08 (0.66), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.005 0.001 PHE A 276 TYR 0.013 0.001 TYR A 35 ARG 0.002 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 39 time to evaluate : 0.313 Fit side-chains REVERT: A 207 LYS cc_start: 0.9122 (mmtp) cc_final: 0.8896 (mmtt) REVERT: A 303 ARG cc_start: 0.7219 (ttt-90) cc_final: 0.6887 (mtp85) REVERT: A 430 LYS cc_start: 0.8330 (ttpt) cc_final: 0.7896 (tptt) REVERT: A 456 ARG cc_start: 0.6871 (ttt180) cc_final: 0.6357 (tpm170) outliers start: 3 outliers final: 3 residues processed: 41 average time/residue: 0.2487 time to fit residues: 11.8718 Evaluate side-chains 40 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 337 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.1980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.0270 overall best weight: 0.3238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.113049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093286 restraints weight = 3913.095| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 1.57 r_work: 0.2825 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3479 Z= 0.164 Angle : 0.468 5.347 4761 Z= 0.239 Chirality : 0.036 0.101 551 Planarity : 0.003 0.024 562 Dihedral : 15.613 176.218 488 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.85 % Allowed : 14.16 % Favored : 84.99 % 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: 0.49 (0.44), residues: 405 helix: 0.98 (0.30), residues: 320 sheet: None (None), residues: 0 loop : -2.06 (0.67), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 331 HIS 0.001 0.000 HIS A 289 PHE 0.006 0.001 PHE A 326 TYR 0.013 0.001 TYR A 35 ARG 0.003 0.000 ARG A 179 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1230.85 seconds wall clock time: 22 minutes 54.21 seconds (1374.21 seconds total)