Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:36:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_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_33389/10_2023/7xq2_33389_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_33389_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xq2_33389/10_2023/7xq2_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-1.21rc1-5097/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: 2.18, per 1000 atoms: 0.65 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: 1.41 Conformation dependent library (CDL) restraints added in 490.6 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: 0.60 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: 0.93 Time building geometry restraints manager: 1.54 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 - 33.81: 1913 33.81 - 67.62: 34 67.62 - 101.43: 3 101.43 - 135.24: 0 135.24 - 169.05: 3 Dihedral angle restraints: 1953 sinusoidal: 749 harmonic: 1204 Sorted by residual: 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 dihedral pdb=" C16 1SY A 602 " pdb=" O17 1SY A 602 " pdb=" P18 1SY A 602 " pdb=" O20 1SY A 602 " ideal model delta sinusoidal sigma weight residual 266.83 107.37 159.46 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 1950 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: 1.440 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: 6.980 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.020 ------------------------------------------------------------------------------- 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 : 15.539 169.049 1179 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 *********************** 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 : 0.370 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 0.2619 time to fit residues: 14.9857 Evaluate side-chains 39 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.326 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3155 time to fit residues: 1.2386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 17 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.0060 overall best weight: 0.4396 ------------------------------------------------------------------------------- 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: 0.7910 moved from start: 0.1987 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= 0.203 Angle : 0.567 7.871 4761 Z= 0.289 Chirality : 0.038 0.125 551 Planarity : 0.005 0.041 562 Dihedral : 14.421 170.976 464 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 11.90 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.32), residues: 405 helix: -2.38 (0.22), residues: 321 sheet: None (None), residues: 0 loop : -2.28 (0.61), residues: 84 *********************** 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 47 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.379 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 46 average time/residue: 0.2294 time to fit residues: 12.5155 Evaluate side-chains 41 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0386 time to fit residues: 0.5886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 0.0030 chunk 40 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 chunk 36 optimal weight: 0.0770 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.2926 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2379 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= 0.151 Angle : 0.486 6.161 4761 Z= 0.245 Chirality : 0.036 0.107 551 Planarity : 0.003 0.030 562 Dihedral : 14.221 178.950 464 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.57 % Allowed : 13.03 % Favored : 86.40 % 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: -1.95 (0.38), residues: 405 helix: -0.91 (0.26), residues: 319 sheet: None (None), residues: 0 loop : -2.14 (0.63), residues: 86 *********************** 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 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.376 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.2293 time to fit residues: 11.5018 Evaluate side-chains 35 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.0980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 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 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3479 Z= 0.237 Angle : 0.517 5.423 4761 Z= 0.259 Chirality : 0.039 0.117 551 Planarity : 0.003 0.027 562 Dihedral : 14.064 177.938 464 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.85 % Allowed : 13.03 % 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: -1.18 (0.40), residues: 405 helix: -0.24 (0.28), residues: 319 sheet: None (None), residues: 0 loop : -2.45 (0.61), residues: 86 *********************** 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 45 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 42 time to evaluate : 0.375 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 44 average time/residue: 0.2071 time to fit residues: 11.0185 Evaluate side-chains 43 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0383 time to fit residues: 0.6679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 16 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 0.0050 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3479 Z= 0.230 Angle : 0.508 6.153 4761 Z= 0.253 Chirality : 0.038 0.115 551 Planarity : 0.003 0.026 562 Dihedral : 13.996 177.613 464 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.28 % Allowed : 13.88 % 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: -0.75 (0.41), residues: 405 helix: 0.09 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.47 (0.62), residues: 84 *********************** 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 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.388 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 38 average time/residue: 0.2363 time to fit residues: 10.6932 Evaluate side-chains 36 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 36 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3479 Z= 0.245 Angle : 0.510 5.362 4761 Z= 0.255 Chirality : 0.039 0.117 551 Planarity : 0.003 0.025 562 Dihedral : 14.002 178.071 464 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.13 % Allowed : 13.60 % 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: -0.50 (0.42), residues: 405 helix: 0.29 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.49 (0.61), residues: 84 *********************** 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 46 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.345 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 46 average time/residue: 0.2196 time to fit residues: 12.0114 Evaluate side-chains 42 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.4980 chunk 25 optimal weight: 0.5980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3479 Z= 0.239 Angle : 0.513 6.925 4761 Z= 0.255 Chirality : 0.039 0.116 551 Planarity : 0.003 0.025 562 Dihedral : 14.007 178.333 464 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.28 % Allowed : 14.73 % 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: -0.31 (0.42), residues: 405 helix: 0.42 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.46 (0.62), residues: 83 *********************** 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 : 0.368 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.2463 time to fit residues: 11.3484 Evaluate side-chains 38 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0366 time to fit residues: 0.5741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.0970 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 28 optimal weight: 0.0170 overall best weight: 0.3816 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3479 Z= 0.176 Angle : 0.488 6.607 4761 Z= 0.242 Chirality : 0.037 0.105 551 Planarity : 0.003 0.024 562 Dihedral : 13.938 177.828 464 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.57 % Allowed : 13.88 % 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: 0.06 (0.43), residues: 405 helix: 0.64 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.11 (0.65), residues: 84 *********************** 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 39 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.377 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 0.2306 time to fit residues: 10.2515 Evaluate side-chains 36 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0365 time to fit residues: 0.5450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.3980 chunk 38 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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: 0.7899 moved from start: 0.2818 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= 0.193 Angle : 0.494 6.448 4761 Z= 0.245 Chirality : 0.037 0.109 551 Planarity : 0.003 0.024 562 Dihedral : 13.934 177.854 464 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 14.73 % 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: 0.16 (0.43), residues: 405 helix: 0.71 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.08 (0.65), residues: 84 *********************** 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 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.404 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2045 time to fit residues: 9.2174 Evaluate side-chains 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.7938 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3479 Z= 0.276 Angle : 0.531 6.028 4761 Z= 0.264 Chirality : 0.040 0.122 551 Planarity : 0.003 0.025 562 Dihedral : 14.030 179.001 464 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % 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: -0.04 (0.43), residues: 405 helix: 0.62 (0.30), residues: 322 sheet: None (None), residues: 0 loop : -2.41 (0.63), residues: 83 ********************** 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 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.2087 time to fit residues: 9.4887 Evaluate side-chains 37 residues out of total 353 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.376 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.0030 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 24 optimal weight: 0.4980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.3390 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.110450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.090189 restraints weight = 3910.507| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 1.62 r_work: 0.2777 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2640 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3479 Z= 0.162 Angle : 0.482 6.262 4761 Z= 0.239 Chirality : 0.037 0.102 551 Planarity : 0.003 0.024 562 Dihedral : 13.927 178.033 464 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 15.01 % 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: 0.34 (0.43), residues: 405 helix: 0.85 (0.30), residues: 321 sheet: None (None), residues: 0 loop : -2.04 (0.65), residues: 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1245.86 seconds wall clock time: 23 minutes 4.27 seconds (1384.27 seconds total)