Starting phenix.real_space_refine on Fri Dec 27 18:29:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr4_34045/12_2024/7yr4_34045.cif" } resolution = 4.12 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4103 2.51 5 N 1064 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4832 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 26, 'TRANS': 565} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1562 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Time building chain proxies: 4.65, per 1000 atoms: 0.73 Number of scatterers: 6394 At special positions: 0 Unit cell: (84.24, 87.36, 118.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1190 8.00 N 1064 7.00 C 4103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.61 Conformation dependent library (CDL) restraints added in 908.5 milliseconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 4 sheets defined 51.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.726A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.594A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.994A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.665A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.003A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.683A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.650A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.564A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 4.251A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.800A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.663A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.174A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 3.992A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.076A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.591A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 600 Proline residue: A 590 - end of helix removed outlier: 4.403A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.624A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA2, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.551A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 272 hydrogen bonds defined for protein. 795 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.53 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 406 1.23 - 1.38: 2252 1.38 - 1.53: 3633 1.53 - 1.68: 229 1.68 - 1.83: 58 Bond restraints: 6578 Sorted by residual: bond pdb=" CG PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 1.503 1.085 0.418 3.40e-02 8.65e+02 1.51e+02 bond pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 1.492 1.217 0.275 5.00e-02 4.00e+02 3.03e+01 bond pdb=" N PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" CB ASN A 601 " pdb=" CG ASN A 601 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.36e+00 bond pdb=" CG LYS D 478 " pdb=" CD LYS D 478 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.06e+00 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.18: 8924 8.18 - 16.36: 11 16.36 - 24.54: 1 24.54 - 32.72: 1 32.72 - 40.90: 1 Bond angle restraints: 8938 Sorted by residual: angle pdb=" N PRO D 373 " pdb=" CD PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 103.20 75.60 27.60 1.50e+00 4.44e-01 3.39e+02 angle pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 106.10 147.00 -40.90 3.20e+00 9.77e-02 1.63e+02 angle pdb=" CA PRO D 373 " pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 104.50 80.22 24.28 1.90e+00 2.77e-01 1.63e+02 angle pdb=" CA PRO D 373 " pdb=" N PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 112.00 103.00 9.00 1.40e+00 5.10e-01 4.13e+01 angle pdb=" C LYS A 600 " pdb=" N ASN A 601 " pdb=" CA ASN A 601 " ideal model delta sigma weight residual 123.05 130.49 -7.44 1.57e+00 4.06e-01 2.25e+01 ... (remaining 8933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3445 17.77 - 35.55: 354 35.55 - 53.32: 58 53.32 - 71.09: 15 71.09 - 88.86: 10 Dihedral angle restraints: 3882 sinusoidal: 1571 harmonic: 2311 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 19.27 73.73 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual 93.00 19.50 73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -146.07 60.07 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 741 0.063 - 0.126: 159 0.126 - 0.189: 28 0.189 - 0.252: 2 0.252 - 0.315: 1 Chirality restraints: 931 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ASN A 601 " pdb=" N ASN A 601 " pdb=" C ASN A 601 " pdb=" CB ASN A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 928 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " 0.031 2.00e-02 2.50e+03 3.06e-02 2.35e+01 pdb=" CG TRP A 477 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 288 " 0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 289 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 459 " -0.017 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 459 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 459 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 459 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 459 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 459 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 459 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 459 " 0.002 2.00e-02 2.50e+03 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 961 2.76 - 3.29: 6316 3.29 - 3.83: 10623 3.83 - 4.36: 12003 4.36 - 4.90: 19898 Nonbonded interactions: 49801 Sorted by model distance: nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.224 3.040 nonbonded pdb=" OH TYR A 83 " pdb=" OH TYR D 489 " model vdw 2.294 3.040 nonbonded pdb=" O SER A 105 " pdb=" OG SER A 113 " model vdw 2.309 3.040 nonbonded pdb=" O HIS A 239 " pdb=" ND2 ASN A 599 " model vdw 2.313 3.120 nonbonded pdb=" O THR D 393 " pdb=" OG1 THR D 523 " model vdw 2.322 3.040 ... (remaining 49796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.200 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.770 Find NCS groups from input model: 0.050 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 0.008 0.418 6578 Z= 0.427 Angle : 1.165 40.904 8938 Z= 0.599 Chirality : 0.055 0.315 931 Planarity : 0.007 0.095 1159 Dihedral : 14.906 88.862 2377 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.40 % 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: -1.79 (0.27), residues: 783 helix: -0.62 (0.25), residues: 350 sheet: -1.30 (0.76), residues: 32 loop : -1.68 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP A 477 HIS 0.005 0.001 HIS D 519 PHE 0.035 0.003 PHE D 497 TYR 0.030 0.003 TYR A 279 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.7503 (mt) cc_final: 0.6836 (mt) REVERT: A 520 LEU cc_start: 0.6720 (mp) cc_final: 0.6272 (tt) REVERT: A 523 PHE cc_start: 0.6854 (m-80) cc_final: 0.6493 (m-80) REVERT: A 543 ASP cc_start: 0.4915 (t0) cc_final: 0.4563 (t0) REVERT: A 587 TYR cc_start: 0.5147 (t80) cc_final: 0.4703 (t80) REVERT: A 592 PHE cc_start: 0.4417 (t80) cc_final: 0.3218 (t80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2389 time to fit residues: 80.5660 Evaluate side-chains 150 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 20.0000 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.0050 chunk 70 optimal weight: 0.4980 overall best weight: 1.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6000 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6578 Z= 0.209 Angle : 0.686 10.169 8938 Z= 0.351 Chirality : 0.044 0.157 931 Planarity : 0.006 0.064 1159 Dihedral : 5.739 30.730 854 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.13 (0.28), residues: 783 helix: -0.02 (0.26), residues: 361 sheet: -0.98 (0.76), residues: 33 loop : -1.41 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 459 HIS 0.007 0.001 HIS A 265 PHE 0.020 0.002 PHE A 525 TYR 0.023 0.002 TYR A 385 ARG 0.005 0.001 ARG A 115 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5858 (ptt) cc_final: 0.5614 (ptt) REVERT: A 216 ASP cc_start: 0.5610 (m-30) cc_final: 0.5317 (m-30) REVERT: A 315 PHE cc_start: 0.6544 (m-10) cc_final: 0.6324 (m-10) REVERT: A 380 GLN cc_start: 0.7042 (tp40) cc_final: 0.6638 (tp40) REVERT: A 408 MET cc_start: 0.7479 (mmm) cc_final: 0.7243 (mmm) REVERT: A 523 PHE cc_start: 0.6571 (m-80) cc_final: 0.6314 (m-80) REVERT: A 587 TYR cc_start: 0.5692 (t80) cc_final: 0.5087 (t80) REVERT: D 417 ASN cc_start: 0.7223 (p0) cc_final: 0.6954 (p0) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.2257 time to fit residues: 54.4961 Evaluate side-chains 132 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 19 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 0.0060 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 239 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS A 556 ASN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6578 Z= 0.166 Angle : 0.653 9.758 8938 Z= 0.331 Chirality : 0.043 0.148 931 Planarity : 0.005 0.049 1159 Dihedral : 5.298 27.011 854 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.29), residues: 783 helix: 0.21 (0.27), residues: 358 sheet: -0.77 (0.81), residues: 33 loop : -1.35 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 459 HIS 0.005 0.001 HIS A 265 PHE 0.017 0.001 PHE A 525 TYR 0.019 0.002 TYR A 515 ARG 0.005 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5482 (ptt) cc_final: 0.5208 (ptt) REVERT: A 315 PHE cc_start: 0.6457 (m-10) cc_final: 0.6080 (m-10) REVERT: A 380 GLN cc_start: 0.7081 (tp40) cc_final: 0.6668 (tp40) REVERT: A 408 MET cc_start: 0.7461 (mmm) cc_final: 0.7217 (mmm) REVERT: A 455 MET cc_start: 0.6965 (ppp) cc_final: 0.6711 (ppp) REVERT: A 587 TYR cc_start: 0.5697 (t80) cc_final: 0.5162 (t80) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2144 time to fit residues: 49.5755 Evaluate side-chains 140 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 63 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A 437 ASN A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.5338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6578 Z= 0.171 Angle : 0.629 8.964 8938 Z= 0.321 Chirality : 0.043 0.197 931 Planarity : 0.005 0.049 1159 Dihedral : 5.048 25.259 854 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -0.70 (0.29), residues: 783 helix: 0.28 (0.27), residues: 362 sheet: -0.60 (0.82), residues: 33 loop : -1.14 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 459 HIS 0.006 0.001 HIS A 265 PHE 0.015 0.001 PHE A 523 TYR 0.020 0.002 TYR A 515 ARG 0.012 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.5532 (ptt) cc_final: 0.5212 (ptt) REVERT: A 315 PHE cc_start: 0.6477 (m-10) cc_final: 0.6272 (m-10) REVERT: A 408 MET cc_start: 0.7538 (mmm) cc_final: 0.7220 (mmm) REVERT: A 455 MET cc_start: 0.6839 (ppp) cc_final: 0.6229 (ppp) REVERT: A 512 PHE cc_start: 0.4512 (m-10) cc_final: 0.4270 (m-10) REVERT: A 520 LEU cc_start: 0.7362 (tt) cc_final: 0.6937 (mt) REVERT: A 587 TYR cc_start: 0.5719 (t80) cc_final: 0.5244 (t80) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.1979 time to fit residues: 43.8352 Evaluate side-chains 139 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 64 optimal weight: 0.0270 chunk 52 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.0570 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 GLN ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6031 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6578 Z= 0.155 Angle : 0.635 6.738 8938 Z= 0.323 Chirality : 0.044 0.190 931 Planarity : 0.004 0.043 1159 Dihedral : 4.959 23.869 854 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.29), residues: 783 helix: 0.46 (0.27), residues: 358 sheet: -0.43 (0.85), residues: 33 loop : -1.21 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 461 HIS 0.003 0.001 HIS A 239 PHE 0.019 0.002 PHE A 230 TYR 0.018 0.001 TYR D 495 ARG 0.010 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 408 MET cc_start: 0.7437 (mmm) cc_final: 0.7220 (mmm) REVERT: A 455 MET cc_start: 0.6907 (ppp) cc_final: 0.5979 (ppp) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1909 time to fit residues: 41.0693 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 30.0000 chunk 39 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 0.0020 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.6336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6578 Z= 0.217 Angle : 0.674 11.608 8938 Z= 0.345 Chirality : 0.044 0.170 931 Planarity : 0.005 0.050 1159 Dihedral : 5.098 23.828 854 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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: -0.58 (0.29), residues: 783 helix: 0.40 (0.27), residues: 363 sheet: -0.29 (0.83), residues: 33 loop : -1.13 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP A 163 HIS 0.008 0.001 HIS A 265 PHE 0.017 0.002 PHE A 230 TYR 0.031 0.002 TYR A 199 ARG 0.008 0.001 ARG D 454 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.7072 (ppp) cc_final: 0.5944 (ppp) REVERT: A 523 PHE cc_start: 0.6757 (m-80) cc_final: 0.6553 (m-80) REVERT: A 587 TYR cc_start: 0.6069 (t80) cc_final: 0.5361 (t80) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.1975 time to fit residues: 40.7547 Evaluate side-chains 130 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 45 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6578 Z= 0.171 Angle : 0.673 9.213 8938 Z= 0.345 Chirality : 0.046 0.213 931 Planarity : 0.004 0.038 1159 Dihedral : 4.882 23.426 854 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: -0.50 (0.30), residues: 783 helix: 0.44 (0.27), residues: 361 sheet: -0.12 (0.85), residues: 33 loop : -1.07 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 461 HIS 0.008 0.001 HIS A 265 PHE 0.018 0.001 PHE A 230 TYR 0.012 0.001 TYR A 515 ARG 0.007 0.001 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 478 TRP cc_start: 0.6432 (m100) cc_final: 0.5838 (m100) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1983 time to fit residues: 41.1389 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.6761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 6578 Z= 0.181 Angle : 0.671 8.261 8938 Z= 0.342 Chirality : 0.045 0.168 931 Planarity : 0.004 0.038 1159 Dihedral : 4.963 23.504 854 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 16.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 0.14 % Allowed : 0.43 % Favored : 99.42 % 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: -0.68 (0.30), residues: 783 helix: 0.27 (0.27), residues: 375 sheet: -0.16 (0.85), residues: 33 loop : -1.19 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 461 HIS 0.009 0.001 HIS A 265 PHE 0.023 0.002 PHE A 356 TYR 0.020 0.002 TYR D 495 ARG 0.005 0.001 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLN cc_start: 0.7075 (tp40) cc_final: 0.6829 (tp40) REVERT: A 455 MET cc_start: 0.6916 (ppp) cc_final: 0.6286 (ppp) REVERT: A 478 TRP cc_start: 0.6410 (m100) cc_final: 0.5786 (m100) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1894 time to fit residues: 39.4520 Evaluate side-chains 136 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 0.0010 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.6977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6578 Z= 0.183 Angle : 0.698 9.380 8938 Z= 0.354 Chirality : 0.045 0.162 931 Planarity : 0.004 0.038 1159 Dihedral : 4.930 23.244 854 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.30), residues: 783 helix: 0.32 (0.27), residues: 373 sheet: -0.15 (0.87), residues: 33 loop : -1.10 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 461 HIS 0.009 0.002 HIS A 505 PHE 0.031 0.002 PHE A 464 TYR 0.025 0.002 TYR A 199 ARG 0.006 0.001 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8978 (ppp) cc_final: 0.8532 (ppp) REVERT: A 478 TRP cc_start: 0.6417 (m100) cc_final: 0.5765 (m100) REVERT: A 505 HIS cc_start: 0.6008 (m90) cc_final: 0.5686 (m170) REVERT: A 523 PHE cc_start: 0.6940 (m-80) cc_final: 0.6529 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1888 time to fit residues: 38.8045 Evaluate side-chains 137 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN A 437 ASN ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.7703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6578 Z= 0.291 Angle : 0.776 8.746 8938 Z= 0.402 Chirality : 0.047 0.171 931 Planarity : 0.005 0.054 1159 Dihedral : 5.451 25.131 854 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.14 % Allowed : 0.58 % Favored : 99.28 % 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: -0.91 (0.29), residues: 783 helix: 0.02 (0.26), residues: 371 sheet: -0.26 (0.85), residues: 33 loop : -1.23 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 69 HIS 0.013 0.002 HIS A 265 PHE 0.033 0.003 PHE A 464 TYR 0.027 0.003 TYR A 199 ARG 0.006 0.001 ARG D 498 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8976 (ppp) cc_final: 0.8474 (ppp) REVERT: A 351 LEU cc_start: 0.7170 (mt) cc_final: 0.6875 (mt) REVERT: A 401 HIS cc_start: 0.6148 (m-70) cc_final: 0.5867 (m-70) REVERT: A 523 PHE cc_start: 0.7111 (m-80) cc_final: 0.6699 (m-80) outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.1899 time to fit residues: 39.8728 Evaluate side-chains 126 residues out of total 691 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 25 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 41 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 535 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.089293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070993 restraints weight = 28044.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.073384 restraints weight = 19647.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.075245 restraints weight = 14865.946| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.7663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6578 Z= 0.193 Angle : 0.723 9.718 8938 Z= 0.370 Chirality : 0.046 0.169 931 Planarity : 0.004 0.039 1159 Dihedral : 5.094 24.474 854 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.14 % Allowed : 0.29 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.29), residues: 783 helix: 0.12 (0.27), residues: 376 sheet: -0.19 (0.84), residues: 34 loop : -1.13 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP A 275 HIS 0.010 0.002 HIS A 505 PHE 0.024 0.002 PHE A 464 TYR 0.021 0.002 TYR D 495 ARG 0.006 0.001 ARG D 498 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1910.92 seconds wall clock time: 35 minutes 34.29 seconds (2134.29 seconds total)