Starting phenix.real_space_refine on Fri Dec 27 12:40:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.map" model { file = "/net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ydq_33756/12_2024/7ydq_33756.cif" } resolution = 4.04 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= 0.003 sd= 0.042 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 28 5.16 5 C 3144 2.51 5 N 760 2.21 5 O 846 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 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: 4778 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 598, 4753 Classifications: {'peptide': 598} Link IDs: {'PTRANS': 21, 'TRANS': 576} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'IRX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.42, per 1000 atoms: 0.72 Number of scatterers: 4778 At special positions: 0 Unit cell: (84.7, 68.2, 119.9, 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 28 16.00 O 846 8.00 N 760 7.00 C 3144 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 - 3.00 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: 1.26 Conformation dependent library (CDL) restraints added in 620.9 milliseconds 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1112 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 1 sheets defined 53.7% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 31 through 58 removed outlier: 3.904A pdb=" N HIS A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.892A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL A 79 " --> pdb=" O CYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 removed outlier: 3.575A pdb=" N PHE A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN A 105 " --> pdb=" O CYS A 101 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 145 removed outlier: 4.119A pdb=" N THR A 118 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N SER A 143 " --> pdb=" O PHE A 139 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 173 removed outlier: 3.798A pdb=" N GLY A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 206 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.676A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 249 Processing helix chain 'A' and resid 249 through 257 removed outlier: 4.273A pdb=" N THR A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.747A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 316 Processing helix chain 'A' and resid 317 through 320 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.987A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 327 " --> pdb=" O ILE A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.900A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.555A pdb=" N PHE A 365 " --> pdb=" O PRO A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 426 through 435 removed outlier: 3.875A pdb=" N LEU A 430 " --> pdb=" O PRO A 426 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N THR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 removed outlier: 3.640A pdb=" N ASP A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 461 Proline residue: A 459 - end of helix Processing helix chain 'A' and resid 613 through 635 removed outlier: 4.055A pdb=" N ILE A 617 " --> pdb=" O LYS A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 382 through 392 removed outlier: 7.326A pdb=" N SER A 517 " --> pdb=" O ARG A 538 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARG A 538 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N ASN A 519 " --> pdb=" O LYS A 536 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N LYS A 536 " --> pdb=" O ASN A 519 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ASN A 491 " --> pdb=" O PRO A 383 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU A 385 " --> pdb=" O ASN A 491 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILE A 493 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU A 387 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU A 495 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ASP A 389 " --> pdb=" O LEU A 495 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N GLY A 497 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASP A 391 " --> pdb=" O GLY A 497 " (cutoff:3.500A) 277 hydrogen bonds defined for protein. 768 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: 1.54 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1461 1.34 - 1.46: 1205 1.46 - 1.58: 2184 1.58 - 1.70: 4 1.70 - 1.82: 43 Bond restraints: 4897 Sorted by residual: bond pdb=" C15 IRX A 701 " pdb=" C16 IRX A 701 " ideal model delta sigma weight residual 1.482 1.633 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 IRX A 701 " pdb=" C8 IRX A 701 " ideal model delta sigma weight residual 1.527 1.670 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" C18 IRX A 701 " pdb=" C19 IRX A 701 " ideal model delta sigma weight residual 1.455 1.596 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C7 IRX A 701 " pdb=" C8 IRX A 701 " ideal model delta sigma weight residual 1.524 1.642 -0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C11 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 1.516 1.444 0.072 2.00e-02 2.50e+03 1.29e+01 ... (remaining 4892 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 6576 3.37 - 6.73: 43 6.73 - 10.10: 13 10.10 - 13.47: 2 13.47 - 16.83: 2 Bond angle restraints: 6636 Sorted by residual: angle pdb=" C12 IRX A 701 " pdb=" N4 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 119.44 136.27 -16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" C10 IRX A 701 " pdb=" C11 IRX A 701 " pdb=" C13 IRX A 701 " ideal model delta sigma weight residual 114.59 99.86 14.73 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 105.48 6.52 1.40e+00 5.10e-01 2.17e+01 angle pdb=" C16 IRX A 701 " pdb=" C15 IRX A 701 " pdb=" N5 IRX A 701 " ideal model delta sigma weight residual 115.43 128.43 -13.00 3.00e+00 1.11e-01 1.88e+01 angle pdb=" C7 IRX A 701 " pdb=" C9 IRX A 701 " pdb=" N4 IRX A 701 " ideal model delta sigma weight residual 113.70 101.29 12.41 3.00e+00 1.11e-01 1.71e+01 ... (remaining 6631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.91: 2374 16.91 - 33.82: 358 33.82 - 50.73: 104 50.73 - 67.63: 17 67.63 - 84.54: 4 Dihedral angle restraints: 2857 sinusoidal: 1130 harmonic: 1727 Sorted by residual: dihedral pdb=" CA HIS A 587 " pdb=" C HIS A 587 " pdb=" N MET A 588 " pdb=" CA MET A 588 " ideal model delta harmonic sigma weight residual 180.00 162.98 17.02 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE A 484 " pdb=" C PHE A 484 " pdb=" N GLU A 485 " pdb=" CA GLU A 485 " ideal model delta harmonic sigma weight residual 180.00 163.52 16.48 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA HIS A 334 " pdb=" C HIS A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 2854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 433 0.029 - 0.058: 220 0.058 - 0.087: 54 0.087 - 0.116: 40 0.116 - 0.145: 10 Chirality restraints: 757 Sorted by residual: chirality pdb=" CA VAL A 589 " pdb=" N VAL A 589 " pdb=" C VAL A 589 " pdb=" CB VAL A 589 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA PHE A 257 " pdb=" N PHE A 257 " pdb=" C PHE A 257 " pdb=" CB PHE A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" CA ILE A 417 " pdb=" N ILE A 417 " pdb=" C ILE A 417 " pdb=" CB ILE A 417 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 754 not shown) Planarity restraints: 825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " 0.080 5.00e-02 4.00e+02 1.19e-01 2.25e+01 pdb=" N PRO A 258 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 649 " -0.041 5.00e-02 4.00e+02 6.16e-02 6.08e+00 pdb=" N PRO A 650 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 650 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 650 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 292 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.47e+00 pdb=" N PRO A 293 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 293 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 293 " 0.026 5.00e-02 4.00e+02 ... (remaining 822 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1135 2.79 - 3.32: 4565 3.32 - 3.84: 7753 3.84 - 4.37: 8514 4.37 - 4.90: 14550 Nonbonded interactions: 36517 Sorted by model distance: nonbonded pdb=" OG SER A 98 " pdb=" OE1 GLU A 196 " model vdw 2.262 3.040 nonbonded pdb=" O SER A 239 " pdb=" OG SER A 239 " model vdw 2.333 3.040 nonbonded pdb=" N GLN A 115 " pdb=" OE1 GLN A 115 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN A 54 " pdb=" OG SER A 160 " model vdw 2.348 3.040 nonbonded pdb=" OD2 ASP A 391 " pdb=" NZ LYS A 396 " model vdw 2.349 3.120 ... (remaining 36512 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.640 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6070 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 : 0.006 0.151 4897 Z= 0.348 Angle : 0.828 16.833 6636 Z= 0.386 Chirality : 0.043 0.145 757 Planarity : 0.006 0.119 825 Dihedral : 17.500 84.544 1745 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.57 % Allowed : 27.41 % Favored : 72.02 % 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: 1.21 (0.37), residues: 590 helix: 1.12 (0.35), residues: 250 sheet: 1.69 (0.46), residues: 119 loop : 0.04 (0.47), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 427 HIS 0.009 0.001 HIS A 587 PHE 0.020 0.002 PHE A 484 TYR 0.010 0.001 TYR A 462 ARG 0.003 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.530 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ARG cc_start: 0.6188 (ttt-90) cc_final: 0.5610 (ttp-170) REVERT: A 462 TYR cc_start: 0.8126 (p90) cc_final: 0.7718 (p90) outliers start: 3 outliers final: 3 residues processed: 60 average time/residue: 0.1936 time to fit residues: 14.8522 Evaluate side-chains 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 8.9990 chunk 44 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 0.0770 chunk 46 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 53 optimal weight: 8.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4897 Z= 0.165 Angle : 0.628 6.226 6636 Z= 0.319 Chirality : 0.043 0.145 757 Planarity : 0.005 0.072 825 Dihedral : 4.686 28.837 639 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.57 % Allowed : 5.10 % Favored : 94.33 % 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 (0.36), residues: 590 helix: 1.08 (0.34), residues: 253 sheet: 1.81 (0.46), residues: 122 loop : -0.10 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 427 HIS 0.005 0.001 HIS A 587 PHE 0.022 0.002 PHE A 139 TYR 0.019 0.001 TYR A 181 ARG 0.002 0.000 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.485 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 GLU cc_start: 0.7145 (pp20) cc_final: 0.6893 (pp20) REVERT: A 340 ILE cc_start: 0.7851 (mm) cc_final: 0.7409 (mm) REVERT: A 385 LEU cc_start: 0.8696 (mm) cc_final: 0.8130 (tt) REVERT: A 443 ARG cc_start: 0.6083 (ttt-90) cc_final: 0.5506 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 79 average time/residue: 0.1839 time to fit residues: 18.5438 Evaluate side-chains 61 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 4897 Z= 0.525 Angle : 0.913 11.343 6636 Z= 0.485 Chirality : 0.056 0.210 757 Planarity : 0.006 0.082 825 Dihedral : 5.264 23.867 639 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.19 % Allowed : 7.75 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.36), residues: 590 helix: -0.16 (0.31), residues: 262 sheet: 1.96 (0.47), residues: 121 loop : -0.39 (0.49), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 53 HIS 0.006 0.001 HIS A 298 PHE 0.035 0.003 PHE A 139 TYR 0.015 0.002 TYR A 65 ARG 0.004 0.001 ARG A 538 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.478 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7920 (m-10) cc_final: 0.7452 (m-80) REVERT: A 115 GLN cc_start: 0.8375 (pm20) cc_final: 0.8135 (pm20) REVERT: A 340 ILE cc_start: 0.8397 (mm) cc_final: 0.7930 (mm) outliers start: 1 outliers final: 1 residues processed: 69 average time/residue: 0.1808 time to fit residues: 15.8208 Evaluate side-chains 54 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 27 optimal weight: 0.0270 chunk 5 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6084 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4897 Z= 0.171 Angle : 0.635 8.722 6636 Z= 0.321 Chirality : 0.043 0.148 757 Planarity : 0.005 0.055 825 Dihedral : 4.608 19.066 639 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.19 % Allowed : 4.54 % Favored : 95.27 % 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: 1.01 (0.36), residues: 590 helix: 0.70 (0.33), residues: 251 sheet: 2.01 (0.46), residues: 121 loop : -0.01 (0.48), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 637 HIS 0.003 0.001 HIS A 108 PHE 0.040 0.002 PHE A 378 TYR 0.009 0.001 TYR A 181 ARG 0.002 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.541 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 GLN cc_start: 0.8237 (pm20) cc_final: 0.7935 (pm20) REVERT: A 340 ILE cc_start: 0.8022 (mm) cc_final: 0.7811 (mm) REVERT: A 436 TYR cc_start: 0.6825 (m-10) cc_final: 0.6580 (m-80) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1894 time to fit residues: 17.6727 Evaluate side-chains 56 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 23 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 19 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 0.0870 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 275 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6238 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4897 Z= 0.320 Angle : 0.749 12.147 6636 Z= 0.388 Chirality : 0.048 0.168 757 Planarity : 0.005 0.054 825 Dihedral : 4.769 20.398 639 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.19 % Allowed : 4.73 % Favored : 95.09 % 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 (0.36), residues: 590 helix: 0.22 (0.32), residues: 258 sheet: 2.10 (0.47), residues: 119 loop : -0.22 (0.48), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 427 HIS 0.004 0.001 HIS A 551 PHE 0.023 0.002 PHE A 139 TYR 0.011 0.001 TYR A 444 ARG 0.004 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.490 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7809 (m-10) cc_final: 0.7402 (m-80) REVERT: A 436 TYR cc_start: 0.6975 (m-10) cc_final: 0.6625 (m-80) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.1862 time to fit residues: 16.7384 Evaluate side-chains 54 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 53 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 26 optimal weight: 0.1980 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.0040 chunk 41 optimal weight: 6.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4897 Z= 0.172 Angle : 0.654 8.807 6636 Z= 0.327 Chirality : 0.043 0.155 757 Planarity : 0.005 0.057 825 Dihedral : 4.487 17.557 639 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.19 % Allowed : 2.65 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.36), residues: 590 helix: 0.77 (0.34), residues: 245 sheet: 2.08 (0.47), residues: 118 loop : 0.01 (0.46), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 427 HIS 0.009 0.001 HIS A 551 PHE 0.028 0.002 PHE A 535 TYR 0.010 0.001 TYR A 444 ARG 0.003 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.497 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7766 (m-10) cc_final: 0.7356 (m-80) REVERT: A 340 ILE cc_start: 0.8095 (mm) cc_final: 0.7858 (mm) REVERT: A 436 TYR cc_start: 0.7095 (m-10) cc_final: 0.6742 (m-80) outliers start: 1 outliers final: 1 residues processed: 71 average time/residue: 0.1914 time to fit residues: 17.5404 Evaluate side-chains 58 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.9990 chunk 48 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6078 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4897 Z= 0.169 Angle : 0.639 7.722 6636 Z= 0.321 Chirality : 0.043 0.149 757 Planarity : 0.004 0.057 825 Dihedral : 4.360 15.720 639 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.19 % Allowed : 2.27 % Favored : 97.54 % 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: 1.12 (0.36), residues: 590 helix: 0.94 (0.34), residues: 245 sheet: 1.93 (0.47), residues: 119 loop : -0.02 (0.46), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 427 HIS 0.008 0.001 HIS A 551 PHE 0.026 0.002 PHE A 535 TYR 0.007 0.001 TYR A 444 ARG 0.004 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.520 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7799 (m-10) cc_final: 0.7389 (m-80) REVERT: A 436 TYR cc_start: 0.7070 (m-10) cc_final: 0.6716 (m-80) outliers start: 1 outliers final: 1 residues processed: 70 average time/residue: 0.2023 time to fit residues: 18.0889 Evaluate side-chains 58 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0670 chunk 36 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.0060 overall best weight: 1.1136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4897 Z= 0.205 Angle : 0.675 7.851 6636 Z= 0.339 Chirality : 0.045 0.180 757 Planarity : 0.004 0.057 825 Dihedral : 4.327 16.260 639 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.19 % Allowed : 0.76 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.36), residues: 590 helix: 0.82 (0.33), residues: 246 sheet: 1.94 (0.46), residues: 119 loop : -0.03 (0.46), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 427 HIS 0.007 0.001 HIS A 551 PHE 0.024 0.002 PHE A 535 TYR 0.006 0.001 TYR A 65 ARG 0.006 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.494 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7744 (m-10) cc_final: 0.7381 (m-80) REVERT: A 340 ILE cc_start: 0.8126 (mm) cc_final: 0.7910 (mm) REVERT: A 436 TYR cc_start: 0.7125 (m-10) cc_final: 0.6716 (m-80) outliers start: 1 outliers final: 1 residues processed: 72 average time/residue: 0.1710 time to fit residues: 15.8202 Evaluate side-chains 56 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 0.7980 chunk 41 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 50 optimal weight: 50.0000 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 ASN ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6235 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 4897 Z= 0.339 Angle : 0.785 7.830 6636 Z= 0.408 Chirality : 0.049 0.188 757 Planarity : 0.005 0.057 825 Dihedral : 4.686 19.317 639 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 0.19 % Allowed : 1.51 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.36), residues: 590 helix: 0.42 (0.33), residues: 248 sheet: 1.92 (0.47), residues: 119 loop : -0.10 (0.46), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 637 HIS 0.008 0.001 HIS A 551 PHE 0.037 0.003 PHE A 139 TYR 0.009 0.002 TYR A 65 ARG 0.005 0.001 ARG A 492 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.538 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7890 (m-10) cc_final: 0.7537 (m-80) REVERT: A 436 TYR cc_start: 0.7183 (m-10) cc_final: 0.6702 (m-80) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.1820 time to fit residues: 15.5119 Evaluate side-chains 53 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 8.9990 chunk 28 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6214 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 4897 Z= 0.290 Angle : 0.750 9.414 6636 Z= 0.384 Chirality : 0.048 0.169 757 Planarity : 0.005 0.058 825 Dihedral : 4.723 19.602 639 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.19 % Allowed : 0.57 % Favored : 99.24 % 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: 0.69 (0.36), residues: 590 helix: 0.42 (0.33), residues: 248 sheet: 1.88 (0.46), residues: 119 loop : -0.16 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 637 HIS 0.007 0.001 HIS A 551 PHE 0.031 0.002 PHE A 139 TYR 0.009 0.001 TYR A 444 ARG 0.005 0.000 ARG A 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1180 Ramachandran restraints generated. 590 Oldfield, 0 Emsley, 590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 64 time to evaluate : 0.542 Fit side-chains TARDY: cannot create tardy model for: "THR A 435 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 111 PHE cc_start: 0.7884 (m-10) cc_final: 0.7576 (m-80) REVERT: A 334 HIS cc_start: 0.8226 (t-90) cc_final: 0.8024 (t70) REVERT: A 436 TYR cc_start: 0.7254 (m-10) cc_final: 0.6728 (m-80) outliers start: 1 outliers final: 1 residues processed: 65 average time/residue: 0.1914 time to fit residues: 16.1627 Evaluate side-chains 53 residues out of total 529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 46 optimal weight: 40.0000 chunk 19 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 342 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 = 0.4733 r_free = 0.4733 target = 0.250898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.204069 restraints weight = 6109.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.202494 restraints weight = 12512.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.204949 restraints weight = 9861.166| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4897 Z= 0.199 Angle : 0.690 8.112 6636 Z= 0.346 Chirality : 0.045 0.149 757 Planarity : 0.005 0.058 825 Dihedral : 4.565 17.665 639 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.19 % Allowed : 0.19 % Favored : 99.62 % 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 (0.36), residues: 590 helix: 0.65 (0.33), residues: 253 sheet: 2.04 (0.47), residues: 117 loop : -0.14 (0.46), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 637 HIS 0.006 0.001 HIS A 551 PHE 0.024 0.002 PHE A 139 TYR 0.008 0.001 TYR A 181 ARG 0.005 0.001 ARG A 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1216.79 seconds wall clock time: 23 minutes 4.55 seconds (1384.55 seconds total)