Starting phenix.real_space_refine on Sat May 10 12:00:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.map" model { file = "/net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8woz_37703/05_2025/8woz_37703.cif" } resolution = 3.25 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= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 36 5.16 5 C 3994 2.51 5 N 1032 2.21 5 O 1181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6244 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4858 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 26, 'TRANS': 569} Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1385 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 160} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.20, per 1000 atoms: 0.67 Number of scatterers: 6244 At special positions: 0 Unit cell: (77.28, 97.98, 107.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 36 16.00 O 1181 8.00 N 1032 7.00 C 3994 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " 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: 1.50 Conformation dependent library (CDL) restraints added in 905.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1450 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 4 sheets defined 54.9% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.876A pdb=" N LEU A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N TYR A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 78 removed outlier: 3.612A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.224A pdb=" N THR A 82 " --> pdb=" O LEU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.868A pdb=" N GLN A 102 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.783A pdb=" N ALA A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 194 removed outlier: 3.712A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.841A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 221 through 247 removed outlier: 3.516A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.659A pdb=" N PHE A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 removed outlier: 4.059A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.841A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.762A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 405 removed outlier: 3.927A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 413 removed outlier: 4.188A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.778A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.512A pdb=" N THR A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 466 " --> pdb=" O MET A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.679A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.832A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 4.524A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 4.613A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.606A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 352 through 356 removed outlier: 3.616A pdb=" N LEU B 355 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR B 356 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 356' Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.358A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU B 377 " --> pdb=" O LEU B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 397 removed outlier: 4.323A pdb=" N ARG B 395 " --> pdb=" O ASP B 392 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.610A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.143A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 341 through 345 Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 441 276 hydrogen bonds defined for protein. 774 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: 1.45 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1261 1.33 - 1.45: 1667 1.45 - 1.57: 3434 1.57 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 6420 Sorted by residual: bond pdb=" N ASP A 292 " pdb=" CA ASP A 292 " ideal model delta sigma weight residual 1.457 1.502 -0.045 1.29e-02 6.01e+03 1.19e+01 bond pdb=" N HIS A 378 " pdb=" CA HIS A 378 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.43e+00 bond pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.31e-02 5.83e+03 6.78e+00 bond pdb=" N VAL A 293 " pdb=" CA VAL A 293 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.38e+00 bond pdb=" C ASP A 292 " pdb=" O ASP A 292 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.26e-02 6.30e+03 4.78e+00 ... (remaining 6415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 8592 2.45 - 4.91: 110 4.91 - 7.36: 18 7.36 - 9.81: 2 9.81 - 12.26: 2 Bond angle restraints: 8724 Sorted by residual: angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.10 -5.30 1.00e+00 1.00e+00 2.81e+01 angle pdb=" C ASP A 292 " pdb=" CA ASP A 292 " pdb=" CB ASP A 292 " ideal model delta sigma weight residual 110.42 99.96 10.46 1.99e+00 2.53e-01 2.76e+01 angle pdb=" C HIS A 378 " pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " ideal model delta sigma weight residual 110.79 102.59 8.20 1.66e+00 3.63e-01 2.44e+01 angle pdb=" O GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 122.19 117.62 4.57 9.60e-01 1.09e+00 2.27e+01 angle pdb=" CA GLY A 377 " pdb=" C GLY A 377 " pdb=" N HIS A 378 " ideal model delta sigma weight residual 117.04 121.49 -4.45 9.90e-01 1.02e+00 2.02e+01 ... (remaining 8719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 3262 17.74 - 35.49: 398 35.49 - 53.23: 113 53.23 - 70.97: 9 70.97 - 88.71: 8 Dihedral angle restraints: 3790 sinusoidal: 1530 harmonic: 2260 Sorted by residual: dihedral pdb=" CB CYS A 344 " pdb=" SG CYS A 344 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual -86.00 -126.19 40.19 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA TRP A 473 " pdb=" C TRP A 473 " pdb=" N MET A 474 " pdb=" CA MET A 474 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS B 467 " pdb=" SG CYS B 467 " pdb=" SG CYS B 474 " pdb=" CB CYS B 474 " ideal model delta sinusoidal sigma weight residual -86.00 -55.24 -30.76 1 1.00e+01 1.00e-02 1.35e+01 ... (remaining 3787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 578 0.035 - 0.071: 246 0.071 - 0.106: 65 0.106 - 0.141: 18 0.141 - 0.176: 3 Chirality restraints: 910 Sorted by residual: chirality pdb=" CG LEU A 267 " pdb=" CB LEU A 267 " pdb=" CD1 LEU A 267 " pdb=" CD2 LEU A 267 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA HIS A 378 " pdb=" N HIS A 378 " pdb=" C HIS A 378 " pdb=" CB HIS A 378 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.29e-01 ... (remaining 907 not shown) Planarity restraints: 1127 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 257 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO A 258 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 398 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.45e+00 pdb=" N PRO B 399 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 399 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 399 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 378 " -0.025 2.00e-02 2.50e+03 2.04e-02 6.24e+00 pdb=" CG HIS A 378 " 0.040 2.00e-02 2.50e+03 pdb=" ND1 HIS A 378 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 378 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 378 " -0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 378 " -0.015 2.00e-02 2.50e+03 ... (remaining 1124 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 143 2.70 - 3.25: 6140 3.25 - 3.80: 9376 3.80 - 4.35: 11814 4.35 - 4.90: 19566 Nonbonded interactions: 47039 Sorted by model distance: nonbonded pdb=" O VAL A 293 " pdb=" OG1 THR A 294 " model vdw 2.147 3.040 nonbonded pdb=" NH1 ARG A 177 " pdb=" O GLU A 495 " model vdw 2.241 3.120 nonbonded pdb=" OG SER B 362 " pdb=" O ALA B 422 " model vdw 2.243 3.040 nonbonded pdb=" ND2 ASN A 137 " pdb=" OE1 GLN A 139 " model vdw 2.249 3.120 nonbonded pdb=" OD1 ASP A 198 " pdb=" N ASP A 201 " model vdw 2.314 3.120 ... (remaining 47034 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.690 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 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 : 0.005 0.292 6426 Z= 0.208 Angle : 0.704 12.263 8732 Z= 0.395 Chirality : 0.042 0.176 910 Planarity : 0.006 0.107 1127 Dihedral : 16.315 88.714 2328 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 22.88 % Favored : 76.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.70 % 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 (0.32), residues: 764 helix: 0.44 (0.28), residues: 381 sheet: 0.84 (0.81), residues: 40 loop : -1.48 (0.35), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 594 HIS 0.012 0.001 HIS A 378 PHE 0.018 0.001 PHE A 72 TYR 0.015 0.001 TYR A 183 ARG 0.002 0.000 ARG A 245 Details of bonding type rmsd hydrogen bonds : bond 0.17050 ( 276) hydrogen bonds : angle 6.19818 ( 774) metal coordination : bond 0.20680 ( 2) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.85294 ( 8) covalent geometry : bond 0.00330 ( 6420) covalent geometry : angle 0.70384 ( 8724) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.621 Fit side-chains REVERT: A 207 TYR cc_start: 0.7010 (m-10) cc_final: 0.6729 (m-10) REVERT: A 247 LYS cc_start: 0.6663 (tptt) cc_final: 0.6414 (mmtt) REVERT: A 539 LEU cc_start: 0.8697 (tp) cc_final: 0.8487 (tt) outliers start: 1 outliers final: 1 residues processed: 118 average time/residue: 0.1686 time to fit residues: 26.6794 Evaluate side-chains 114 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 4.9990 chunk 23 optimal weight: 4.9990 chunk 36 optimal weight: 0.2980 chunk 44 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** 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 = 0.4069 r_free = 0.4069 target = 0.159399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.138345 restraints weight = 9638.776| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.44 r_work: 0.3706 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.131 Angle : 0.581 11.315 8732 Z= 0.299 Chirality : 0.041 0.161 910 Planarity : 0.005 0.073 1127 Dihedral : 4.650 56.200 843 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.08 % Allowed : 20.95 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.39 (0.31), residues: 764 helix: 0.65 (0.27), residues: 389 sheet: 0.87 (0.80), residues: 42 loop : -1.52 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.016 0.001 PHE A 603 TYR 0.014 0.001 TYR A 183 ARG 0.004 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.05543 ( 276) hydrogen bonds : angle 4.32960 ( 774) metal coordination : bond 0.00408 ( 2) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.84542 ( 8) covalent geometry : bond 0.00282 ( 6420) covalent geometry : angle 0.58112 ( 8724) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.618 Fit side-chains REVERT: A 471 GLU cc_start: 0.8142 (pm20) cc_final: 0.7798 (pm20) REVERT: A 539 LEU cc_start: 0.8805 (tp) cc_final: 0.8586 (tt) outliers start: 14 outliers final: 5 residues processed: 126 average time/residue: 0.1565 time to fit residues: 26.9398 Evaluate side-chains 115 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 110 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain B residue 337 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 57 optimal weight: 0.0870 chunk 62 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 0.0370 chunk 24 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.159725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.138552 restraints weight = 9759.415| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 2.46 r_work: 0.3710 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.122 Angle : 0.567 10.998 8732 Z= 0.291 Chirality : 0.041 0.149 910 Planarity : 0.005 0.061 1127 Dihedral : 4.108 15.871 841 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.53 % Allowed : 20.80 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.23 (0.31), residues: 764 helix: 0.81 (0.27), residues: 388 sheet: 1.01 (0.81), residues: 42 loop : -1.48 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 594 HIS 0.004 0.001 HIS A 241 PHE 0.015 0.001 PHE A 603 TYR 0.014 0.001 TYR A 183 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05178 ( 276) hydrogen bonds : angle 4.14151 ( 774) metal coordination : bond 0.00233 ( 2) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.75919 ( 8) covalent geometry : bond 0.00262 ( 6420) covalent geometry : angle 0.56690 ( 8724) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.713 Fit side-chains REVERT: A 190 MET cc_start: 0.7611 (tmm) cc_final: 0.7211 (tmm) REVERT: A 364 VAL cc_start: 0.6679 (OUTLIER) cc_final: 0.6352 (t) REVERT: A 471 GLU cc_start: 0.8177 (pm20) cc_final: 0.7814 (pm20) REVERT: A 594 TRP cc_start: 0.7286 (OUTLIER) cc_final: 0.6909 (t-100) outliers start: 17 outliers final: 8 residues processed: 127 average time/residue: 0.1820 time to fit residues: 31.1999 Evaluate side-chains 121 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 594 TRP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 60 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 6 optimal weight: 0.0070 chunk 43 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 28 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 54 optimal weight: 0.1980 chunk 14 optimal weight: 1.9990 overall best weight: 0.2798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.139601 restraints weight = 9877.840| |-----------------------------------------------------------------------------| r_work (start): 0.3835 rms_B_bonded: 2.49 r_work: 0.3725 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6426 Z= 0.112 Angle : 0.545 9.929 8732 Z= 0.280 Chirality : 0.040 0.153 910 Planarity : 0.005 0.055 1127 Dihedral : 4.001 14.567 841 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.67 % Allowed : 20.06 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.12 (0.31), residues: 764 helix: 0.92 (0.27), residues: 385 sheet: 1.09 (0.83), residues: 42 loop : -1.44 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 594 HIS 0.003 0.001 HIS A 241 PHE 0.019 0.001 PHE A 438 TYR 0.015 0.001 TYR A 252 ARG 0.002 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.04643 ( 276) hydrogen bonds : angle 4.00042 ( 774) metal coordination : bond 0.00160 ( 2) SS BOND : bond 0.00093 ( 4) SS BOND : angle 0.69931 ( 8) covalent geometry : bond 0.00241 ( 6420) covalent geometry : angle 0.54502 ( 8724) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.616 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8160 (t0) cc_final: 0.7875 (t0) REVERT: A 190 MET cc_start: 0.7643 (tmm) cc_final: 0.7315 (tmm) REVERT: A 364 VAL cc_start: 0.6633 (OUTLIER) cc_final: 0.6310 (t) REVERT: A 419 LYS cc_start: 0.8223 (ttmt) cc_final: 0.8018 (tptt) REVERT: A 471 GLU cc_start: 0.8181 (pm20) cc_final: 0.7793 (pm20) REVERT: A 495 GLU cc_start: 0.6442 (tp30) cc_final: 0.5868 (tp30) outliers start: 18 outliers final: 12 residues processed: 132 average time/residue: 0.1607 time to fit residues: 28.8676 Evaluate side-chains 124 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 21 optimal weight: 0.2980 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** 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 = 0.4047 r_free = 0.4047 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136260 restraints weight = 9657.630| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.42 r_work: 0.3678 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6426 Z= 0.156 Angle : 0.588 11.154 8732 Z= 0.299 Chirality : 0.042 0.131 910 Planarity : 0.005 0.056 1127 Dihedral : 4.149 16.118 841 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.42 % Allowed : 20.36 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.19 (0.31), residues: 764 helix: 0.91 (0.27), residues: 380 sheet: 0.82 (0.83), residues: 44 loop : -1.48 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.007 0.001 HIS A 378 PHE 0.020 0.002 PHE A 438 TYR 0.018 0.002 TYR B 338 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05965 ( 276) hydrogen bonds : angle 4.10725 ( 774) metal coordination : bond 0.00424 ( 2) SS BOND : bond 0.00180 ( 4) SS BOND : angle 0.80198 ( 8) covalent geometry : bond 0.00352 ( 6420) covalent geometry : angle 0.58768 ( 8724) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 364 VAL cc_start: 0.6908 (OUTLIER) cc_final: 0.6571 (t) REVERT: A 367 ASP cc_start: 0.7055 (m-30) cc_final: 0.6802 (m-30) REVERT: A 419 LYS cc_start: 0.8395 (ttmt) cc_final: 0.8150 (tptt) REVERT: A 471 GLU cc_start: 0.8522 (pm20) cc_final: 0.8044 (pm20) REVERT: A 495 GLU cc_start: 0.6677 (tp30) cc_final: 0.6304 (tp30) outliers start: 23 outliers final: 14 residues processed: 140 average time/residue: 0.1662 time to fit residues: 31.4660 Evaluate side-chains 132 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 21 optimal weight: 0.2980 chunk 66 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 0.3980 chunk 62 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** 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 = 0.4061 r_free = 0.4061 target = 0.158678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.137599 restraints weight = 9722.625| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.42 r_work: 0.3696 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6426 Z= 0.128 Angle : 0.571 10.757 8732 Z= 0.293 Chirality : 0.041 0.169 910 Planarity : 0.005 0.056 1127 Dihedral : 4.112 15.318 841 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.53 % Allowed : 21.69 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.09 (0.31), residues: 764 helix: 0.98 (0.27), residues: 378 sheet: 0.92 (0.84), residues: 44 loop : -1.41 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 PHE 0.022 0.001 PHE A 438 TYR 0.016 0.001 TYR A 183 ARG 0.005 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.05233 ( 276) hydrogen bonds : angle 4.02899 ( 774) metal coordination : bond 0.00276 ( 2) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.72236 ( 8) covalent geometry : bond 0.00287 ( 6420) covalent geometry : angle 0.57087 ( 8724) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 117 time to evaluate : 0.567 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.7679 (tmm) cc_final: 0.7217 (tmm) REVERT: A 202 TYR cc_start: 0.7644 (t80) cc_final: 0.7434 (t80) REVERT: A 357 ARG cc_start: 0.7293 (mtt180) cc_final: 0.7043 (mtt180) REVERT: A 364 VAL cc_start: 0.6561 (OUTLIER) cc_final: 0.6231 (t) REVERT: A 419 LYS cc_start: 0.8220 (ttmt) cc_final: 0.8010 (tptt) REVERT: A 470 LYS cc_start: 0.7187 (mmtm) cc_final: 0.6929 (mmtm) REVERT: A 471 GLU cc_start: 0.8276 (pm20) cc_final: 0.7815 (pm20) REVERT: A 495 GLU cc_start: 0.6425 (tp30) cc_final: 0.6071 (tp30) outliers start: 17 outliers final: 13 residues processed: 129 average time/residue: 0.1715 time to fit residues: 30.0431 Evaluate side-chains 128 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 483 GLU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.156294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.135207 restraints weight = 9714.961| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.43 r_work: 0.3664 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6426 Z= 0.161 Angle : 0.599 11.277 8732 Z= 0.309 Chirality : 0.042 0.163 910 Planarity : 0.005 0.056 1127 Dihedral : 4.240 16.523 841 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.67 % Allowed : 22.73 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.27 (0.31), residues: 764 helix: 0.81 (0.27), residues: 380 sheet: 0.96 (0.83), residues: 44 loop : -1.51 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 165 HIS 0.008 0.001 HIS A 378 PHE 0.024 0.002 PHE A 438 TYR 0.019 0.002 TYR A 183 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.06139 ( 276) hydrogen bonds : angle 4.08300 ( 774) metal coordination : bond 0.00394 ( 2) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.75771 ( 8) covalent geometry : bond 0.00367 ( 6420) covalent geometry : angle 0.59885 ( 8724) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: A 419 LYS cc_start: 0.8399 (ttmt) cc_final: 0.8144 (tptt) REVERT: A 471 GLU cc_start: 0.8516 (pm20) cc_final: 0.8026 (pm20) REVERT: A 485 VAL cc_start: 0.7878 (t) cc_final: 0.7468 (t) REVERT: A 495 GLU cc_start: 0.6709 (tp30) cc_final: 0.6340 (tp30) outliers start: 18 outliers final: 13 residues processed: 138 average time/residue: 0.1682 time to fit residues: 31.2238 Evaluate side-chains 136 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 0.0970 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 ASN B 409 ASN B 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.158242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.137146 restraints weight = 9682.896| |-----------------------------------------------------------------------------| r_work (start): 0.3802 rms_B_bonded: 2.46 r_work: 0.3693 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6426 Z= 0.127 Angle : 0.581 10.639 8732 Z= 0.298 Chirality : 0.041 0.173 910 Planarity : 0.005 0.056 1127 Dihedral : 4.166 15.558 841 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.12 % Allowed : 22.14 % Favored : 74.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.09 (0.31), residues: 764 helix: 0.97 (0.27), residues: 378 sheet: 0.97 (0.83), residues: 44 loop : -1.41 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.004 0.001 HIS A 378 PHE 0.026 0.001 PHE A 438 TYR 0.020 0.001 TYR A 215 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 276) hydrogen bonds : angle 3.97927 ( 774) metal coordination : bond 0.00202 ( 2) SS BOND : bond 0.00132 ( 4) SS BOND : angle 0.70911 ( 8) covalent geometry : bond 0.00280 ( 6420) covalent geometry : angle 0.58087 ( 8724) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 364 VAL cc_start: 0.6409 (OUTLIER) cc_final: 0.6090 (t) REVERT: A 367 ASP cc_start: 0.6521 (m-30) cc_final: 0.6259 (m-30) REVERT: A 419 LYS cc_start: 0.8221 (ttmt) cc_final: 0.8009 (tptt) REVERT: A 471 GLU cc_start: 0.8279 (pm20) cc_final: 0.7817 (pm20) REVERT: A 485 VAL cc_start: 0.7736 (t) cc_final: 0.7381 (t) REVERT: A 495 GLU cc_start: 0.6443 (tp30) cc_final: 0.6078 (tp30) REVERT: A 596 LYS cc_start: 0.8422 (mtpt) cc_final: 0.8089 (mttp) outliers start: 21 outliers final: 13 residues processed: 133 average time/residue: 0.1587 time to fit residues: 28.7236 Evaluate side-chains 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 317 SER Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 0.6980 chunk 52 optimal weight: 0.0770 chunk 31 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 12 optimal weight: 0.0570 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 overall best weight: 0.2634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 368 ASN B 409 ASN B 424 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.160474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.139542 restraints weight = 9802.102| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.42 r_work: 0.3727 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6426 Z= 0.118 Angle : 0.580 9.790 8732 Z= 0.295 Chirality : 0.040 0.157 910 Planarity : 0.005 0.055 1127 Dihedral : 4.019 14.638 841 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.23 % Allowed : 23.48 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.09 (0.31), residues: 764 helix: 1.19 (0.28), residues: 371 sheet: 0.90 (0.83), residues: 44 loop : -1.33 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 165 HIS 0.003 0.001 HIS A 378 PHE 0.027 0.001 PHE A 438 TYR 0.014 0.001 TYR A 183 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 276) hydrogen bonds : angle 3.92202 ( 774) metal coordination : bond 0.00129 ( 2) SS BOND : bond 0.00084 ( 4) SS BOND : angle 0.73063 ( 8) covalent geometry : bond 0.00261 ( 6420) covalent geometry : angle 0.57976 ( 8724) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 0.611 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8142 (t0) cc_final: 0.7900 (t0) REVERT: A 207 TYR cc_start: 0.6793 (m-10) cc_final: 0.6508 (m-10) REVERT: A 357 ARG cc_start: 0.7235 (mtt180) cc_final: 0.6943 (mtt180) REVERT: A 364 VAL cc_start: 0.6383 (OUTLIER) cc_final: 0.6063 (t) REVERT: A 471 GLU cc_start: 0.8210 (pm20) cc_final: 0.7785 (pm20) REVERT: A 495 GLU cc_start: 0.6388 (tp30) cc_final: 0.6036 (tp30) REVERT: A 596 LYS cc_start: 0.8354 (mtpt) cc_final: 0.8140 (mttp) outliers start: 15 outliers final: 12 residues processed: 124 average time/residue: 0.1752 time to fit residues: 29.3738 Evaluate side-chains 130 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 409 ASN ** 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 = 0.4055 r_free = 0.4055 target = 0.157762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.136640 restraints weight = 9784.592| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 2.45 r_work: 0.3692 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6426 Z= 0.148 Angle : 0.607 10.248 8732 Z= 0.309 Chirality : 0.042 0.135 910 Planarity : 0.005 0.055 1127 Dihedral : 4.092 15.655 841 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 2.23 % Allowed : 23.92 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: -0.03 (0.31), residues: 764 helix: 1.09 (0.27), residues: 372 sheet: 0.91 (0.83), residues: 42 loop : -1.40 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 165 HIS 0.006 0.001 HIS A 378 PHE 0.027 0.002 PHE A 438 TYR 0.019 0.001 TYR A 183 ARG 0.002 0.000 ARG A 169 Details of bonding type rmsd hydrogen bonds : bond 0.05541 ( 276) hydrogen bonds : angle 4.01384 ( 774) metal coordination : bond 0.00302 ( 2) SS BOND : bond 0.00158 ( 4) SS BOND : angle 0.74937 ( 8) covalent geometry : bond 0.00338 ( 6420) covalent geometry : angle 0.60675 ( 8724) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8128 (t0) cc_final: 0.7879 (t0) REVERT: A 364 VAL cc_start: 0.6348 (OUTLIER) cc_final: 0.6038 (t) REVERT: A 471 GLU cc_start: 0.8208 (pm20) cc_final: 0.7994 (pm20) REVERT: A 485 VAL cc_start: 0.7743 (t) cc_final: 0.7401 (t) REVERT: A 495 GLU cc_start: 0.6475 (tp30) cc_final: 0.6095 (tp30) outliers start: 15 outliers final: 13 residues processed: 132 average time/residue: 0.1730 time to fit residues: 30.5501 Evaluate side-chains 135 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 154 LYS Chi-restraints excluded: chain A residue 203 TRP Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 539 LEU Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 54 optimal weight: 0.0020 chunk 34 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 64 optimal weight: 4.9990 chunk 12 optimal weight: 0.1980 chunk 26 optimal weight: 0.0470 chunk 43 optimal weight: 0.0770 chunk 66 optimal weight: 0.0670 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN A 534 GLN B 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.162866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.141786 restraints weight = 9961.386| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.49 r_work: 0.3761 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6426 Z= 0.116 Angle : 0.580 8.856 8732 Z= 0.295 Chirality : 0.040 0.149 910 Planarity : 0.005 0.054 1127 Dihedral : 3.918 13.713 841 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.38 % Allowed : 23.77 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % 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: 0.09 (0.31), residues: 764 helix: 1.27 (0.28), residues: 365 sheet: 0.77 (0.83), residues: 42 loop : -1.36 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 328 HIS 0.004 0.001 HIS A 378 PHE 0.029 0.001 PHE A 438 TYR 0.013 0.001 TYR A 183 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 276) hydrogen bonds : angle 3.87954 ( 774) metal coordination : bond 0.00039 ( 2) SS BOND : bond 0.00110 ( 4) SS BOND : angle 0.70252 ( 8) covalent geometry : bond 0.00256 ( 6420) covalent geometry : angle 0.57995 ( 8724) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3091.28 seconds wall clock time: 54 minutes 19.02 seconds (3259.02 seconds total)