Starting phenix.real_space_refine on Tue Mar 11 19:24:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc2_37090/03_2025/8kc2_37090.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 4135 2.51 5 N 1074 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6471 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4854 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1560 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' ZN': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.39, per 1000 atoms: 0.99 Number of scatterers: 6471 At special positions: 0 Unit cell: (97.68, 76.56, 121.44, 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 1225 8.00 N 1074 7.00 C 4135 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A 702 " - " ASN A 53 " " NAG A 703 " - " ASN A 82 " " NAG B 1 " - " ASN A 546 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 378 " 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1488 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 6 sheets defined 51.8% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 19 through 51 removed outlier: 3.963A pdb=" N GLU A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN A 24 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 38 " --> pdb=" O GLN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 removed outlier: 3.540A pdb=" N LYS A 68 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 83 No H-bonds generated for 'chain 'A' and resid 82 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.523A pdb=" N VAL A 88 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 102 removed outlier: 3.552A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 130 Processing helix chain 'A' and resid 147 through 155 Processing helix chain 'A' and resid 157 through 192 removed outlier: 3.570A pdb=" N LYS A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.003A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 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 221 through 248 removed outlier: 3.572A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Proline residue: A 235 - end of helix 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 282 removed outlier: 3.676A pdb=" N TYR A 279 " --> pdb=" O THR A 276 " (cutoff:3.500A) Proline residue: A 280 - end of helix Processing helix chain 'A' and resid 294 through 300 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.556A pdb=" N ILE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.813A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 375 removed outlier: 3.844A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.000A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 432 through 444 removed outlier: 3.518A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 474 through 484 removed outlier: 3.501A pdb=" N GLU A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 482 " --> pdb=" O TRP A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.381A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLN A 524 " --> pdb=" O ILE A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 558 removed outlier: 3.622A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.844A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.566A 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 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 removed outlier: 5.241A pdb=" N ARG E 408 " --> pdb=" O ASN E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 removed outlier: 3.560A pdb=" N TYR E 421 " --> pdb=" O ASN E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.908A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.558A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 376 " --> pdb=" O ALA E 435 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'E' and resid 473 through 474 261 hydrogen bonds defined for protein. 744 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: 1.86 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2077 1.35 - 1.47: 1713 1.47 - 1.59: 2803 1.59 - 1.72: 0 1.72 - 1.84: 56 Bond restraints: 6649 Sorted by residual: bond pdb=" C1 NAG A 703 " pdb=" O5 NAG A 703 " ideal model delta sigma weight residual 1.406 1.485 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.25e+01 bond pdb=" CE1 HIS A 378 " pdb=" NE2 HIS A 378 " ideal model delta sigma weight residual 1.321 1.356 -0.035 1.00e-02 1.00e+04 1.24e+01 bond pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 1.457 1.504 -0.047 1.40e-02 5.10e+03 1.15e+01 bond pdb=" CE1 HIS A 373 " pdb=" NE2 HIS A 373 " ideal model delta sigma weight residual 1.321 1.354 -0.033 1.00e-02 1.00e+04 1.09e+01 ... (remaining 6644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 8748 2.00 - 3.99: 240 3.99 - 5.99: 41 5.99 - 7.99: 4 7.99 - 9.99: 2 Bond angle restraints: 9035 Sorted by residual: angle pdb=" C ALA A 413 " pdb=" N THR A 414 " pdb=" CA THR A 414 " ideal model delta sigma weight residual 120.49 130.48 -9.99 1.42e+00 4.96e-01 4.95e+01 angle pdb=" C MET A 383 " pdb=" N ALA A 384 " pdb=" CA ALA A 384 " ideal model delta sigma weight residual 120.29 110.38 9.91 1.42e+00 4.96e-01 4.87e+01 angle pdb=" CA HIS A 378 " pdb=" CB HIS A 378 " pdb=" CG HIS A 378 " ideal model delta sigma weight residual 113.80 119.25 -5.45 1.00e+00 1.00e+00 2.97e+01 angle pdb=" CA PHE A 400 " pdb=" CB PHE A 400 " pdb=" CG PHE A 400 " ideal model delta sigma weight residual 113.80 118.84 -5.04 1.00e+00 1.00e+00 2.54e+01 angle pdb=" N PHE A 400 " pdb=" CA PHE A 400 " pdb=" C PHE A 400 " ideal model delta sigma weight residual 114.04 108.07 5.97 1.24e+00 6.50e-01 2.32e+01 ... (remaining 9030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.24: 3745 24.24 - 48.48: 200 48.48 - 72.72: 33 72.72 - 96.96: 6 96.96 - 121.20: 3 Dihedral angle restraints: 3987 sinusoidal: 1666 harmonic: 2321 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 -175.16 89.16 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" CA ASN E 360 " pdb=" C ASN E 360 " pdb=" N CYS E 361 " pdb=" CA CYS E 361 " ideal model delta harmonic sigma weight residual -180.00 -151.72 -28.28 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " pdb=" SG CYS E 432 " pdb=" CB CYS E 432 " ideal model delta sinusoidal sigma weight residual 93.00 46.79 46.21 1 1.00e+01 1.00e-02 2.96e+01 ... (remaining 3984 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 715 0.049 - 0.098: 175 0.098 - 0.147: 58 0.147 - 0.196: 3 0.196 - 0.245: 1 Chirality restraints: 952 Sorted by residual: chirality pdb=" C1 NAG A 703 " pdb=" ND2 ASN A 82 " pdb=" C2 NAG A 703 " pdb=" O5 NAG A 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.51e+00 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 2.70 -0.19 2.00e-01 2.50e+01 8.73e-01 chirality pdb=" CA MET A 383 " pdb=" N MET A 383 " pdb=" C MET A 383 " pdb=" CB MET A 383 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 949 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 518 " 0.402 9.50e-02 1.11e+02 1.80e-01 1.99e+01 pdb=" NE ARG A 518 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 518 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 518 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.032 5.00e-02 4.00e+02 4.83e-02 3.73e+00 pdb=" N PRO A 389 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO A 415 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.025 5.00e-02 4.00e+02 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 17 2.44 - 3.06: 3972 3.06 - 3.67: 9148 3.67 - 4.29: 13433 4.29 - 4.90: 23562 Nonbonded interactions: 50132 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 701 " model vdw 1.829 2.230 nonbonded pdb=" O VAL E 445 " pdb=" OG SER E 446 " model vdw 2.203 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD2 ASP A 509 " model vdw 2.248 3.040 nonbonded pdb=" NZ LYS E 378 " pdb=" OH TYR E 380 " model vdw 2.285 3.120 nonbonded pdb=" OE2 GLU A 57 " pdb=" O6 NAG A 702 " model vdw 2.289 3.040 ... (remaining 50127 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: 9.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 23.770 Find NCS groups from input model: 0.050 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: 0.000 Load rotamer database and sin/cos tables:14.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 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 0.079 6649 Z= 0.292 Angle : 0.752 9.987 9035 Z= 0.465 Chirality : 0.048 0.245 952 Planarity : 0.007 0.180 1170 Dihedral : 14.838 121.200 2478 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.87 % Favored : 93.00 % Rotamer: Outliers : 0.87 % Allowed : 1.31 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.30), residues: 786 helix: 0.37 (0.28), residues: 380 sheet: 1.20 (0.89), residues: 35 loop : -1.85 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 473 HIS 0.010 0.002 HIS A 378 PHE 0.024 0.002 PHE A 400 TYR 0.019 0.002 TYR A 521 ARG 0.006 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 171 time to evaluate : 0.654 Fit side-chains REVERT: A 206 ASP cc_start: 0.7217 (t70) cc_final: 0.6895 (t0) REVERT: A 341 LYS cc_start: 0.8243 (pttp) cc_final: 0.7999 (pttp) REVERT: E 401 VAL cc_start: 0.8681 (p) cc_final: 0.8454 (t) outliers start: 6 outliers final: 3 residues processed: 175 average time/residue: 1.3631 time to fit residues: 248.8239 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 153 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 394 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 0.0000 chunk 32 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 39 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.3980 chunk 23 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.0040 chunk 70 optimal weight: 0.9980 overall best weight: 0.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN A 89 GLN A 299 ASN A 578 ASN A 601 ASN E 460 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.116183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106997 restraints weight = 9158.519| |-----------------------------------------------------------------------------| r_work (start): 0.3478 rms_B_bonded: 1.64 r_work: 0.3379 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6649 Z= 0.195 Angle : 0.580 7.976 9035 Z= 0.305 Chirality : 0.044 0.317 952 Planarity : 0.004 0.048 1170 Dihedral : 9.132 107.905 957 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.62 % Allowed : 11.92 % Favored : 85.47 % 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: -0.52 (0.31), residues: 786 helix: 0.84 (0.28), residues: 374 sheet: 0.98 (0.89), residues: 36 loop : -1.79 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 28 TYR 0.021 0.001 TYR A 385 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.747 Fit side-chains REVERT: A 34 GLN cc_start: 0.7645 (OUTLIER) cc_final: 0.7156 (tp40) REVERT: A 95 ARG cc_start: 0.8423 (mtt90) cc_final: 0.8196 (mtt90) REVERT: A 206 ASP cc_start: 0.7776 (t70) cc_final: 0.7548 (t0) REVERT: A 323 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8384 (mmp) REVERT: A 341 LYS cc_start: 0.8435 (pttp) cc_final: 0.8185 (pttp) REVERT: A 597 GLU cc_start: 0.8150 (tp30) cc_final: 0.7856 (tm-30) REVERT: A 608 THR cc_start: 0.8578 (OUTLIER) cc_final: 0.8354 (m) outliers start: 18 outliers final: 5 residues processed: 161 average time/residue: 1.2827 time to fit residues: 215.9683 Evaluate side-chains 155 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 408 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.0670 chunk 62 optimal weight: 0.0370 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 8 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.1980 chunk 41 optimal weight: 0.9990 overall best weight: 0.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN E 394 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.117252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.107858 restraints weight = 9307.895| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.67 r_work: 0.3390 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6649 Z= 0.160 Angle : 0.537 9.722 9035 Z= 0.279 Chirality : 0.042 0.313 952 Planarity : 0.004 0.051 1170 Dihedral : 7.651 92.737 955 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.91 % Allowed : 13.37 % Favored : 83.72 % 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: -0.30 (0.31), residues: 786 helix: 1.10 (0.29), residues: 373 sheet: 1.04 (0.92), residues: 36 loop : -1.76 (0.31), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE A 32 TYR 0.020 0.001 TYR A 385 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7922 (tmt) REVERT: A 206 ASP cc_start: 0.7809 (t70) cc_final: 0.7547 (t0) REVERT: A 323 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8292 (mmp) REVERT: A 341 LYS cc_start: 0.8413 (pttp) cc_final: 0.8182 (pttp) REVERT: A 597 GLU cc_start: 0.8172 (tp30) cc_final: 0.7874 (tm-30) REVERT: E 460 ASN cc_start: 0.8127 (m-40) cc_final: 0.7657 (m110) outliers start: 20 outliers final: 10 residues processed: 162 average time/residue: 1.3504 time to fit residues: 229.5596 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 17 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 98 GLN A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.114127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.104833 restraints weight = 9299.381| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.67 r_work: 0.3345 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6649 Z= 0.244 Angle : 0.585 9.670 9035 Z= 0.302 Chirality : 0.044 0.173 952 Planarity : 0.004 0.053 1170 Dihedral : 5.731 49.025 952 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.20 % Allowed : 14.53 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.31), residues: 786 helix: 1.07 (0.28), residues: 377 sheet: 1.04 (0.92), residues: 36 loop : -1.78 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.027 0.002 TYR A 521 ARG 0.004 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 155 time to evaluate : 0.726 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7952 (tmt) REVERT: A 206 ASP cc_start: 0.7850 (t70) cc_final: 0.7559 (t0) REVERT: A 323 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (mmp) REVERT: A 334 THR cc_start: 0.8564 (m) cc_final: 0.8307 (p) REVERT: A 341 LYS cc_start: 0.8401 (pttp) cc_final: 0.8176 (pttp) REVERT: A 350 ASP cc_start: 0.8159 (t0) cc_final: 0.7957 (t70) REVERT: A 597 GLU cc_start: 0.8177 (tp30) cc_final: 0.7888 (tm-30) outliers start: 22 outliers final: 10 residues processed: 166 average time/residue: 1.3108 time to fit residues: 227.7720 Evaluate side-chains 166 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.2980 chunk 73 optimal weight: 0.0970 chunk 64 optimal weight: 0.0670 chunk 1 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 3 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS A 578 ASN A 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.114580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105280 restraints weight = 9154.462| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.65 r_work: 0.3355 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 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 0.040 6649 Z= 0.196 Angle : 0.559 7.064 9035 Z= 0.291 Chirality : 0.043 0.187 952 Planarity : 0.004 0.053 1170 Dihedral : 5.706 46.155 952 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.78 % Allowed : 14.68 % Favored : 81.54 % 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: -0.26 (0.31), residues: 786 helix: 1.14 (0.28), residues: 377 sheet: 0.92 (0.92), residues: 36 loop : -1.75 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.034 0.001 TYR A 521 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8242 (tmt) cc_final: 0.7938 (tmt) REVERT: A 206 ASP cc_start: 0.7837 (t70) cc_final: 0.7574 (t0) REVERT: A 323 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8260 (mmp) REVERT: A 334 THR cc_start: 0.8555 (m) cc_final: 0.8253 (p) REVERT: A 341 LYS cc_start: 0.8436 (pttp) cc_final: 0.8198 (pttp) REVERT: A 514 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.7658 (ptp90) REVERT: A 581 VAL cc_start: 0.8182 (OUTLIER) cc_final: 0.7981 (t) REVERT: A 597 GLU cc_start: 0.8173 (tp30) cc_final: 0.7891 (tm-30) REVERT: E 401 VAL cc_start: 0.8666 (OUTLIER) cc_final: 0.8343 (t) outliers start: 26 outliers final: 12 residues processed: 163 average time/residue: 1.2063 time to fit residues: 206.2133 Evaluate side-chains 170 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 GLU Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 24 optimal weight: 0.0770 chunk 51 optimal weight: 0.8980 chunk 57 optimal weight: 0.3980 chunk 69 optimal weight: 0.1980 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 0.3980 chunk 21 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 35 optimal weight: 0.0970 chunk 70 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.2136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.114388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.105148 restraints weight = 9082.432| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.64 r_work: 0.3351 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6649 Z= 0.192 Angle : 0.549 6.528 9035 Z= 0.288 Chirality : 0.042 0.171 952 Planarity : 0.004 0.053 1170 Dihedral : 4.737 46.392 952 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 3.63 % Allowed : 15.26 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.31), residues: 786 helix: 1.21 (0.28), residues: 377 sheet: 0.88 (0.92), residues: 36 loop : -1.75 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.024 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7606 (tttm) cc_final: 0.7396 (tttp) REVERT: A 190 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7984 (tmt) REVERT: A 206 ASP cc_start: 0.7863 (t70) cc_final: 0.7624 (t0) REVERT: A 334 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8280 (p) REVERT: A 514 ARG cc_start: 0.8504 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: A 581 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7993 (t) REVERT: A 597 GLU cc_start: 0.8175 (tp30) cc_final: 0.7894 (tm-30) REVERT: E 401 VAL cc_start: 0.8669 (OUTLIER) cc_final: 0.8350 (t) outliers start: 25 outliers final: 12 residues processed: 159 average time/residue: 1.2386 time to fit residues: 206.4109 Evaluate side-chains 166 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 190 MET Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.2980 chunk 16 optimal weight: 0.2980 chunk 50 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 chunk 58 optimal weight: 0.1980 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 0.1980 chunk 75 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 overall best weight: 0.2380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 401 HIS A 578 ASN A 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.114061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.104798 restraints weight = 9101.732| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.65 r_work: 0.3346 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3211 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6649 Z= 0.206 Angle : 0.558 8.066 9035 Z= 0.292 Chirality : 0.043 0.191 952 Planarity : 0.004 0.053 1170 Dihedral : 4.851 46.341 952 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.05 % Allowed : 15.99 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.31), residues: 786 helix: 1.32 (0.28), residues: 368 sheet: 0.84 (0.91), residues: 36 loop : -1.70 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 28 TYR 0.032 0.001 TYR A 521 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7876 (t70) cc_final: 0.7662 (t0) REVERT: A 334 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 514 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7621 (ptp90) REVERT: A 536 ASP cc_start: 0.8030 (p0) cc_final: 0.7739 (p0) REVERT: A 597 GLU cc_start: 0.8176 (tp30) cc_final: 0.7892 (tm-30) REVERT: E 401 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8360 (t) REVERT: E 442 ASP cc_start: 0.8521 (m-30) cc_final: 0.8321 (m-30) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 1.2389 time to fit residues: 201.2181 Evaluate side-chains 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 44 optimal weight: 0.3980 chunk 40 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 0.0050 overall best weight: 0.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.113072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.103832 restraints weight = 9102.724| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 1.65 r_work: 0.3322 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6649 Z= 0.238 Angle : 0.583 7.470 9035 Z= 0.307 Chirality : 0.044 0.173 952 Planarity : 0.004 0.054 1170 Dihedral : 4.764 46.178 952 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.91 % Allowed : 16.57 % Favored : 80.52 % 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: -0.18 (0.31), residues: 786 helix: 1.30 (0.28), residues: 369 sheet: 0.75 (0.90), residues: 36 loop : -1.72 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 28 TYR 0.037 0.002 TYR A 521 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.672 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7890 (t70) cc_final: 0.7603 (t0) REVERT: A 334 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (p) REVERT: A 514 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7629 (ptp90) REVERT: A 536 ASP cc_start: 0.8037 (p0) cc_final: 0.7771 (p0) REVERT: A 597 GLU cc_start: 0.8182 (tp30) cc_final: 0.7910 (tm-30) REVERT: E 401 VAL cc_start: 0.8698 (OUTLIER) cc_final: 0.8393 (t) REVERT: E 442 ASP cc_start: 0.8538 (m-30) cc_final: 0.8335 (m-30) outliers start: 20 outliers final: 14 residues processed: 157 average time/residue: 1.3408 time to fit residues: 221.1466 Evaluate side-chains 163 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 37 optimal weight: 0.1980 chunk 18 optimal weight: 0.3980 chunk 52 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 13 optimal weight: 0.0980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.112871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.103620 restraints weight = 9198.389| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.65 r_work: 0.3323 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6649 Z= 0.249 Angle : 0.594 7.487 9035 Z= 0.314 Chirality : 0.044 0.191 952 Planarity : 0.004 0.054 1170 Dihedral : 4.779 46.144 952 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.62 % Allowed : 16.86 % Favored : 80.52 % 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 (0.30), residues: 786 helix: 1.27 (0.28), residues: 370 sheet: 0.67 (0.89), residues: 36 loop : -1.75 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 28 TYR 0.043 0.002 TYR A 521 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 190 MET cc_start: 0.8213 (tmt) cc_final: 0.7952 (tmt) REVERT: A 206 ASP cc_start: 0.7905 (t70) cc_final: 0.7617 (t0) REVERT: A 334 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8337 (p) REVERT: A 514 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7631 (ptp90) REVERT: A 536 ASP cc_start: 0.8040 (p0) cc_final: 0.7781 (p0) REVERT: A 597 GLU cc_start: 0.8181 (tp30) cc_final: 0.7915 (tm-30) REVERT: E 401 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8400 (t) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 1.2768 time to fit residues: 201.7506 Evaluate side-chains 159 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 514 ARG Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 360 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 514 SER Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.0000 chunk 74 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.0980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 32 optimal weight: 0.0040 overall best weight: 0.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.106593 restraints weight = 9297.282| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 1.68 r_work: 0.3372 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6649 Z= 0.159 Angle : 0.535 5.822 9035 Z= 0.283 Chirality : 0.042 0.223 952 Planarity : 0.004 0.054 1170 Dihedral : 4.542 45.061 952 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.60 % Allowed : 18.60 % Favored : 79.80 % 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: -0.07 (0.31), residues: 786 helix: 1.43 (0.28), residues: 369 sheet: 0.75 (0.91), residues: 36 loop : -1.71 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 163 HIS 0.003 0.000 HIS A 241 PHE 0.007 0.001 PHE A 32 TYR 0.030 0.001 TYR A 521 ARG 0.002 0.000 ARG E 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1572 Ramachandran restraints generated. 786 Oldfield, 0 Emsley, 786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7887 (t70) cc_final: 0.7537 (t0) REVERT: A 334 THR cc_start: 0.8538 (OUTLIER) cc_final: 0.8315 (p) REVERT: A 536 ASP cc_start: 0.7988 (p0) cc_final: 0.7738 (p0) REVERT: A 597 GLU cc_start: 0.8217 (tp30) cc_final: 0.7957 (tm-30) REVERT: E 401 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8218 (t) outliers start: 11 outliers final: 7 residues processed: 149 average time/residue: 1.2639 time to fit residues: 197.3380 Evaluate side-chains 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 600 LYS Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 401 VAL Chi-restraints excluded: chain E residue 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 42 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.3980 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 76 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.113297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.103937 restraints weight = 9292.692| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.67 r_work: 0.3329 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6649 Z= 0.249 Angle : 0.596 7.344 9035 Z= 0.316 Chirality : 0.044 0.212 952 Planarity : 0.004 0.054 1170 Dihedral : 4.614 45.783 952 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.89 % Allowed : 19.04 % Favored : 79.07 % 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: -0.14 (0.31), residues: 786 helix: 1.38 (0.28), residues: 369 sheet: 0.59 (0.90), residues: 36 loop : -1.75 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.009 0.001 PHE A 28 TYR 0.040 0.002 TYR A 521 ARG 0.003 0.000 ARG A 273 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6713.43 seconds wall clock time: 114 minutes 46.61 seconds (6886.61 seconds total)