Starting phenix.real_space_refine on Tue Feb 11 19:57:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kc2_37090/02_2025/8kc2_37090.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kc2_37090/02_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_37090/02_2025/8kc2_37090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kc2_37090/02_2025/8kc2_37090.map" model { file = "/net/cci-nas-00/data/ceres_data/8kc2_37090/02_2025/8kc2_37090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kc2_37090/02_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-5592/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: 6.55, per 1000 atoms: 1.01 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: 1.72 Conformation dependent library (CDL) restraints added in 1.1 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: 0.67 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: 1.68 Time building geometry restraints manager: 1.96 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: 7.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.340 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.500 ------------------------------------------------------------------------------- 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 : 0.662 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: 1.3070 time to fit residues: 238.9310 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 : 0.639 ------------------------------------------------------------------------------- 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: 0.0070 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: 0.1214 ------------------------------------------------------------------------------- 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 493 HIS A 578 ASN A 601 ASN E 460 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.117602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108298 restraints weight = 9201.537| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.68 r_work: 0.3393 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6649 Z= 0.169 Angle : 0.564 8.177 9035 Z= 0.295 Chirality : 0.043 0.296 952 Planarity : 0.004 0.049 1170 Dihedral : 9.025 105.998 957 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.76 % Allowed : 11.48 % Favored : 85.76 % 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: -0.47 (0.31), residues: 786 helix: 0.85 (0.29), residues: 373 sheet: 0.84 (0.88), residues: 36 loop : -1.67 (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 0.008 0.001 PHE E 377 TYR 0.020 0.001 TYR A 385 ARG 0.002 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 175 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.682 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7557 (OUTLIER) cc_final: 0.7107 (tp40) REVERT: A 206 ASP cc_start: 0.7770 (t70) cc_final: 0.7456 (t0) REVERT: A 323 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8370 (tpt) REVERT: A 341 LYS cc_start: 0.8447 (pttp) cc_final: 0.8193 (pttp) REVERT: A 597 GLU cc_start: 0.8214 (tp30) cc_final: 0.7907 (tm-30) REVERT: A 608 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8300 (m) REVERT: E 460 ASN cc_start: 0.8032 (m-40) cc_final: 0.7546 (m110) outliers start: 19 outliers final: 6 residues processed: 163 average time/residue: 1.2714 time to fit residues: 217.3438 Evaluate side-chains 153 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 144 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 398 GLU Chi-restraints excluded: chain A residue 401 HIS Chi-restraints excluded: chain A residue 608 THR Chi-restraints excluded: chain E residue 335 LEU 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: 0.6980 chunk 32 optimal weight: 0.0980 chunk 51 optimal weight: 0.5980 chunk 62 optimal weight: 0.0020 chunk 52 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 overall best weight: 0.2346 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.115410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.106106 restraints weight = 9309.685| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.66 r_work: 0.3383 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1493 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= 0.206 Angle : 0.570 9.711 9035 Z= 0.297 Chirality : 0.043 0.298 952 Planarity : 0.004 0.051 1170 Dihedral : 7.989 96.281 955 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 3.20 % Allowed : 13.08 % 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: -0.41 (0.31), residues: 786 helix: 1.01 (0.28), residues: 377 sheet: 1.01 (0.91), residues: 36 loop : -1.84 (0.31), residues: 373 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 0.010 0.001 PHE A 32 TYR 0.027 0.001 TYR A 521 ARG 0.004 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 179 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 31 LYS cc_start: 0.7563 (ttpp) cc_final: 0.7327 (tttp) REVERT: A 34 GLN cc_start: 0.7583 (OUTLIER) cc_final: 0.7065 (tp40) REVERT: A 95 ARG cc_start: 0.8393 (mtt90) cc_final: 0.8159 (mtt90) REVERT: A 206 ASP cc_start: 0.7771 (t70) cc_final: 0.7515 (t0) REVERT: A 323 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8326 (mmp) REVERT: A 341 LYS cc_start: 0.8396 (pttp) cc_final: 0.8170 (pttp) REVERT: A 597 GLU cc_start: 0.8194 (tp30) cc_final: 0.7895 (tm-30) outliers start: 22 outliers final: 10 residues processed: 165 average time/residue: 1.3423 time to fit residues: 231.6296 Evaluate side-chains 164 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLN Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 183 TYR 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 A residue 568 LEU Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 408 ARG 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: 0.8980 chunk 32 optimal weight: 0.4980 chunk 43 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 0.0980 chunk 29 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 ** E 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.103514 restraints weight = 9249.682| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.65 r_work: 0.3325 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6649 Z= 0.282 Angle : 0.612 9.115 9035 Z= 0.320 Chirality : 0.046 0.325 952 Planarity : 0.004 0.054 1170 Dihedral : 7.729 99.947 955 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 4.65 % Allowed : 13.52 % Favored : 81.83 % 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: -0.39 (0.31), residues: 786 helix: 1.01 (0.28), residues: 378 sheet: 1.01 (0.92), residues: 36 loop : -1.81 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.002 PHE A 400 TYR 0.037 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 187 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 155 time to evaluate : 0.694 Fit side-chains REVERT: A 95 ARG cc_start: 0.8397 (mtt90) cc_final: 0.8183 (mtt90) REVERT: A 206 ASP cc_start: 0.7851 (t70) cc_final: 0.7581 (t0) REVERT: A 323 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8316 (mmp) REVERT: A 341 LYS cc_start: 0.8437 (pttp) cc_final: 0.8203 (pttp) REVERT: A 350 ASP cc_start: 0.8183 (t0) cc_final: 0.7977 (t70) REVERT: A 514 ARG cc_start: 0.8551 (OUTLIER) cc_final: 0.7610 (ptp90) REVERT: A 597 GLU cc_start: 0.8190 (tp30) cc_final: 0.7911 (tm-30) REVERT: E 401 VAL cc_start: 0.8710 (p) cc_final: 0.8421 (t) outliers start: 32 outliers final: 15 residues processed: 167 average time/residue: 1.3186 time to fit residues: 230.0981 Evaluate side-chains 168 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 305 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 600 LYS Chi-restraints excluded: chain E residue 336 CYS Chi-restraints excluded: chain E residue 354 ASN Chi-restraints excluded: chain E residue 366 SER Chi-restraints excluded: chain E residue 367 VAL Chi-restraints excluded: chain E residue 408 ARG Chi-restraints excluded: chain E residue 409 GLN Chi-restraints excluded: chain E residue 417 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.3980 chunk 73 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 45 optimal weight: 0.3980 chunk 3 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.3980 ------------------------------------------------------------------------------- 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 E 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.102983 restraints weight = 9091.474| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.63 r_work: 0.3316 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6649 Z= 0.295 Angle : 0.612 9.126 9035 Z= 0.320 Chirality : 0.046 0.309 952 Planarity : 0.005 0.056 1170 Dihedral : 7.404 98.792 952 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.78 % Allowed : 14.39 % Favored : 81.83 % 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: -0.40 (0.30), residues: 786 helix: 1.03 (0.28), residues: 378 sheet: 0.77 (0.91), residues: 36 loop : -1.82 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.002 PHE A 28 TYR 0.024 0.002 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 175 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.688 Fit side-chains REVERT: A 206 ASP cc_start: 0.7866 (t70) cc_final: 0.7601 (t0) REVERT: A 323 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8306 (mmp) REVERT: A 350 ASP cc_start: 0.8179 (t0) cc_final: 0.7977 (t70) REVERT: A 514 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7580 (ptp90) REVERT: A 536 ASP cc_start: 0.8046 (p0) cc_final: 0.7766 (p0) REVERT: A 581 VAL cc_start: 0.8226 (OUTLIER) cc_final: 0.8001 (t) REVERT: A 597 GLU cc_start: 0.8193 (tp30) cc_final: 0.7918 (tm-30) REVERT: E 401 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8412 (t) outliers start: 26 outliers final: 12 residues processed: 160 average time/residue: 1.3302 time to fit residues: 222.6514 Evaluate side-chains 166 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 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 408 ARG 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: 0.1980 chunk 51 optimal weight: 0.0370 chunk 57 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 40 optimal weight: 0.0060 chunk 21 optimal weight: 0.4980 chunk 15 optimal weight: 0.4980 chunk 35 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 chunk 23 optimal weight: 0.0070 overall best weight: 0.0468 ------------------------------------------------------------------------------- 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 E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.107875 restraints weight = 9102.598| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.65 r_work: 0.3394 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2188 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= 0.143 Angle : 0.531 9.788 9035 Z= 0.273 Chirality : 0.041 0.295 952 Planarity : 0.004 0.053 1170 Dihedral : 6.850 93.373 952 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.62 % Allowed : 16.42 % 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: -0.03 (0.31), residues: 786 helix: 1.39 (0.28), residues: 366 sheet: 0.87 (0.93), residues: 36 loop : -1.60 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.002 0.000 HIS A 374 PHE 0.007 0.001 PHE A 452 TYR 0.020 0.001 TYR A 521 ARG 0.004 0.000 ARG A 95 *********************** 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 162 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7862 (t70) cc_final: 0.7633 (t0) REVERT: A 323 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8243 (tpt) REVERT: A 536 ASP cc_start: 0.7969 (p0) cc_final: 0.7690 (p0) REVERT: A 597 GLU cc_start: 0.8219 (tp30) cc_final: 0.7951 (tm-30) REVERT: E 401 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8156 (t) outliers start: 18 outliers final: 9 residues processed: 153 average time/residue: 1.3454 time to fit residues: 215.9458 Evaluate side-chains 152 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR 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 366 SER Chi-restraints excluded: chain E residue 394 ASN Chi-restraints excluded: chain E residue 401 VAL 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: 0.0980 chunk 50 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 0.0980 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 61 optimal weight: 0.0060 overall best weight: 0.1596 ------------------------------------------------------------------------------- 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 = 0.3614 r_free = 0.3614 target = 0.115842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.106511 restraints weight = 9096.958| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.65 r_work: 0.3370 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6649 Z= 0.172 Angle : 0.553 10.264 9035 Z= 0.285 Chirality : 0.043 0.318 952 Planarity : 0.004 0.054 1170 Dihedral : 6.141 78.062 952 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.03 % Allowed : 17.88 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.31), residues: 786 helix: 1.43 (0.28), residues: 368 sheet: 0.73 (0.91), residues: 36 loop : -1.63 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.034 0.001 TYR A 521 ARG 0.009 0.000 ARG A 95 *********************** 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 155 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.717 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7866 (t70) cc_final: 0.7588 (t0) REVERT: A 536 ASP cc_start: 0.8024 (p0) cc_final: 0.7740 (p0) REVERT: A 597 GLU cc_start: 0.8212 (tp30) cc_final: 0.7944 (tm-30) REVERT: E 401 VAL cc_start: 0.8596 (OUTLIER) cc_final: 0.8226 (t) REVERT: E 500 THR cc_start: 0.8773 (OUTLIER) cc_final: 0.8572 (p) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 1.3004 time to fit residues: 201.4537 Evaluate side-chains 148 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR 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 500 THR 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: 0.0370 chunk 20 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 chunk 51 optimal weight: 0.6980 chunk 14 optimal weight: 0.1980 chunk 44 optimal weight: 0.2980 chunk 40 optimal weight: 0.3980 chunk 77 optimal weight: 0.0370 chunk 11 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 chunk 19 optimal weight: 0.1980 overall best weight: 0.1134 ------------------------------------------------------------------------------- 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 = 0.3626 r_free = 0.3626 target = 0.116679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.107276 restraints weight = 9129.514| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.68 r_work: 0.3382 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6649 Z= 0.154 Angle : 0.541 9.354 9035 Z= 0.278 Chirality : 0.041 0.192 952 Planarity : 0.004 0.053 1170 Dihedral : 5.146 48.527 952 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.18 % Allowed : 18.75 % 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: 0.06 (0.31), residues: 786 helix: 1.51 (0.28), residues: 368 sheet: 0.73 (0.91), residues: 36 loop : -1.60 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 163 HIS 0.003 0.000 HIS A 241 PHE 0.007 0.001 PHE A 32 TYR 0.024 0.001 TYR A 521 ARG 0.005 0.000 ARG A 95 *********************** 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 156 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7861 (t70) cc_final: 0.7517 (t0) REVERT: A 536 ASP cc_start: 0.8009 (p0) cc_final: 0.7727 (p0) REVERT: A 597 GLU cc_start: 0.8221 (tp30) cc_final: 0.7961 (tm-30) REVERT: E 401 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8227 (t) REVERT: E 460 ASN cc_start: 0.8167 (m-40) cc_final: 0.7714 (m110) REVERT: E 500 THR cc_start: 0.8767 (OUTLIER) cc_final: 0.8553 (p) outliers start: 15 outliers final: 10 residues processed: 150 average time/residue: 1.2835 time to fit residues: 202.7305 Evaluate side-chains 149 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 398 GLU Chi-restraints excluded: chain A residue 517 THR 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 500 THR 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: 0.0870 chunk 18 optimal weight: 0.4980 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 25 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.112118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.102773 restraints weight = 9162.164| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 1.66 r_work: 0.3311 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6649 Z= 0.294 Angle : 0.630 8.254 9035 Z= 0.329 Chirality : 0.045 0.192 952 Planarity : 0.004 0.055 1170 Dihedral : 5.051 46.723 952 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.33 % Allowed : 18.31 % Favored : 79.36 % 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: -0.08 (0.31), residues: 786 helix: 1.44 (0.28), residues: 368 sheet: 0.53 (0.90), residues: 36 loop : -1.71 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.002 PHE A 400 TYR 0.042 0.002 TYR A 521 ARG 0.006 0.001 ARG A 95 *********************** 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: 16 poor density : 146 time to evaluate : 0.798 Fit side-chains revert: symmetry clash REVERT: A 20 ILE cc_start: 0.8002 (mm) cc_final: 0.7615 (tt) REVERT: A 206 ASP cc_start: 0.7891 (t70) cc_final: 0.7598 (t0) REVERT: A 536 ASP cc_start: 0.8078 (p0) cc_final: 0.7806 (p0) REVERT: A 597 GLU cc_start: 0.8212 (tp30) cc_final: 0.7952 (tm-30) REVERT: E 401 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8424 (t) outliers start: 16 outliers final: 9 residues processed: 153 average time/residue: 1.3758 time to fit residues: 220.1476 Evaluate side-chains 151 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 398 GLU 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 517 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 45 optimal weight: 0.2980 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 67 optimal weight: 0.0970 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 50 optimal weight: 0.4980 chunk 71 optimal weight: 0.1980 chunk 13 optimal weight: 0.0040 chunk 73 optimal weight: 0.8980 chunk 32 optimal weight: 0.1980 overall best weight: 0.1590 ------------------------------------------------------------------------------- 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 E 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.114820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.105434 restraints weight = 9247.227| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.67 r_work: 0.3355 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6649 Z= 0.173 Angle : 0.559 5.964 9035 Z= 0.292 Chirality : 0.042 0.209 952 Planarity : 0.004 0.054 1170 Dihedral : 4.734 45.108 952 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.03 % Allowed : 18.90 % 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: 0.01 (0.31), residues: 786 helix: 1.50 (0.28), residues: 370 sheet: 0.54 (0.89), residues: 36 loop : -1.66 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.040 0.001 TYR A 521 ARG 0.005 0.000 ARG A 95 ********************** 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 150 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7870 (t70) cc_final: 0.7530 (t0) REVERT: A 536 ASP cc_start: 0.8022 (p0) cc_final: 0.7768 (p0) REVERT: A 597 GLU cc_start: 0.8205 (tp30) cc_final: 0.7952 (tm-30) REVERT: E 401 VAL cc_start: 0.8650 (OUTLIER) cc_final: 0.8314 (t) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 1.4168 time to fit residues: 210.5074 Evaluate side-chains 147 residues out of total 688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 136 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 398 GLU 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 394 ASN 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: 0.0980 chunk 62 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 43 optimal weight: 0.0870 chunk 23 optimal weight: 0.6980 chunk 74 optimal weight: 0.0030 chunk 40 optimal weight: 0.3980 chunk 76 optimal weight: 0.0470 chunk 29 optimal weight: 0.3980 chunk 0 optimal weight: 0.9990 overall best weight: 0.0866 ------------------------------------------------------------------------------- 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 = 0.3600 r_free = 0.3600 target = 0.114854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.105406 restraints weight = 9327.271| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 1.68 r_work: 0.3353 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 6649 Z= 0.209 Angle : 0.988 59.199 9035 Z= 0.590 Chirality : 0.053 0.972 952 Planarity : 0.004 0.054 1170 Dihedral : 4.780 45.134 952 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.74 % Allowed : 19.04 % Favored : 79.22 % Cbeta Deviations : 0.13 % 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: 0.01 (0.31), residues: 786 helix: 1.51 (0.28), residues: 370 sheet: 0.53 (0.89), residues: 36 loop : -1.67 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 241 PHE 0.008 0.001 PHE A 32 TYR 0.040 0.001 TYR A 521 ARG 0.003 0.000 ARG A 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6248.17 seconds wall clock time: 111 minutes 38.77 seconds (6698.77 seconds total)