Starting phenix.real_space_refine on Sat Aug 3 01:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_37090.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_37090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_37090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_37090.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kc2_37090/08_2024/8kc2_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 Residue "A TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.75, per 1000 atoms: 0.89 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 - 3.50 Amino acid : False - 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: 2.49 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: 0.71 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: 1.63 Time building geometry restraints manager: 2.75 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: 98.36 - 105.52: 133 105.52 - 112.67: 3298 112.67 - 119.82: 2387 119.82 - 126.98: 3113 126.98 - 134.13: 104 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: 13.550 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.920 Find NCS groups from input model: 0.070 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:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.130 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 6 poor density : 171 time to evaluate : 0.659 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: 1.2449 time to fit residues: 227.7684 Evaluate side-chains 156 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 153 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 fitting. rotamer outliers: 19 poor density : 156 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6709 (tp40) REVERT: A 206 ASP cc_start: 0.7201 (t70) cc_final: 0.6849 (t0) REVERT: A 341 LYS cc_start: 0.8286 (pttp) cc_final: 0.8013 (pttp) REVERT: A 597 GLU cc_start: 0.7636 (tp30) cc_final: 0.7299 (tm-30) REVERT: A 608 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8202 (m) REVERT: E 460 ASN cc_start: 0.7841 (m-40) cc_final: 0.7639 (m110) outliers start: 19 outliers final: 6 residues processed: 163 average time/residue: 1.2200 time to fit residues: 208.7148 Evaluate side-chains 152 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 144 time to evaluate : 0.724 ------------------------------------------------------------------------------- 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 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 39 optimal weight: 0.0980 chunk 21 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.2980 chunk 76 optimal weight: 0.1980 chunk 63 optimal weight: 0.0270 chunk 24 optimal weight: 0.2980 chunk 56 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 overall best weight: 0.1838 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1515 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= 0.182 Angle : 0.557 9.302 9035 Z= 0.289 Chirality : 0.043 0.339 952 Planarity : 0.004 0.051 1170 Dihedral : 7.912 96.007 955 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.20 % Allowed : 13.23 % Favored : 83.58 % 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: -0.32 (0.31), residues: 786 helix: 1.06 (0.28), residues: 375 sheet: 0.98 (0.91), residues: 36 loop : -1.74 (0.31), residues: 375 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 0.028 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 177 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7191 (t70) cc_final: 0.6894 (t0) REVERT: A 341 LYS cc_start: 0.8262 (pttp) cc_final: 0.8015 (pttp) REVERT: A 597 GLU cc_start: 0.7593 (tp30) cc_final: 0.7256 (tm-30) outliers start: 22 outliers final: 9 residues processed: 164 average time/residue: 1.2223 time to fit residues: 210.1538 Evaluate side-chains 156 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 147 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LYS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 305 GLU 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 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 36 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 417 ASN E 460 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 6649 Z= 0.406 Angle : 0.673 8.866 9035 Z= 0.352 Chirality : 0.048 0.177 952 Planarity : 0.005 0.056 1170 Dihedral : 5.856 48.033 952 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 4.22 % Allowed : 12.94 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.30), residues: 786 helix: 0.97 (0.28), residues: 376 sheet: 0.89 (0.90), residues: 36 loop : -1.91 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 473 HIS 0.007 0.001 HIS A 241 PHE 0.015 0.002 PHE A 400 TYR 0.035 0.002 TYR A 521 ARG 0.006 0.001 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 185 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 0.742 Fit side-chains REVERT: A 206 ASP cc_start: 0.7306 (t70) cc_final: 0.6998 (t0) REVERT: A 282 THR cc_start: 0.8036 (OUTLIER) cc_final: 0.7828 (p) REVERT: A 341 LYS cc_start: 0.8292 (pttp) cc_final: 0.8055 (pttp) REVERT: A 350 ASP cc_start: 0.7828 (t0) cc_final: 0.7613 (t70) REVERT: A 514 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7138 (ptp90) REVERT: A 536 ASP cc_start: 0.7625 (p0) cc_final: 0.7353 (p0) REVERT: A 597 GLU cc_start: 0.7592 (tp30) cc_final: 0.7276 (tm-30) REVERT: E 401 VAL cc_start: 0.8651 (p) cc_final: 0.8419 (t) outliers start: 29 outliers final: 11 residues processed: 169 average time/residue: 1.3216 time to fit residues: 233.4639 Evaluate side-chains 171 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 305 GLU 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 408 ARG Chi-restraints excluded: chain E residue 417 ASN Chi-restraints excluded: chain E residue 483 VAL Chi-restraints excluded: chain E residue 503 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 1 optimal weight: 0.0980 chunk 56 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 578 ASN A 601 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6649 Z= 0.322 Angle : 0.634 8.760 9035 Z= 0.332 Chirality : 0.046 0.174 952 Planarity : 0.005 0.057 1170 Dihedral : 5.910 47.399 952 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 3.92 % Allowed : 14.83 % Favored : 81.25 % 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: -0.46 (0.30), residues: 786 helix: 0.97 (0.28), residues: 372 sheet: 0.76 (0.90), residues: 36 loop : -1.81 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 473 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.002 PHE A 400 TYR 0.025 0.002 TYR A 521 ARG 0.004 0.001 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 180 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 153 time to evaluate : 0.790 Fit side-chains REVERT: A 206 ASP cc_start: 0.7312 (t70) cc_final: 0.7021 (t0) REVERT: A 282 THR cc_start: 0.8022 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 334 THR cc_start: 0.8416 (m) cc_final: 0.8180 (p) REVERT: A 347 THR cc_start: 0.8551 (m) cc_final: 0.8275 (p) REVERT: A 350 ASP cc_start: 0.7808 (t0) cc_final: 0.7603 (t70) REVERT: A 514 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7131 (ptp90) REVERT: A 536 ASP cc_start: 0.7630 (p0) cc_final: 0.7352 (p0) REVERT: A 581 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7815 (t) REVERT: A 597 GLU cc_start: 0.7560 (tp30) cc_final: 0.7252 (tm-30) REVERT: E 401 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8381 (t) REVERT: E 442 ASP cc_start: 0.8412 (m-30) cc_final: 0.8160 (m-30) outliers start: 27 outliers final: 14 residues processed: 165 average time/residue: 1.2609 time to fit residues: 217.8012 Evaluate side-chains 168 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.561 ------------------------------------------------------------------------------- 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 282 THR Chi-restraints excluded: chain A residue 297 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 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.4980 chunk 62 optimal weight: 0.0770 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 0.0010 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 72 optimal weight: 0.4980 chunk 8 optimal weight: 0.0010 chunk 42 optimal weight: 0.2980 overall best weight: 0.1750 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2156 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= 0.186 Angle : 0.560 6.693 9035 Z= 0.292 Chirality : 0.042 0.174 952 Planarity : 0.004 0.056 1170 Dihedral : 5.136 45.830 952 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.78 % Allowed : 15.70 % 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: -0.30 (0.30), residues: 786 helix: 1.10 (0.28), residues: 377 sheet: 0.81 (0.92), residues: 36 loop : -1.75 (0.30), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 163 HIS 0.004 0.001 HIS A 241 PHE 0.009 0.001 PHE A 32 TYR 0.021 0.001 TYR A 521 ARG 0.002 0.000 ARG E 457 *********************** 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 171 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7315 (t70) cc_final: 0.6994 (t0) REVERT: A 334 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8086 (p) REVERT: A 347 THR cc_start: 0.8563 (m) cc_final: 0.8310 (p) REVERT: A 350 ASP cc_start: 0.7807 (t0) cc_final: 0.7599 (t0) REVERT: A 536 ASP cc_start: 0.7591 (p0) cc_final: 0.7326 (p0) REVERT: A 581 VAL cc_start: 0.8026 (OUTLIER) cc_final: 0.7782 (t) REVERT: A 597 GLU cc_start: 0.7555 (tp30) cc_final: 0.7259 (tm-30) REVERT: E 401 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8278 (t) REVERT: E 442 ASP cc_start: 0.8389 (m-30) cc_final: 0.8144 (m-30) outliers start: 26 outliers final: 9 residues processed: 157 average time/residue: 1.2555 time to fit residues: 206.4321 Evaluate side-chains 155 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 143 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 208 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 581 VAL 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 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 55 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 45 optimal weight: 0.0870 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 overall best weight: 0.4158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 6649 Z= 0.306 Angle : 0.625 8.691 9035 Z= 0.329 Chirality : 0.045 0.173 952 Planarity : 0.005 0.057 1170 Dihedral : 5.057 47.117 952 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 2.91 % Allowed : 16.42 % Favored : 80.67 % 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 (0.30), residues: 786 helix: 1.08 (0.28), residues: 378 sheet: 0.68 (0.91), residues: 36 loop : -1.77 (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 400 TYR 0.045 0.002 TYR A 521 ARG 0.003 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 fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 ASP cc_start: 0.7335 (t70) cc_final: 0.7023 (t0) REVERT: A 334 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 347 THR cc_start: 0.8604 (m) cc_final: 0.8275 (p) REVERT: A 350 ASP cc_start: 0.7814 (t0) cc_final: 0.7602 (t0) REVERT: A 514 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7124 (ptp90) REVERT: A 536 ASP cc_start: 0.7632 (p0) cc_final: 0.7365 (p0) REVERT: A 597 GLU cc_start: 0.7576 (tp30) cc_final: 0.7280 (tm-30) REVERT: E 401 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8370 (t) REVERT: E 442 ASP cc_start: 0.8423 (m-30) cc_final: 0.8175 (m-30) outliers start: 20 outliers final: 9 residues processed: 157 average time/residue: 1.3059 time to fit residues: 214.1414 Evaluate side-chains 157 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU 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 600 LYS 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 409 GLN 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 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 59 optimal weight: 0.0970 chunk 68 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 65 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 89 GLN A 578 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6649 Z= 0.272 Angle : 0.607 7.908 9035 Z= 0.320 Chirality : 0.045 0.174 952 Planarity : 0.005 0.057 1170 Dihedral : 5.010 46.087 952 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % 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: -0.34 (0.30), residues: 786 helix: 1.09 (0.28), residues: 379 sheet: 0.63 (0.90), residues: 36 loop : -1.79 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 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 0.002 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 167 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 147 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6697 (mt-10) REVERT: A 95 ARG cc_start: 0.8086 (mtt90) cc_final: 0.7845 (mtt90) REVERT: A 206 ASP cc_start: 0.7337 (t70) cc_final: 0.7041 (t0) REVERT: A 334 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8095 (p) REVERT: A 347 THR cc_start: 0.8601 (m) cc_final: 0.8257 (p) REVERT: A 514 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7106 (ptp90) REVERT: A 536 ASP cc_start: 0.7631 (p0) cc_final: 0.7372 (p0) REVERT: A 597 GLU cc_start: 0.7570 (tp30) cc_final: 0.7273 (tm-30) REVERT: E 401 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8347 (t) REVERT: E 442 ASP cc_start: 0.8433 (m-30) cc_final: 0.8189 (m-30) outliers start: 20 outliers final: 11 residues processed: 156 average time/residue: 1.3435 time to fit residues: 218.9120 Evaluate side-chains 160 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 GLN 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 600 LYS 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 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 30 optimal weight: 0.2980 chunk 55 optimal weight: 0.0170 chunk 21 optimal weight: 0.4980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6649 Z= 0.288 Angle : 0.618 8.121 9035 Z= 0.325 Chirality : 0.045 0.174 952 Planarity : 0.005 0.057 1170 Dihedral : 5.001 46.403 952 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 2.47 % Allowed : 17.30 % Favored : 80.23 % 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: -0.35 (0.30), residues: 786 helix: 1.12 (0.28), residues: 379 sheet: 0.59 (0.90), residues: 36 loop : -1.83 (0.30), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.002 PHE A 28 TYR 0.035 0.002 TYR A 521 ARG 0.003 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 165 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 148 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8085 (mtt90) cc_final: 0.7843 (mtt90) REVERT: A 206 ASP cc_start: 0.7343 (t70) cc_final: 0.7032 (t0) REVERT: A 334 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 347 THR cc_start: 0.8596 (m) cc_final: 0.8260 (p) REVERT: A 514 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7108 (ptp90) REVERT: A 536 ASP cc_start: 0.7633 (p0) cc_final: 0.7372 (p0) REVERT: A 597 GLU cc_start: 0.7568 (tp30) cc_final: 0.7273 (tm-30) REVERT: E 401 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8358 (t) REVERT: E 442 ASP cc_start: 0.8445 (m-30) cc_final: 0.8204 (m-30) outliers start: 17 outliers final: 11 residues processed: 154 average time/residue: 1.2546 time to fit residues: 201.5795 Evaluate side-chains 160 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU 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 600 LYS 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 409 GLN 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 77 optimal weight: 0.3980 chunk 71 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 18 optimal weight: 0.0270 chunk 57 optimal weight: 0.4980 chunk 9 optimal weight: 0.4980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 477 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6649 Z= 0.288 Angle : 0.616 8.197 9035 Z= 0.324 Chirality : 0.045 0.174 952 Planarity : 0.005 0.057 1170 Dihedral : 5.015 45.668 952 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 2.18 % Allowed : 18.02 % 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: -0.30 (0.30), residues: 786 helix: 1.18 (0.28), residues: 373 sheet: 0.54 (0.91), residues: 36 loop : -1.77 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.002 PHE A 28 TYR 0.035 0.002 TYR A 521 ARG 0.003 0.000 ARG A 273 ********************** 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 163 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 ARG cc_start: 0.8082 (mtt90) cc_final: 0.7821 (mtt90) REVERT: A 206 ASP cc_start: 0.7336 (t70) cc_final: 0.7019 (t0) REVERT: A 334 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8105 (p) REVERT: A 347 THR cc_start: 0.8600 (m) cc_final: 0.8257 (p) REVERT: A 514 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7104 (ptp90) REVERT: A 536 ASP cc_start: 0.7620 (p0) cc_final: 0.7361 (p0) REVERT: A 597 GLU cc_start: 0.7562 (tp30) cc_final: 0.7270 (tm-30) REVERT: E 401 VAL cc_start: 0.8622 (OUTLIER) cc_final: 0.8353 (t) REVERT: E 442 ASP cc_start: 0.8450 (m-30) cc_final: 0.8228 (m-30) outliers start: 15 outliers final: 10 residues processed: 153 average time/residue: 1.3998 time to fit residues: 223.7634 Evaluate side-chains 160 residues out of total 688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 171 GLU 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 600 LYS 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 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 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.3980 chunk 3 optimal weight: 0.1980 chunk 44 optimal weight: 0.9990 chunk 70 optimal weight: 0.0670 chunk 41 optimal weight: 0.9990 overall best weight: 0.3518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 89 GLN A 429 GLN A 531 GLN A 578 ASN A 601 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.110514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.101514 restraints weight = 9229.271| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 1.63 r_work: 0.3299 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2507 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= 0.272 Angle : 0.609 8.053 9035 Z= 0.321 Chirality : 0.045 0.174 952 Planarity : 0.005 0.057 1170 Dihedral : 4.986 45.726 952 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.18 % Allowed : 18.02 % 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: -0.30 (0.30), residues: 786 helix: 1.18 (0.28), residues: 373 sheet: 0.52 (0.91), residues: 36 loop : -1.77 (0.30), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 163 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 28 TYR 0.033 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: 4072.58 seconds wall clock time: 72 minutes 48.14 seconds (4368.14 seconds total)