Starting phenix.real_space_refine on Sun Aug 4 22:18:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8we1_37470/08_2024/8we1_37470.cif" } resolution = 2.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6332 atoms to isotropic. 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 37 5.16 5 C 4194 2.51 5 N 1077 2.21 5 O 1250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 37": "OE1" <-> "OE2" Residue "A TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 140": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 231": "OE1" <-> "OE2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "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: 6559 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4872 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} Conformer: "B" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 568} bond proxies already assigned to first conformer: 4987 Chain: "B" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1550 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" 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: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS A 34 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 34 " occ=0.50 Time building chain proxies: 6.63, per 1000 atoms: 1.01 Number of scatterers: 6559 At special positions: 0 Unit cell: (74.8, 87.55, 124.95, 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 37 16.00 O 1250 8.00 N 1077 7.00 C 4194 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 B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 2.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 53.1% alpha, 5.6% 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 20 through 53 removed outlier: 4.510A pdb=" N ASP A 38 " --> pdb=" O AHIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.784A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.072A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.831A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.554A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 175 No H-bonds generated for 'chain 'A' and resid 173 through 175' Processing helix chain 'A' and resid 176 through 194 removed outlier: 3.608A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.837A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.947A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.594A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.935A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.679A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.275A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.532A pdb=" N CYS A 542 " --> pdb=" O LEU A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.611A pdb=" N GLY A 551 " --> pdb=" O SER A 547 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.685A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 385 through 389 removed outlier: 3.773A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.793A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.299A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.101A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.725A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 289 hydrogen bonds defined for protein. 820 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: 1.70 Time building geometry restraints manager: 3.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2079 1.34 - 1.46: 1687 1.46 - 1.58: 2920 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6744 Sorted by residual: bond pdb=" CE1BHIS A 34 " pdb=" NE2BHIS A 34 " ideal model delta sigma weight residual 1.321 1.360 -0.039 1.00e-02 1.00e+04 1.55e+01 bond pdb=" CE1AHIS A 34 " pdb=" NE2AHIS A 34 " ideal model delta sigma weight residual 1.321 1.358 -0.037 1.00e-02 1.00e+04 1.36e+01 bond pdb=" N GLN A 24 " pdb=" CA GLN A 24 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.21e-02 6.83e+03 9.89e+00 bond pdb=" N ASN B 477 " pdb=" CA ASN B 477 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.75e+00 bond pdb=" N GLN B 493 " pdb=" CA GLN B 493 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.26e-02 6.30e+03 5.85e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 100.07 - 106.87: 224 106.87 - 113.67: 3574 113.67 - 120.47: 2700 120.47 - 127.27: 2577 127.27 - 134.07: 96 Bond angle restraints: 9171 Sorted by residual: angle pdb=" C TYR A 83 " pdb=" N PRO A 84 " pdb=" CA PRO A 84 " ideal model delta sigma weight residual 119.78 123.81 -4.03 1.03e+00 9.43e-01 1.53e+01 angle pdb=" CB MET A 408 " pdb=" CG MET A 408 " pdb=" SD MET A 408 " ideal model delta sigma weight residual 112.70 124.31 -11.61 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CA AHIS A 34 " pdb=" C AHIS A 34 " pdb=" O AHIS A 34 " ideal model delta sigma weight residual 119.97 116.07 3.90 1.15e+00 7.56e-01 1.15e+01 angle pdb=" CA GLU A 150 " pdb=" CB GLU A 150 " pdb=" CG GLU A 150 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 111.51 116.17 -4.66 1.58e+00 4.01e-01 8.69e+00 ... (remaining 9166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.39: 3590 21.39 - 42.78: 399 42.78 - 64.16: 90 64.16 - 85.55: 17 85.55 - 106.94: 7 Dihedral angle restraints: 4103 sinusoidal: 1777 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLN A 139 " pdb=" C GLN A 139 " pdb=" N GLU A 140 " pdb=" CA GLU A 140 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" C5 NAG A 901 " ideal model delta sinusoidal sigma weight residual 53.78 -53.16 106.94 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" C2 NAG A 901 " pdb=" C3 NAG A 901 " pdb=" C4 NAG A 901 " pdb=" O4 NAG A 901 " ideal model delta sinusoidal sigma weight residual 175.11 68.48 106.63 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 4100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 843 0.059 - 0.118: 130 0.118 - 0.178: 12 0.178 - 0.237: 1 0.237 - 0.296: 1 Chirality restraints: 987 Sorted by residual: chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ASN B 477 " pdb=" N ASN B 477 " pdb=" C ASN B 477 " pdb=" CB ASN B 477 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 984 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA AHIS A 34 " 0.028 2.00e-02 2.50e+03 5.63e-02 3.17e+01 pdb=" C AHIS A 34 " -0.097 2.00e-02 2.50e+03 pdb=" O AHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" N GLU A 35 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 414 " -0.039 5.00e-02 4.00e+02 5.88e-02 5.53e+00 pdb=" N PRO A 415 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO A 415 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 415 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA BHIS A 34 " -0.010 2.00e-02 2.50e+03 2.10e-02 4.41e+00 pdb=" C BHIS A 34 " 0.036 2.00e-02 2.50e+03 pdb=" O BHIS A 34 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU A 35 " -0.013 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 52 2.58 - 3.16: 5107 3.16 - 3.74: 10141 3.74 - 4.32: 13701 4.32 - 4.90: 23083 Nonbonded interactions: 52084 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.001 2.230 nonbonded pdb=" OD1 ASP A 494 " pdb=" OG1 THR A 496 " model vdw 2.164 3.040 nonbonded pdb=" OH TYR A 183 " pdb=" OD1 ASP A 509 " model vdw 2.165 3.040 nonbonded pdb=" OG SER A 109 " pdb=" OD1 ASP A 111 " model vdw 2.177 3.040 nonbonded pdb=" O ALA A 501 " pdb=" OG SER A 507 " model vdw 2.188 3.040 ... (remaining 52079 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 27.250 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 : 0.004 0.039 6744 Z= 0.237 Angle : 0.609 11.611 9171 Z= 0.325 Chirality : 0.044 0.296 987 Planarity : 0.004 0.059 1177 Dihedral : 18.672 106.937 2590 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.89 % Allowed : 25.36 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.67 (0.31), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.79 (0.76), residues: 45 loop : -0.79 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE B 347 TYR 0.025 0.001 TYR A 521 ARG 0.006 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 0.725 Fit side-chains REVERT: B 364 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6739 (p0) outliers start: 27 outliers final: 23 residues processed: 186 average time/residue: 1.0394 time to fit residues: 204.2318 Evaluate side-chains 178 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LYS Chi-restraints excluded: chain A residue 111 ASP Chi-restraints excluded: chain A residue 145 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 303 ASP Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 420 SER Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 441 LYS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 61 ASN A 81 GLN A 154 ASN A 210 ASN A 374 HIS A 580 ASN A 586 ASN B 439 ASN B 448 ASN B 450 ASN B 487 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.0735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6744 Z= 0.206 Angle : 0.572 12.454 9171 Z= 0.284 Chirality : 0.044 0.251 987 Planarity : 0.004 0.058 1177 Dihedral : 10.553 76.210 1118 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.19 % Allowed : 22.33 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.62 (0.30), residues: 790 helix: 1.60 (0.28), residues: 370 sheet: 0.51 (0.74), residues: 45 loop : -0.82 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 347 TYR 0.021 0.001 TYR A 521 ARG 0.004 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 164 time to evaluate : 0.731 Fit side-chains REVERT: B 364 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7091 (p0) REVERT: B 370 ASN cc_start: 0.8152 (p0) cc_final: 0.7942 (p0) outliers start: 36 outliers final: 27 residues processed: 182 average time/residue: 1.0521 time to fit residues: 202.4451 Evaluate side-chains 180 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 194 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 0.4980 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 340 GLN A 580 ASN A 586 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6744 Z= 0.181 Angle : 0.549 11.724 9171 Z= 0.269 Chirality : 0.043 0.299 987 Planarity : 0.004 0.056 1177 Dihedral : 7.497 56.537 1095 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.19 % Allowed : 22.77 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.64 (0.30), residues: 790 helix: 1.64 (0.27), residues: 370 sheet: 0.28 (0.73), residues: 45 loop : -0.80 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.009 0.001 PHE B 347 TYR 0.018 0.001 TYR A 521 ARG 0.005 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 163 time to evaluate : 0.570 Fit side-chains REVERT: B 370 ASN cc_start: 0.8129 (p0) cc_final: 0.7912 (p0) REVERT: B 424 LYS cc_start: 0.7937 (tppt) cc_final: 0.7705 (tppt) outliers start: 36 outliers final: 26 residues processed: 178 average time/residue: 1.0676 time to fit residues: 200.4472 Evaluate side-chains 179 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6744 Z= 0.203 Angle : 0.547 11.686 9171 Z= 0.272 Chirality : 0.044 0.311 987 Planarity : 0.004 0.059 1177 Dihedral : 6.546 57.483 1088 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 4.76 % Allowed : 23.49 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.63 (0.30), residues: 790 helix: 1.65 (0.27), residues: 370 sheet: 0.42 (0.73), residues: 45 loop : -0.85 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 69 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 347 TYR 0.019 0.001 TYR A 521 ARG 0.006 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 159 time to evaluate : 0.740 Fit side-chains REVERT: B 370 ASN cc_start: 0.8120 (p0) cc_final: 0.7872 (p0) outliers start: 33 outliers final: 23 residues processed: 172 average time/residue: 1.0539 time to fit residues: 191.4697 Evaluate side-chains 176 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 153 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.8980 chunk 56 optimal weight: 0.0770 chunk 31 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6744 Z= 0.156 Angle : 0.528 11.594 9171 Z= 0.260 Chirality : 0.043 0.288 987 Planarity : 0.004 0.055 1177 Dihedral : 5.989 53.340 1083 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.61 % Allowed : 23.63 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.66 (0.30), residues: 790 helix: 1.63 (0.27), residues: 376 sheet: 0.49 (0.74), residues: 45 loop : -0.84 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 PHE 0.007 0.001 PHE A 72 TYR 0.020 0.001 TYR A 521 ARG 0.006 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 162 time to evaluate : 0.714 Fit side-chains REVERT: A 190 MET cc_start: 0.7451 (tmm) cc_final: 0.7234 (tmm) REVERT: B 370 ASN cc_start: 0.8125 (p0) cc_final: 0.7867 (p0) outliers start: 32 outliers final: 23 residues processed: 176 average time/residue: 1.0499 time to fit residues: 195.3792 Evaluate side-chains 179 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 0.0870 chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 8 optimal weight: 0.0970 chunk 42 optimal weight: 0.9980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 210 ASN A 586 ASN B 354 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 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 : 0.002 0.034 6744 Z= 0.158 Angle : 0.544 12.498 9171 Z= 0.267 Chirality : 0.043 0.285 987 Planarity : 0.004 0.054 1177 Dihedral : 5.923 53.374 1083 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.90 % Allowed : 23.63 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.66 (0.30), residues: 790 helix: 1.67 (0.27), residues: 376 sheet: 0.55 (0.75), residues: 45 loop : -0.90 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 168 HIS 0.005 0.001 HIS A 241 PHE 0.008 0.001 PHE B 347 TYR 0.022 0.001 TYR A 521 ARG 0.007 0.000 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.735 Fit side-chains REVERT: A 190 MET cc_start: 0.7456 (tmm) cc_final: 0.7247 (tmm) REVERT: B 370 ASN cc_start: 0.8116 (p0) cc_final: 0.7855 (p0) outliers start: 34 outliers final: 24 residues processed: 167 average time/residue: 1.1007 time to fit residues: 194.0691 Evaluate side-chains 178 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS 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: 0.8980 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6744 Z= 0.253 Angle : 0.576 12.499 9171 Z= 0.285 Chirality : 0.045 0.307 987 Planarity : 0.004 0.056 1177 Dihedral : 5.938 54.483 1081 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.04 % Allowed : 23.63 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.43 (0.30), residues: 790 helix: 1.44 (0.27), residues: 382 sheet: 0.62 (0.73), residues: 45 loop : -1.03 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.007 0.001 HIS A 241 PHE 0.009 0.001 PHE B 347 TYR 0.021 0.002 TYR A 521 ARG 0.007 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 159 time to evaluate : 0.757 Fit side-chains REVERT: B 370 ASN cc_start: 0.8114 (p0) cc_final: 0.7842 (p0) REVERT: B 424 LYS cc_start: 0.7966 (tppt) cc_final: 0.7735 (tppt) outliers start: 35 outliers final: 27 residues processed: 172 average time/residue: 1.0889 time to fit residues: 197.6719 Evaluate side-chains 181 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6744 Z= 0.254 Angle : 0.580 12.575 9171 Z= 0.289 Chirality : 0.045 0.315 987 Planarity : 0.004 0.057 1177 Dihedral : 5.929 54.468 1081 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 5.04 % Allowed : 24.35 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.36 (0.30), residues: 790 helix: 1.39 (0.27), residues: 382 sheet: 0.70 (0.74), residues: 45 loop : -1.10 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 168 HIS 0.007 0.001 HIS A 241 PHE 0.008 0.001 PHE B 342 TYR 0.020 0.002 TYR A 521 ARG 0.007 0.001 ARG A 559 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 157 time to evaluate : 0.679 Fit side-chains REVERT: A 197 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 370 ASN cc_start: 0.8115 (p0) cc_final: 0.7840 (p0) REVERT: B 424 LYS cc_start: 0.8023 (tppt) cc_final: 0.7772 (tppt) outliers start: 35 outliers final: 25 residues processed: 173 average time/residue: 1.0616 time to fit residues: 193.7930 Evaluate side-chains 180 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 197 GLU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 154 ASN A 194 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6744 Z= 0.193 Angle : 0.567 12.707 9171 Z= 0.280 Chirality : 0.044 0.301 987 Planarity : 0.004 0.056 1177 Dihedral : 5.698 53.318 1079 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.18 % Allowed : 25.36 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 0.44 (0.30), residues: 790 helix: 1.53 (0.27), residues: 376 sheet: 0.74 (0.75), residues: 45 loop : -1.09 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 203 HIS 0.006 0.001 HIS A 241 PHE 0.009 0.001 PHE B 456 TYR 0.019 0.001 TYR A 521 ARG 0.011 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 0.829 Fit side-chains REVERT: B 370 ASN cc_start: 0.8116 (p0) cc_final: 0.7847 (p0) REVERT: B 424 LYS cc_start: 0.7983 (tppt) cc_final: 0.7750 (tppt) outliers start: 29 outliers final: 24 residues processed: 171 average time/residue: 1.0375 time to fit residues: 187.5768 Evaluate side-chains 179 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 155 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0670 chunk 71 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.0870 chunk 37 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 194 ASN A 586 ASN B 448 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6744 Z= 0.168 Angle : 0.565 12.915 9171 Z= 0.276 Chirality : 0.043 0.289 987 Planarity : 0.004 0.055 1177 Dihedral : 5.478 52.959 1077 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.46 % Allowed : 26.08 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.30), residues: 790 helix: 1.46 (0.27), residues: 382 sheet: 0.73 (0.75), residues: 45 loop : -1.02 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 203 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE B 456 TYR 0.022 0.001 TYR A 521 ARG 0.011 0.001 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1580 Ramachandran restraints generated. 790 Oldfield, 0 Emsley, 790 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 0.753 Fit side-chains REVERT: B 370 ASN cc_start: 0.8119 (p0) cc_final: 0.7857 (p0) outliers start: 24 outliers final: 22 residues processed: 166 average time/residue: 1.0665 time to fit residues: 187.5201 Evaluate side-chains 176 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 154 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 102 GLN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 290 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 343 VAL Chi-restraints excluded: chain A residue 376 MET Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 440 LYS Chi-restraints excluded: chain B residue 461 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 478 LYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 63 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.0670 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 0.5726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 ASN A 194 ASN A 210 ASN A 586 ASN B 354 ASN B 448 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.139088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.120712 restraints weight = 12855.365| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.38 r_work: 0.3569 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6744 Z= 0.198 Angle : 0.581 12.757 9171 Z= 0.285 Chirality : 0.044 0.295 987 Planarity : 0.004 0.056 1177 Dihedral : 5.469 53.386 1077 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.60 % Allowed : 25.94 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 790 helix: 1.57 (0.27), residues: 376 sheet: 0.79 (0.75), residues: 45 loop : -1.06 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 168 HIS 0.006 0.001 HIS A 241 PHE 0.008 0.001 PHE B 456 TYR 0.023 0.001 TYR A 521 ARG 0.010 0.001 ARG A 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.79 seconds wall clock time: 65 minutes 4.65 seconds (3904.65 seconds total)