Starting phenix.real_space_refine on Wed Mar 4 16:28:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xcp_33125/03_2026/7xcp_33125.map" } resolution = 3.05 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.002 sd= 0.072 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 8261 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 44 5.16 5 C 5274 2.51 5 N 1362 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8261 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 4869 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: 4990 Chain: "B" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1565 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "H" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 912 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} 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: "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 Time building chain proxies: 2.30, per 1000 atoms: 0.28 Number of scatterers: 8261 At special positions: 0 Unit cell: (73.59, 89.646, 117.744, 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 44 16.00 O 1580 8.00 N 1362 7.00 C 5274 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 701 " - " ASN A 53 " " NAG A 702 " - " ASN A 90 " " NAG A 703 " - " ASN A 322 " " NAG A 705 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 569.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 704 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 704 " - pdb=" NE2 HIS A 374 " 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 44.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.637A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 81 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.811A pdb=" N GLY A 104 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.536A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 194 Proline residue: A 178 - end of helix 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 252 removed outlier: 3.811A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (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 301 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.788A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.056A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.758A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 3.836A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 444 Processing helix chain 'A' and resid 445 through 466 removed outlier: 3.624A pdb=" N THR A 449 " --> pdb=" O THR A 445 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 450 " --> pdb=" O ILE A 446 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.609A pdb=" N LYS A 481 " --> pdb=" O TRP A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 Processing helix chain 'A' and resid 513 through 533 removed outlier: 3.822A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 526 " --> pdb=" O GLN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.802A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.830A 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 600 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.837A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.615A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.614A pdb=" N SER H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.955A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.641A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 5.948A 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 352 removed outlier: 5.971A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.940A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.964A pdb=" N ASP H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N MET H 34 " --> pdb=" O THR H 50 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.713A pdb=" N TYR H 109 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP H 99 " --> pdb=" O PHE H 107 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE H 107 " --> pdb=" O ASP H 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.587A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.587A pdb=" N LEU L 11 " --> pdb=" O ASP L 106 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR L 98 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1097 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: 1.24 Time building geometry restraints manager: 0.85 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: 2611 1.34 - 1.46: 1645 1.46 - 1.58: 4164 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 8488 Sorted by residual: bond pdb=" N LYS B 386 " pdb=" CA LYS B 386 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.13e+00 bond pdb=" N ASP H 33 " pdb=" CA ASP H 33 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.22e-02 6.72e+03 5.35e+00 bond pdb=" N SER H 31 " pdb=" CA SER H 31 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.29e-02 6.01e+03 4.61e+00 bond pdb=" CA SER H 31 " pdb=" CB SER H 31 " ideal model delta sigma weight residual 1.530 1.496 0.035 1.69e-02 3.50e+03 4.17e+00 bond pdb=" CA SER H 30 " pdb=" CB SER H 30 " ideal model delta sigma weight residual 1.525 1.497 0.028 1.36e-02 5.41e+03 4.15e+00 ... (remaining 8483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 11360 2.00 - 4.00: 151 4.00 - 6.01: 19 6.01 - 8.01: 3 8.01 - 10.01: 4 Bond angle restraints: 11537 Sorted by residual: angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 114.75 106.54 8.21 1.26e+00 6.30e-01 4.25e+01 angle pdb=" C TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta sigma weight residual 109.50 119.51 -10.01 1.69e+00 3.50e-01 3.51e+01 angle pdb=" N LEU B 368 " pdb=" CA LEU B 368 " pdb=" C LEU B 368 " ideal model delta sigma weight residual 114.09 106.60 7.49 1.55e+00 4.16e-01 2.33e+01 angle pdb=" C ASN B 388 " pdb=" CA ASN B 388 " pdb=" CB ASN B 388 " ideal model delta sigma weight residual 110.42 117.25 -6.83 1.99e+00 2.53e-01 1.18e+01 angle pdb=" CA PHE B 375 " pdb=" C PHE B 375 " pdb=" N THR B 376 " ideal model delta sigma weight residual 119.80 115.34 4.46 1.34e+00 5.57e-01 1.11e+01 ... (remaining 11532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 4559 17.43 - 34.85: 413 34.85 - 52.28: 86 52.28 - 69.71: 19 69.71 - 87.13: 11 Dihedral angle restraints: 5088 sinusoidal: 2114 harmonic: 2974 Sorted by residual: dihedral pdb=" CA PHE B 374 " pdb=" C PHE B 374 " pdb=" N PHE B 375 " pdb=" CA PHE B 375 " ideal model delta harmonic sigma weight residual 180.00 148.95 31.05 0 5.00e+00 4.00e-02 3.86e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 95 " pdb=" CB CYS H 95 " ideal model delta sinusoidal sigma weight residual 93.00 55.26 37.74 1 1.00e+01 1.00e-02 2.01e+01 dihedral pdb=" C TYR H 32 " pdb=" N TYR H 32 " pdb=" CA TYR H 32 " pdb=" CB TYR H 32 " ideal model delta harmonic sigma weight residual -122.60 -132.83 10.23 0 2.50e+00 1.60e-01 1.68e+01 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1063 0.057 - 0.113: 152 0.113 - 0.170: 16 0.170 - 0.227: 2 0.227 - 0.284: 1 Chirality restraints: 1234 Sorted by residual: chirality pdb=" CA TYR H 32 " pdb=" N TYR H 32 " pdb=" C TYR H 32 " pdb=" CB TYR H 32 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ASN B 388 " pdb=" N ASN B 388 " pdb=" C ASN B 388 " pdb=" CB ASN B 388 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.41e-01 chirality pdb=" CB ILE A 446 " pdb=" CA ILE A 446 " pdb=" CG1 ILE A 446 " pdb=" CG2 ILE A 446 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.00e-01 ... (remaining 1231 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 29 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C PHE H 29 " -0.068 2.00e-02 2.50e+03 pdb=" O PHE H 29 " 0.026 2.00e-02 2.50e+03 pdb=" N SER H 30 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 32 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C TYR H 32 " -0.055 2.00e-02 2.50e+03 pdb=" O TYR H 32 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP H 33 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 372 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.62e+00 pdb=" N PRO B 373 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 373 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 373 " 0.041 5.00e-02 4.00e+02 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 338 2.73 - 3.27: 8302 3.27 - 3.81: 14303 3.81 - 4.36: 17338 4.36 - 4.90: 29648 Nonbonded interactions: 69929 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 704 " model vdw 2.182 2.230 nonbonded pdb=" OD2 ASP B 398 " pdb=" OH TYR B 423 " model vdw 2.246 3.040 nonbonded pdb=" O ILE A 151 " pdb=" OG SER A 155 " model vdw 2.255 3.040 nonbonded pdb=" O PHE B 490 " pdb=" NH1 ARG B 493 " model vdw 2.258 3.120 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.274 3.040 ... (remaining 69924 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=0.49 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: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.210 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.003 0.036 8506 Z= 0.146 Angle : 0.577 10.012 11576 Z= 0.311 Chirality : 0.041 0.284 1234 Planarity : 0.005 0.073 1481 Dihedral : 14.238 87.133 3163 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 0.23 % Allowed : 0.45 % Favored : 99.32 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.27), residues: 1010 helix: 1.24 (0.27), residues: 387 sheet: 0.30 (0.44), residues: 147 loop : 0.02 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 493 TYR 0.036 0.001 TYR H 32 PHE 0.010 0.001 PHE A 369 TRP 0.027 0.002 TRP H 110 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8488) covalent geometry : angle 0.57607 (11537) SS BOND : bond 0.00162 ( 9) SS BOND : angle 0.50991 ( 18) hydrogen bonds : bond 0.15535 ( 389) hydrogen bonds : angle 6.45715 ( 1097) metal coordination : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00543 ( 1) link_BETA1-4 : angle 1.12295 ( 3) link_NAG-ASN : bond 0.00122 ( 6) link_NAG-ASN : angle 1.14095 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: A 243 TYR cc_start: 0.7527 (t80) cc_final: 0.7282 (t80) REVERT: A 474 MET cc_start: 0.5467 (mmp) cc_final: 0.4810 (tpp) REVERT: B 374 PHE cc_start: 0.4238 (m-80) cc_final: 0.3973 (m-80) REVERT: B 503 VAL cc_start: 0.8213 (t) cc_final: 0.7828 (m) outliers start: 2 outliers final: 2 residues processed: 129 average time/residue: 0.0764 time to fit residues: 14.4024 Evaluate side-chains 118 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 116 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 31 SER Chi-restraints excluded: chain H residue 33 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.215997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181595 restraints weight = 9235.377| |-----------------------------------------------------------------------------| r_work (start): 0.4041 rms_B_bonded: 1.84 r_work: 0.3846 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3706 r_free = 0.3706 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8506 Z= 0.162 Angle : 0.553 8.784 11576 Z= 0.289 Chirality : 0.043 0.296 1234 Planarity : 0.005 0.073 1481 Dihedral : 5.253 40.449 1264 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 1.02 % Allowed : 6.45 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.27), residues: 1010 helix: 1.27 (0.26), residues: 395 sheet: 0.72 (0.45), residues: 145 loop : 0.05 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 97 TYR 0.018 0.002 TYR B 495 PHE 0.022 0.002 PHE A 230 TRP 0.023 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 8488) covalent geometry : angle 0.55125 (11537) SS BOND : bond 0.00316 ( 9) SS BOND : angle 0.56623 ( 18) hydrogen bonds : bond 0.04476 ( 389) hydrogen bonds : angle 4.96866 ( 1097) metal coordination : bond 0.00149 ( 2) link_BETA1-4 : bond 0.00647 ( 1) link_BETA1-4 : angle 1.22784 ( 3) link_NAG-ASN : bond 0.00243 ( 6) link_NAG-ASN : angle 1.20314 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.206 Fit side-chains REVERT: A 243 TYR cc_start: 0.7875 (t80) cc_final: 0.7473 (t80) REVERT: B 374 PHE cc_start: 0.4847 (m-80) cc_final: 0.4596 (m-80) outliers start: 9 outliers final: 6 residues processed: 124 average time/residue: 0.0865 time to fit residues: 15.0395 Evaluate side-chains 122 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 110 TRP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 52 optimal weight: 3.9990 chunk 79 optimal weight: 0.0010 chunk 76 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 508 ASN A 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.178701 restraints weight = 11166.844| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 2.18 r_work: 0.3798 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8506 Z= 0.167 Angle : 0.555 8.902 11576 Z= 0.289 Chirality : 0.042 0.222 1234 Planarity : 0.005 0.063 1481 Dihedral : 4.906 40.128 1263 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 1.24 % Allowed : 9.28 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.27), residues: 1010 helix: 1.13 (0.26), residues: 402 sheet: 0.55 (0.43), residues: 161 loop : 0.05 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 97 TYR 0.018 0.002 TYR L 49 PHE 0.025 0.002 PHE A 230 TRP 0.021 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8488) covalent geometry : angle 0.55257 (11537) SS BOND : bond 0.00334 ( 9) SS BOND : angle 0.59676 ( 18) hydrogen bonds : bond 0.04436 ( 389) hydrogen bonds : angle 4.84693 ( 1097) metal coordination : bond 0.00212 ( 2) link_BETA1-4 : bond 0.00242 ( 1) link_BETA1-4 : angle 1.32128 ( 3) link_NAG-ASN : bond 0.00234 ( 6) link_NAG-ASN : angle 1.42619 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.283 Fit side-chains REVERT: A 243 TYR cc_start: 0.7901 (t80) cc_final: 0.7523 (t80) REVERT: A 474 MET cc_start: 0.5385 (mmp) cc_final: 0.4717 (tpp) REVERT: B 356 LYS cc_start: 0.7548 (ttmt) cc_final: 0.7310 (ttmm) REVERT: B 374 PHE cc_start: 0.4772 (m-80) cc_final: 0.4491 (m-80) outliers start: 11 outliers final: 6 residues processed: 131 average time/residue: 0.0845 time to fit residues: 15.6214 Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 120 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 89 optimal weight: 0.0170 chunk 71 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.216457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.181943 restraints weight = 15246.614| |-----------------------------------------------------------------------------| r_work (start): 0.4060 rms_B_bonded: 3.40 r_work: 0.3734 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8506 Z= 0.113 Angle : 0.509 9.106 11576 Z= 0.264 Chirality : 0.041 0.208 1234 Planarity : 0.005 0.059 1481 Dihedral : 4.519 36.074 1263 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.79 % Allowed : 10.63 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.27), residues: 1010 helix: 1.40 (0.27), residues: 384 sheet: 0.49 (0.44), residues: 154 loop : 0.02 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.019 0.001 TYR L 49 PHE 0.022 0.001 PHE A 230 TRP 0.024 0.001 TRP A 165 HIS 0.003 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8488) covalent geometry : angle 0.50713 (11537) SS BOND : bond 0.00271 ( 9) SS BOND : angle 0.47235 ( 18) hydrogen bonds : bond 0.03870 ( 389) hydrogen bonds : angle 4.74869 ( 1097) metal coordination : bond 0.00092 ( 2) link_BETA1-4 : bond 0.00496 ( 1) link_BETA1-4 : angle 1.15903 ( 3) link_NAG-ASN : bond 0.00208 ( 6) link_NAG-ASN : angle 1.23204 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.287 Fit side-chains REVERT: A 35 GLU cc_start: 0.7295 (mp0) cc_final: 0.6945 (mp0) REVERT: A 243 TYR cc_start: 0.7894 (t80) cc_final: 0.7503 (t80) REVERT: A 474 MET cc_start: 0.5435 (mmp) cc_final: 0.4741 (tpp) REVERT: B 374 PHE cc_start: 0.4888 (m-80) cc_final: 0.4513 (m-80) REVERT: B 390 LEU cc_start: 0.5730 (OUTLIER) cc_final: 0.5329 (tt) outliers start: 7 outliers final: 6 residues processed: 130 average time/residue: 0.0907 time to fit residues: 16.3534 Evaluate side-chains 125 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS A 508 ASN A 531 GLN B 477 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.206662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173272 restraints weight = 15347.367| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 4.00 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3971 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3971 r_free = 0.3971 target_work(ls_wunit_k1) = 0.173 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3971 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 8506 Z= 0.328 Angle : 0.696 7.584 11576 Z= 0.363 Chirality : 0.048 0.213 1234 Planarity : 0.006 0.077 1481 Dihedral : 5.572 46.561 1263 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 1.81 % Allowed : 10.63 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.27), residues: 1010 helix: 0.67 (0.26), residues: 396 sheet: 0.09 (0.42), residues: 163 loop : -0.11 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 460 TYR 0.026 0.002 TYR A 381 PHE 0.028 0.003 PHE A 230 TRP 0.023 0.002 TRP A 165 HIS 0.011 0.002 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00759 ( 8488) covalent geometry : angle 0.69088 (11537) SS BOND : bond 0.00518 ( 9) SS BOND : angle 0.95485 ( 18) hydrogen bonds : bond 0.05436 ( 389) hydrogen bonds : angle 5.21619 ( 1097) metal coordination : bond 0.00536 ( 2) link_BETA1-4 : bond 0.00406 ( 1) link_BETA1-4 : angle 2.31141 ( 3) link_NAG-ASN : bond 0.00438 ( 6) link_NAG-ASN : angle 2.03018 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.241 Fit side-chains REVERT: A 190 MET cc_start: 0.6671 (ttp) cc_final: 0.6376 (ttp) outliers start: 16 outliers final: 11 residues processed: 134 average time/residue: 0.0829 time to fit residues: 15.7804 Evaluate side-chains 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 27 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 5 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.212602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.177279 restraints weight = 9112.952| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.94 r_work: 0.3792 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8506 Z= 0.139 Angle : 0.553 9.243 11576 Z= 0.284 Chirality : 0.041 0.178 1234 Planarity : 0.005 0.071 1481 Dihedral : 4.860 37.730 1263 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.24 % Allowed : 12.67 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.27), residues: 1010 helix: 0.96 (0.26), residues: 391 sheet: 0.03 (0.42), residues: 164 loop : -0.14 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.018 0.001 TYR L 49 PHE 0.025 0.002 PHE A 230 TRP 0.023 0.001 TRP A 165 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8488) covalent geometry : angle 0.54929 (11537) SS BOND : bond 0.00312 ( 9) SS BOND : angle 0.57867 ( 18) hydrogen bonds : bond 0.04194 ( 389) hydrogen bonds : angle 4.90636 ( 1097) metal coordination : bond 0.00160 ( 2) link_BETA1-4 : bond 0.00320 ( 1) link_BETA1-4 : angle 1.35401 ( 3) link_NAG-ASN : bond 0.00262 ( 6) link_NAG-ASN : angle 1.57233 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.320 Fit side-chains REVERT: A 243 TYR cc_start: 0.7754 (t80) cc_final: 0.7465 (t80) REVERT: A 474 MET cc_start: 0.5374 (mmp) cc_final: 0.4651 (tpp) outliers start: 11 outliers final: 9 residues processed: 130 average time/residue: 0.0750 time to fit residues: 14.2280 Evaluate side-chains 125 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 116 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.209416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.174199 restraints weight = 9253.092| |-----------------------------------------------------------------------------| r_work (start): 0.3955 rms_B_bonded: 1.97 r_work: 0.3744 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8506 Z= 0.216 Angle : 0.610 8.849 11576 Z= 0.314 Chirality : 0.044 0.181 1234 Planarity : 0.005 0.068 1481 Dihedral : 5.097 42.666 1263 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.58 % Allowed : 12.78 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 1010 helix: 0.84 (0.26), residues: 391 sheet: -0.04 (0.42), residues: 164 loop : -0.16 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 97 TYR 0.020 0.002 TYR L 49 PHE 0.027 0.002 PHE A 230 TRP 0.024 0.001 TRP A 165 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 8488) covalent geometry : angle 0.60569 (11537) SS BOND : bond 0.00420 ( 9) SS BOND : angle 0.69595 ( 18) hydrogen bonds : bond 0.04720 ( 389) hydrogen bonds : angle 5.02105 ( 1097) metal coordination : bond 0.00337 ( 2) link_BETA1-4 : bond 0.00345 ( 1) link_BETA1-4 : angle 1.83843 ( 3) link_NAG-ASN : bond 0.00374 ( 6) link_NAG-ASN : angle 1.74626 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.295 Fit side-chains REVERT: A 474 MET cc_start: 0.5485 (mmp) cc_final: 0.4800 (tpp) outliers start: 14 outliers final: 11 residues processed: 130 average time/residue: 0.0768 time to fit residues: 14.6248 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain L residue 52 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.212697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182706 restraints weight = 19557.416| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 4.50 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4075 r_free = 0.4075 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8506 Z= 0.140 Angle : 0.556 9.585 11576 Z= 0.285 Chirality : 0.042 0.189 1234 Planarity : 0.005 0.067 1481 Dihedral : 4.782 39.693 1263 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.47 % Allowed : 13.01 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.27), residues: 1010 helix: 0.97 (0.26), residues: 397 sheet: -0.09 (0.42), residues: 164 loop : -0.07 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.021 0.001 TYR L 49 PHE 0.024 0.002 PHE A 230 TRP 0.025 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8488) covalent geometry : angle 0.55293 (11537) SS BOND : bond 0.00321 ( 9) SS BOND : angle 0.58669 ( 18) hydrogen bonds : bond 0.04131 ( 389) hydrogen bonds : angle 4.87217 ( 1097) metal coordination : bond 0.00150 ( 2) link_BETA1-4 : bond 0.00373 ( 1) link_BETA1-4 : angle 1.45352 ( 3) link_NAG-ASN : bond 0.00254 ( 6) link_NAG-ASN : angle 1.51658 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.319 Fit side-chains REVERT: A 243 TYR cc_start: 0.7762 (t80) cc_final: 0.7554 (t80) REVERT: A 474 MET cc_start: 0.5566 (mmp) cc_final: 0.4993 (tpp) REVERT: A 519 THR cc_start: 0.8035 (m) cc_final: 0.7824 (p) REVERT: B 390 LEU cc_start: 0.5713 (OUTLIER) cc_final: 0.5389 (tt) outliers start: 13 outliers final: 11 residues processed: 129 average time/residue: 0.0784 time to fit residues: 14.6678 Evaluate side-chains 130 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 62 optimal weight: 0.0040 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 17 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 77 optimal weight: 0.4980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.216616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.181237 restraints weight = 15261.815| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 3.91 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4025 r_free = 0.4025 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4025 r_free = 0.4025 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8506 Z= 0.111 Angle : 0.528 10.050 11576 Z= 0.270 Chirality : 0.041 0.168 1234 Planarity : 0.005 0.080 1481 Dihedral : 4.510 39.345 1263 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.24 % Allowed : 13.35 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.27), residues: 1010 helix: 1.22 (0.26), residues: 393 sheet: 0.12 (0.43), residues: 154 loop : 0.08 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 97 TYR 0.023 0.001 TYR L 49 PHE 0.022 0.001 PHE A 230 TRP 0.027 0.001 TRP A 165 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8488) covalent geometry : angle 0.52524 (11537) SS BOND : bond 0.00279 ( 9) SS BOND : angle 0.56700 ( 18) hydrogen bonds : bond 0.03765 ( 389) hydrogen bonds : angle 4.77582 ( 1097) metal coordination : bond 0.00073 ( 2) link_BETA1-4 : bond 0.00431 ( 1) link_BETA1-4 : angle 1.28688 ( 3) link_NAG-ASN : bond 0.00235 ( 6) link_NAG-ASN : angle 1.30609 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 125 time to evaluate : 0.247 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 132 average time/residue: 0.0832 time to fit residues: 15.7680 Evaluate side-chains 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 84 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.213613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.177955 restraints weight = 11096.759| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 2.39 r_work: 0.3771 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8506 Z= 0.121 Angle : 0.538 9.926 11576 Z= 0.274 Chirality : 0.041 0.167 1234 Planarity : 0.005 0.081 1481 Dihedral : 4.498 40.789 1263 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.24 % Allowed : 13.91 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.27), residues: 1010 helix: 1.14 (0.26), residues: 402 sheet: 0.11 (0.43), residues: 154 loop : 0.02 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 493 TYR 0.028 0.002 TYR B 489 PHE 0.022 0.001 PHE A 230 TRP 0.026 0.001 TRP A 165 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8488) covalent geometry : angle 0.53485 (11537) SS BOND : bond 0.00305 ( 9) SS BOND : angle 0.67840 ( 18) hydrogen bonds : bond 0.03832 ( 389) hydrogen bonds : angle 4.76199 ( 1097) metal coordination : bond 0.00116 ( 2) link_BETA1-4 : bond 0.00335 ( 1) link_BETA1-4 : angle 1.39234 ( 3) link_NAG-ASN : bond 0.00238 ( 6) link_NAG-ASN : angle 1.34484 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2020 Ramachandran restraints generated. 1010 Oldfield, 0 Emsley, 1010 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.310 Fit side-chains REVERT: A 243 TYR cc_start: 0.7835 (t80) cc_final: 0.7447 (t80) REVERT: A 519 THR cc_start: 0.8614 (m) cc_final: 0.8322 (p) REVERT: B 390 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.5407 (tt) REVERT: B 489 TYR cc_start: 0.7001 (m-80) cc_final: 0.6736 (m-80) REVERT: H 81 GLN cc_start: 0.7936 (mm110) cc_final: 0.7606 (tp40) outliers start: 11 outliers final: 10 residues processed: 129 average time/residue: 0.0792 time to fit residues: 14.6791 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 579 MET Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 114 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.1980 chunk 19 optimal weight: 0.0870 chunk 59 optimal weight: 0.3980 chunk 15 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 531 GLN L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.217244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.182248 restraints weight = 11138.532| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 2.35 r_work: 0.3827 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3826 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3826 r_free = 0.3826 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3826 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8506 Z= 0.102 Angle : 0.517 10.143 11576 Z= 0.264 Chirality : 0.040 0.168 1234 Planarity : 0.005 0.079 1481 Dihedral : 4.305 37.875 1263 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.13 % Allowed : 14.14 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1010 helix: 1.37 (0.27), residues: 392 sheet: 0.02 (0.42), residues: 164 loop : 0.13 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 493 TYR 0.029 0.001 TYR B 489 PHE 0.020 0.001 PHE A 230 TRP 0.026 0.001 TRP A 165 HIS 0.004 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 8488) covalent geometry : angle 0.51405 (11537) SS BOND : bond 0.00258 ( 9) SS BOND : angle 0.64828 ( 18) hydrogen bonds : bond 0.03511 ( 389) hydrogen bonds : angle 4.69734 ( 1097) metal coordination : bond 0.00075 ( 2) link_BETA1-4 : bond 0.00326 ( 1) link_BETA1-4 : angle 1.12775 ( 3) link_NAG-ASN : bond 0.00179 ( 6) link_NAG-ASN : angle 1.27678 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2158.57 seconds wall clock time: 37 minutes 37.25 seconds (2257.25 seconds total)