Starting phenix.real_space_refine on Fri Jul 3 15:35:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xcp_33125/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.cif" model { file = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_2026/7xcp_33125.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xcp_33125/07_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-6108/lib/python3.11/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 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 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 chiralities: 1 Time building chain proxies: 2.56, per 1000 atoms: 0.31 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: 0.85 Conformation dependent library (CDL) restraints added in 391.9 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: 0.34 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: 1.28 Time building geometry restraints manager: 1.08 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: 4431 17.43 - 34.85: 400 34.85 - 52.28: 82 52.28 - 69.71: 17 69.71 - 87.13: 11 Dihedral angle restraints: 4941 sinusoidal: 1967 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 4938 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 10.700 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 14.305 87.133 3016 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/Z covalent geometry : bond 0.00267 / 0.15 ( 8488) covalent geometry : angle 0.57607 / 0.31 (11537) SS BOND : bond 0.00162 / 0.09 ( 9) SS BOND : angle 0.50991 / 0.35 ( 18) hydrogen bonds : bond 0.15535 / 10.63 ( 389) hydrogen bonds : angle 6.45715 / 4.62 ( 1097) metal coordination : bond 0.00037 / 0.02 ( 2) link_BETA1-4 : bond 0.00543 / 0.29 ( 1) link_BETA1-4 : angle 1.12295 / 0.59 ( 3) link_NAG-ASN : bond 0.00122 / 0.07 ( 6) link_NAG-ASN : angle 1.14095 / 0.67 ( 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 : 0.296 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: 0.0734 time to fit residues: 13.8505 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 : 0.234 ------------------------------------------------------------------------------- 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... A 397 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.215621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.181069 restraints weight = 9227.989| |-----------------------------------------------------------------------------| r_work (start): 0.4036 rms_B_bonded: 1.86 r_work: 0.3842 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3700 r_free = 0.3700 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 = 0.3700 r_free = 0.3700 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8506 Z= 0.162 Angle : 0.556 8.910 11576 Z= 0.290 Chirality : 0.043 0.303 1234 Planarity : 0.005 0.073 1481 Dihedral : 4.409 38.373 1117 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 1.24 % Allowed : 6.33 % Favored : 92.42 % 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: 0.87 (0.27), residues: 1010 helix: 1.25 (0.26), residues: 396 sheet: 0.72 (0.45), residues: 145 loop : 0.06 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 97 TYR 0.018 0.002 TYR B 495 PHE 0.022 0.002 PHE A 230 TRP 0.022 0.001 TRP A 165 HIS 0.005 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 8488) covalent geometry : angle 0.55392 / 0.29 (11537) SS BOND : bond 0.00300 / 0.16 ( 9) SS BOND : angle 0.54673 / 0.33 ( 18) hydrogen bonds : bond 0.04446 / 3.05 ( 389) hydrogen bonds : angle 4.95250 / 3.57 ( 1097) metal coordination : bond 0.00231 / 0.11 ( 2) link_BETA1-4 : bond 0.00596 / 0.31 ( 1) link_BETA1-4 : angle 1.03877 / 0.53 ( 3) link_NAG-ASN : bond 0.00221 / 0.11 ( 6) link_NAG-ASN : angle 1.28295 / 0.79 ( 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 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.310 Fit side-chains REVERT: A 243 TYR cc_start: 0.7902 (t80) cc_final: 0.7499 (t80) REVERT: A 474 MET cc_start: 0.5450 (mmp) cc_final: 0.4622 (tpp) REVERT: B 374 PHE cc_start: 0.4860 (m-80) cc_final: 0.4611 (m-80) outliers start: 11 outliers final: 5 residues processed: 123 average time/residue: 0.0841 time to fit residues: 14.3565 Evaluate side-chains 119 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 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: 9.9990 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 0.0870 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 overall best weight: 1.1160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4377 r_free = 0.4377 target = 0.214863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.180321 restraints weight = 11249.409| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.33 r_work: 0.3783 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8506 Z= 0.156 Angle : 0.547 8.446 11576 Z= 0.283 Chirality : 0.042 0.214 1234 Planarity : 0.005 0.063 1481 Dihedral : 4.296 30.218 1116 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.57 % Favored : 96.33 % Rotamer: Outliers : 1.02 % Allowed : 9.28 % Favored : 89.71 % 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: 0.82 (0.27), residues: 1010 helix: 1.18 (0.26), residues: 402 sheet: 0.77 (0.44), residues: 151 loop : 0.01 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 97 TYR 0.021 0.002 TYR B 351 PHE 0.023 0.002 PHE A 230 TRP 0.020 0.001 TRP A 165 HIS 0.004 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 8488) covalent geometry : angle 0.54397 / 0.28 (11537) SS BOND : bond 0.00318 / 0.17 ( 9) SS BOND : angle 0.55762 / 0.33 ( 18) hydrogen bonds : bond 0.04305 / 2.95 ( 389) hydrogen bonds : angle 4.83906 / 3.48 ( 1097) metal coordination : bond 0.00207 / 0.10 ( 2) link_BETA1-4 : bond 0.00471 / 0.25 ( 1) link_BETA1-4 : angle 1.17784 / 0.61 ( 3) link_NAG-ASN : bond 0.00198 / 0.10 ( 6) link_NAG-ASN : angle 1.38389 / 0.84 ( 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 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.294 Fit side-chains REVERT: A 243 TYR cc_start: 0.7877 (t80) cc_final: 0.7473 (t80) REVERT: A 397 ASN cc_start: 0.8336 (p0) cc_final: 0.8132 (p0) REVERT: A 474 MET cc_start: 0.5447 (mmp) cc_final: 0.4760 (tpp) REVERT: B 356 LYS cc_start: 0.7545 (ttmt) cc_final: 0.7321 (ttmm) REVERT: B 374 PHE cc_start: 0.4819 (m-80) cc_final: 0.4547 (m-80) REVERT: B 390 LEU cc_start: 0.5835 (OUTLIER) cc_final: 0.5615 (tt) outliers start: 9 outliers final: 6 residues processed: 128 average time/residue: 0.0725 time to fit residues: 13.3977 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 : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain H residue 33 ASP Chi-restraints excluded: chain H residue 110 TRP 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: 0.0980 chunk 71 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.214137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.182817 restraints weight = 15149.580| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.19 r_work: 0.3743 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1541 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= 0.112 Angle : 0.506 9.299 11576 Z= 0.262 Chirality : 0.040 0.184 1234 Planarity : 0.005 0.058 1481 Dihedral : 4.132 28.903 1116 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.79 % Allowed : 10.86 % Favored : 88.35 % 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: 0.93 (0.27), residues: 1010 helix: 1.40 (0.26), residues: 390 sheet: 0.52 (0.44), residues: 154 loop : 0.08 (0.30), residues: 466 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 0.022 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/Z covalent geometry : bond 0.00243 / 0.11 ( 8488) covalent geometry : angle 0.50409 / 0.26 (11537) SS BOND : bond 0.00264 / 0.14 ( 9) SS BOND : angle 0.46738 / 0.28 ( 18) hydrogen bonds : bond 0.03826 / 2.63 ( 389) hydrogen bonds : angle 4.68633 / 3.36 ( 1097) metal coordination : bond 0.00123 / 0.06 ( 2) link_BETA1-4 : bond 0.00376 / 0.20 ( 1) link_BETA1-4 : angle 0.96469 / 0.50 ( 3) link_NAG-ASN : bond 0.00200 / 0.10 ( 6) link_NAG-ASN : angle 1.19476 / 0.72 ( 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 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.323 Fit side-chains REVERT: A 243 TYR cc_start: 0.7893 (t80) cc_final: 0.7491 (t80) REVERT: A 474 MET cc_start: 0.5440 (mmp) cc_final: 0.4749 (tpp) REVERT: B 374 PHE cc_start: 0.4869 (m-80) cc_final: 0.4490 (m-80) outliers start: 7 outliers final: 6 residues processed: 128 average time/residue: 0.0906 time to fit residues: 16.4038 Evaluate side-chains 124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 579 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 70 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 27 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 0.3980 chunk 73 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.214577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.180346 restraints weight = 15356.355| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 3.58 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8506 Z= 0.115 Angle : 0.507 8.605 11576 Z= 0.261 Chirality : 0.040 0.180 1234 Planarity : 0.005 0.074 1481 Dihedral : 4.075 28.481 1116 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.02 % Allowed : 10.75 % Favored : 88.24 % 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: 0.92 (0.27), residues: 1010 helix: 1.44 (0.26), residues: 396 sheet: 0.41 (0.44), residues: 154 loop : 0.05 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.021 0.001 TYR L 49 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/Z covalent geometry : bond 0.00253 / 0.11 ( 8488) covalent geometry : angle 0.50481 / 0.26 (11537) SS BOND : bond 0.00274 / 0.15 ( 9) SS BOND : angle 0.46010 / 0.28 ( 18) hydrogen bonds : bond 0.03809 / 2.63 ( 389) hydrogen bonds : angle 4.58904 / 3.29 ( 1097) metal coordination : bond 0.00128 / 0.06 ( 2) link_BETA1-4 : bond 0.00376 / 0.20 ( 1) link_BETA1-4 : angle 1.00644 / 0.52 ( 3) link_NAG-ASN : bond 0.00205 / 0.11 ( 6) link_NAG-ASN : angle 1.21159 / 0.74 ( 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 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.298 Fit side-chains REVERT: A 243 TYR cc_start: 0.7790 (t80) cc_final: 0.7548 (t80) REVERT: A 474 MET cc_start: 0.5403 (mmp) cc_final: 0.4897 (tpp) REVERT: B 374 PHE cc_start: 0.4250 (m-80) cc_final: 0.3987 (m-80) outliers start: 9 outliers final: 7 residues processed: 127 average time/residue: 0.0920 time to fit residues: 16.6720 Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 119 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 75 optimal weight: 0.0770 chunk 63 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 83 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.214336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.182122 restraints weight = 8974.216| |-----------------------------------------------------------------------------| r_work (start): 0.4065 rms_B_bonded: 1.79 r_work: 0.3862 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3878 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3878 r_free = 0.3878 target_work(ls_wunit_k1) = 0.163 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3878 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8506 Z= 0.111 Angle : 0.498 8.617 11576 Z= 0.256 Chirality : 0.040 0.177 1234 Planarity : 0.005 0.075 1481 Dihedral : 4.031 27.584 1116 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.47 % Allowed : 10.86 % Favored : 87.67 % 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: 0.89 (0.27), residues: 1010 helix: 1.45 (0.26), residues: 396 sheet: 0.40 (0.44), residues: 154 loop : 0.01 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 457 TYR 0.022 0.001 TYR L 49 PHE 0.021 0.001 PHE A 230 TRP 0.026 0.001 TRP A 165 HIS 0.002 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8488) covalent geometry : angle 0.49583 / 0.26 (11537) SS BOND : bond 0.00266 / 0.15 ( 9) SS BOND : angle 0.44748 / 0.28 ( 18) hydrogen bonds : bond 0.03719 / 2.56 ( 389) hydrogen bonds : angle 4.55368 / 3.26 ( 1097) metal coordination : bond 0.00113 / 0.05 ( 2) link_BETA1-4 : bond 0.00421 / 0.22 ( 1) link_BETA1-4 : angle 1.02090 / 0.53 ( 3) link_NAG-ASN : bond 0.00187 / 0.10 ( 6) link_NAG-ASN : angle 1.21621 / 0.73 ( 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 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.317 Fit side-chains REVERT: A 243 TYR cc_start: 0.7837 (t80) cc_final: 0.7452 (t80) REVERT: A 474 MET cc_start: 0.5360 (mmp) cc_final: 0.4755 (tpp) REVERT: B 390 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.5350 (tt) REVERT: B 423 TYR cc_start: 0.7966 (t80) cc_final: 0.7542 (t80) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.0828 time to fit residues: 15.9245 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 48 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 47 optimal weight: 0.0050 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 94 optimal weight: 20.0000 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 HIS 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 = 0.4384 r_free = 0.4384 target = 0.214984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182395 restraints weight = 9135.022| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 1.73 r_work: 0.3880 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3744 rms_B_bonded: 4.85 restraints_weight: 0.2500 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) = 0.151 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1752 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= 0.106 Angle : 0.498 9.525 11576 Z= 0.255 Chirality : 0.040 0.171 1234 Planarity : 0.004 0.074 1481 Dihedral : 3.994 26.432 1116 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.47 % Allowed : 11.65 % Favored : 86.88 % 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: 0.89 (0.27), residues: 1010 helix: 1.45 (0.26), residues: 396 sheet: 0.38 (0.44), residues: 154 loop : 0.00 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.021 0.001 TYR L 49 PHE 0.019 0.001 PHE A 230 TRP 0.026 0.001 TRP A 165 HIS 0.002 0.001 HIS A 378 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 8488) covalent geometry : angle 0.49609 / 0.26 (11537) SS BOND : bond 0.00262 / 0.14 ( 9) SS BOND : angle 0.43544 / 0.27 ( 18) hydrogen bonds : bond 0.03655 / 2.53 ( 389) hydrogen bonds : angle 4.50355 / 3.23 ( 1097) metal coordination : bond 0.00112 / 0.05 ( 2) link_BETA1-4 : bond 0.00339 / 0.18 ( 1) link_BETA1-4 : angle 0.96399 / 0.50 ( 3) link_NAG-ASN : bond 0.00199 / 0.10 ( 6) link_NAG-ASN : angle 1.19841 / 0.72 ( 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: 13 poor density : 123 time to evaluate : 0.309 Fit side-chains REVERT: A 123 MET cc_start: 0.7417 (mmm) cc_final: 0.7216 (mmm) REVERT: A 243 TYR cc_start: 0.7895 (t80) cc_final: 0.7486 (t80) REVERT: A 277 ASN cc_start: 0.8575 (m110) cc_final: 0.8319 (m-40) REVERT: A 474 MET cc_start: 0.5455 (mmp) cc_final: 0.4780 (tpp) REVERT: B 390 LEU cc_start: 0.5722 (OUTLIER) cc_final: 0.5360 (tt) REVERT: B 423 TYR cc_start: 0.8034 (t80) cc_final: 0.7470 (t80) outliers start: 13 outliers final: 9 residues processed: 131 average time/residue: 0.0821 time to fit residues: 15.7030 Evaluate side-chains 129 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 119 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.0040 chunk 13 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 0.4980 chunk 66 optimal weight: 0.0070 overall best weight: 0.6612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN B 477 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.215373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180354 restraints weight = 19715.635| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 4.88 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4053 r_free = 0.4053 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1829 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= 0.116 Angle : 0.510 10.032 11576 Z= 0.259 Chirality : 0.040 0.159 1234 Planarity : 0.004 0.076 1481 Dihedral : 4.015 26.815 1116 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 1.47 % Allowed : 12.10 % Favored : 86.43 % 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: 1.45 (0.26), residues: 396 sheet: 0.34 (0.43), residues: 154 loop : -0.01 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.023 0.001 TYR L 49 PHE 0.020 0.001 PHE A 230 TRP 0.028 0.001 TRP A 165 HIS 0.003 0.001 HIS A 241 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 8488) covalent geometry : angle 0.50772 / 0.26 (11537) SS BOND : bond 0.00268 / 0.15 ( 9) SS BOND : angle 0.45013 / 0.28 ( 18) hydrogen bonds : bond 0.03740 / 2.58 ( 389) hydrogen bonds : angle 4.49983 / 3.23 ( 1097) metal coordination : bond 0.00114 / 0.05 ( 2) link_BETA1-4 : bond 0.00370 / 0.19 ( 1) link_BETA1-4 : angle 1.02876 / 0.53 ( 3) link_NAG-ASN : bond 0.00200 / 0.10 ( 6) link_NAG-ASN : angle 1.25682 / 0.76 ( 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 138 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.274 Fit side-chains REVERT: A 243 TYR cc_start: 0.7838 (t80) cc_final: 0.7573 (t80) REVERT: A 474 MET cc_start: 0.5413 (mmp) cc_final: 0.4876 (tpp) REVERT: B 390 LEU cc_start: 0.5565 (OUTLIER) cc_final: 0.5277 (tt) outliers start: 13 outliers final: 10 residues processed: 132 average time/residue: 0.0757 time to fit residues: 14.3787 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 : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 9.9990 chunk 62 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.215071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.180711 restraints weight = 15371.869| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 3.81 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4058 r_free = 0.4058 target_work(ls_wunit_k1) = 0.180 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.4058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8506 Z= 0.119 Angle : 0.525 10.769 11576 Z= 0.266 Chirality : 0.040 0.188 1234 Planarity : 0.004 0.077 1481 Dihedral : 4.051 26.662 1116 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % 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: 0.85 (0.27), residues: 1010 helix: 1.40 (0.26), residues: 397 sheet: 0.32 (0.43), residues: 154 loop : 0.01 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 97 TYR 0.022 0.001 TYR L 49 PHE 0.020 0.001 PHE A 230 TRP 0.028 0.001 TRP A 165 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 8488) covalent geometry : angle 0.52319 / 0.27 (11537) SS BOND : bond 0.00263 / 0.14 ( 9) SS BOND : angle 0.44613 / 0.28 ( 18) hydrogen bonds : bond 0.03733 / 2.58 ( 389) hydrogen bonds : angle 4.52152 / 3.24 ( 1097) metal coordination : bond 0.00114 / 0.05 ( 2) link_BETA1-4 : bond 0.00380 / 0.20 ( 1) link_BETA1-4 : angle 1.03129 / 0.54 ( 3) link_NAG-ASN : bond 0.00181 / 0.09 ( 6) link_NAG-ASN : angle 1.27529 / 0.76 ( 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 132 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 0.305 Fit side-chains REVERT: A 243 TYR cc_start: 0.7819 (t80) cc_final: 0.7551 (t80) REVERT: A 474 MET cc_start: 0.5410 (mmp) cc_final: 0.4922 (tpp) REVERT: B 390 LEU cc_start: 0.5527 (OUTLIER) cc_final: 0.5221 (tt) outliers start: 11 outliers final: 10 residues processed: 127 average time/residue: 0.0722 time to fit residues: 13.3837 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 : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 2 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 15 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.214737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.182902 restraints weight = 11044.025| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 2.16 r_work: 0.3835 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8506 Z= 0.113 Angle : 0.532 12.833 11576 Z= 0.267 Chirality : 0.040 0.156 1234 Planarity : 0.004 0.077 1481 Dihedral : 4.032 26.127 1116 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.47 % Allowed : 12.90 % 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: 0.85 (0.27), residues: 1010 helix: 1.40 (0.26), residues: 397 sheet: 0.30 (0.43), residues: 154 loop : 0.02 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 115 TYR 0.023 0.001 TYR L 49 PHE 0.020 0.001 PHE A 230 TRP 0.028 0.001 TRP A 165 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 8488) covalent geometry : angle 0.53032 / 0.27 (11537) SS BOND : bond 0.00250 / 0.14 ( 9) SS BOND : angle 0.44467 / 0.28 ( 18) hydrogen bonds : bond 0.03684 / 2.55 ( 389) hydrogen bonds : angle 4.50310 / 3.23 ( 1097) metal coordination : bond 0.00091 / 0.04 ( 2) link_BETA1-4 : bond 0.00294 / 0.15 ( 1) link_BETA1-4 : angle 0.97219 / 0.51 ( 3) link_NAG-ASN : bond 0.00195 / 0.10 ( 6) link_NAG-ASN : angle 1.22123 / 0.73 ( 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 131 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 118 time to evaluate : 0.289 Fit side-chains REVERT: A 115 ARG cc_start: 0.6356 (tpt90) cc_final: 0.6046 (tpt90) REVERT: A 243 TYR cc_start: 0.7871 (t80) cc_final: 0.7470 (t80) REVERT: A 474 MET cc_start: 0.5388 (mmp) cc_final: 0.4783 (tpp) REVERT: A 519 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8304 (p) REVERT: B 390 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5372 (tt) outliers start: 13 outliers final: 9 residues processed: 124 average time/residue: 0.0756 time to fit residues: 13.5799 Evaluate side-chains 126 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 115 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 519 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 54 optimal weight: 0.0040 chunk 19 optimal weight: 0.0070 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 61 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.4810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 531 GLN L 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.216636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182673 restraints weight = 11244.006| |-----------------------------------------------------------------------------| r_work (start): 0.4075 rms_B_bonded: 2.30 r_work: 0.3832 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3846 r_free = 0.3846 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8506 Z= 0.108 Angle : 0.527 12.929 11576 Z= 0.263 Chirality : 0.040 0.155 1234 Planarity : 0.004 0.077 1481 Dihedral : 3.985 25.193 1116 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.36 % Allowed : 12.90 % Favored : 85.75 % 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: 0.95 (0.27), residues: 1010 helix: 1.52 (0.26), residues: 388 sheet: 0.29 (0.43), residues: 154 loop : 0.10 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 115 TYR 0.023 0.001 TYR L 49 PHE 0.019 0.001 PHE A 230 TRP 0.028 0.001 TRP A 165 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 ( 8488) covalent geometry : angle 0.52508 / 0.26 (11537) SS BOND : bond 0.00241 / 0.13 ( 9) SS BOND : angle 0.42647 / 0.26 ( 18) hydrogen bonds : bond 0.03599 / 2.49 ( 389) hydrogen bonds : angle 4.47113 / 3.20 ( 1097) metal coordination : bond 0.00068 / 0.03 ( 2) link_BETA1-4 : bond 0.00376 / 0.20 ( 1) link_BETA1-4 : angle 0.96363 / 0.50 ( 3) link_NAG-ASN : bond 0.00203 / 0.10 ( 6) link_NAG-ASN : angle 1.23407 / 0.73 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2216.92 seconds wall clock time: 38 minutes 44.22 seconds (2324.22 seconds total)