Starting phenix.real_space_refine on Wed May 14 09:00:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdz_37468/05_2025/8wdz_37468.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 6336 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 37 5.16 5 C 4195 2.51 5 N 1078 2.21 5 O 1248 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 6559 Number of models: 1 Model: "" Number of chains: 6 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: 1553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1553 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 57 Unusual residues: {' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.30, per 1000 atoms: 0.96 Number of scatterers: 6559 At special positions: 0 Unit cell: (76.5, 87.55, 124.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 37 16.00 O 1248 8.00 N 1078 7.00 C 4195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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 D 1 " - " NAG D 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 901 " - " ASN A 53 " " NAG A 902 " - " ASN A 90 " " NAG A 903 " - " ASN A 322 " " NAG A 904 " - " ASN A 432 " " NAG B 601 " - " ASN B 343 " " NAG C 1 " - " ASN A 103 " " NAG D 1 " - " ASN A 546 " Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 905 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 378 " pdb="ZN ZN A 905 " - pdb=" NE2 HIS A 374 " 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1492 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 54.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.528A pdb=" N GLN A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU A 37 " --> pdb=" O ASN A 33 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP A 38 " --> pdb=" O HIS A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.667A pdb=" N GLU A 87 " --> pdb=" O PRO A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 101 removed outlier: 3.783A pdb=" N GLN A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.949A pdb=" N SER A 106 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL A 107 " --> pdb=" O GLY A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 129 Processing helix chain 'A' and resid 147 through 154 Processing helix chain 'A' and resid 157 through 172 removed outlier: 3.762A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG A 169 " --> pdb=" O TRP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 194 removed outlier: 3.895A pdb=" N LEU A 176 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 177 " --> pdb=" O GLY A 173 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.687A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'A' and resid 220 through 249 removed outlier: 3.716A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 232 " --> pdb=" O HIS A 228 " (cutoff:3.500A) Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.727A pdb=" N VAL A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 331 removed outlier: 3.757A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 removed outlier: 3.624A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N TYR A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 411 removed outlier: 3.860A pdb=" N VAL A 404 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 removed outlier: 3.839A pdb=" N GLU A 435 " --> pdb=" O ASP A 431 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 466 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 513 through 533 removed outlier: 4.083A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A 524 " --> pdb=" O LEU A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.922A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.798A pdb=" N VAL A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 removed outlier: 3.530A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 599 Processing helix chain 'B' and resid 366 through 370 Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.024A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.443A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 347 through 352 removed outlier: 6.066A pdb=" N ASP A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.181A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'B' and resid 473 through 474 290 hydrogen bonds defined for protein. 821 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: 1.66 Time building geometry restraints manager: 2.04 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: 2082 1.34 - 1.46: 1737 1.46 - 1.58: 2867 1.58 - 1.70: 0 1.70 - 1.82: 58 Bond restraints: 6744 Sorted by residual: bond pdb=" CA SER B 494 " pdb=" CB SER B 494 " ideal model delta sigma weight residual 1.530 1.478 0.052 1.43e-02 4.89e+03 1.32e+01 bond pdb=" CE1 HIS A 401 " pdb=" NE2 HIS A 401 " ideal model delta sigma weight residual 1.321 1.355 -0.034 1.00e-02 1.00e+04 1.17e+01 bond pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta sigma weight residual 1.456 1.498 -0.041 1.31e-02 5.83e+03 9.86e+00 bond pdb=" N HIS A 401 " pdb=" CA HIS A 401 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.30e-02 5.92e+03 7.66e+00 bond pdb=" N SER B 494 " pdb=" CA SER B 494 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.23e-02 6.61e+03 6.31e+00 ... (remaining 6739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 8782 1.27 - 2.55: 292 2.55 - 3.82: 70 3.82 - 5.09: 20 5.09 - 6.36: 6 Bond angle restraints: 9170 Sorted by residual: angle pdb=" N GLU A 227 " pdb=" CA GLU A 227 " pdb=" CB GLU A 227 " ideal model delta sigma weight residual 110.12 115.10 -4.98 1.47e+00 4.63e-01 1.15e+01 angle pdb=" N LYS A 419 " pdb=" CA LYS A 419 " pdb=" C LYS A 419 " ideal model delta sigma weight residual 111.36 107.81 3.55 1.09e+00 8.42e-01 1.06e+01 angle pdb=" C ASN B 487 " pdb=" CA ASN B 487 " pdb=" CB ASN B 487 " ideal model delta sigma weight residual 110.42 116.78 -6.36 1.99e+00 2.53e-01 1.02e+01 angle pdb=" C GLN A 24 " pdb=" N ALA A 25 " pdb=" CA ALA A 25 " ideal model delta sigma weight residual 120.29 124.78 -4.49 1.42e+00 4.96e-01 1.00e+01 angle pdb=" N ASN B 487 " pdb=" CA ASN B 487 " pdb=" C ASN B 487 " ideal model delta sigma weight residual 110.80 104.71 6.09 2.13e+00 2.20e-01 8.18e+00 ... (remaining 9165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.33: 3709 17.33 - 34.66: 307 34.66 - 51.99: 68 51.99 - 69.32: 15 69.32 - 86.65: 7 Dihedral angle restraints: 4106 sinusoidal: 1780 harmonic: 2326 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 141.81 -48.81 1 1.00e+01 1.00e-02 3.28e+01 dihedral pdb=" CA CYS A 141 " pdb=" C CYS A 141 " pdb=" N LEU A 142 " pdb=" CA LEU A 142 " ideal model delta harmonic sigma weight residual -180.00 -158.05 -21.95 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 4103 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 709 0.043 - 0.087: 206 0.087 - 0.130: 64 0.130 - 0.173: 6 0.173 - 0.216: 2 Chirality restraints: 987 Sorted by residual: chirality pdb=" C1 NAG A 902 " pdb=" ND2 ASN A 90 " pdb=" C2 NAG A 902 " pdb=" O5 NAG A 902 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CB ILE B 410 " pdb=" CA ILE B 410 " pdb=" CG1 ILE B 410 " pdb=" CG2 ILE B 410 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.19 2.00e-01 2.50e+01 8.97e-01 chirality pdb=" C1 NAG A 901 " pdb=" ND2 ASN A 53 " pdb=" C2 NAG A 901 " pdb=" O5 NAG A 901 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-01 2.50e+01 5.65e-01 ... (remaining 984 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 486 " -0.015 2.00e-02 2.50e+03 2.94e-02 8.66e+00 pdb=" C VAL B 486 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL B 486 " -0.019 2.00e-02 2.50e+03 pdb=" N ASN B 487 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 302 " -0.017 2.00e-02 2.50e+03 1.69e-02 7.18e+00 pdb=" CG TRP A 302 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP A 302 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 302 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 302 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 302 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 302 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 302 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 302 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 400 " 0.013 2.00e-02 2.50e+03 2.45e-02 6.01e+00 pdb=" C PHE A 400 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 400 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS A 401 " 0.014 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 38 2.58 - 3.16: 5188 3.16 - 3.74: 9740 3.74 - 4.32: 13628 4.32 - 4.90: 22976 Nonbonded interactions: 51570 Sorted by model distance: nonbonded pdb=" OE2 GLU A 402 " pdb="ZN ZN A 905 " model vdw 2.004 2.230 nonbonded pdb=" OH TYR A 217 " pdb=" OD2 ASP A 225 " model vdw 2.262 3.040 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP A 431 " model vdw 2.304 3.120 nonbonded pdb=" O ILE A 151 " pdb=" OG SER A 155 " model vdw 2.306 3.040 nonbonded pdb=" OD1 ASN A 90 " pdb=" N2 NAG A 902 " model vdw 2.318 3.120 ... (remaining 51565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.960 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:9.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.210 6763 Z= 0.223 Angle : 0.607 8.126 9214 Z= 0.316 Chirality : 0.044 0.216 987 Planarity : 0.004 0.055 1176 Dihedral : 13.558 86.655 2593 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.30), residues: 788 helix: 1.02 (0.27), residues: 356 sheet: 1.71 (0.75), residues: 50 loop : -1.15 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP A 302 HIS 0.006 0.001 HIS A 374 PHE 0.011 0.001 PHE A 308 TYR 0.012 0.001 TYR A 183 ARG 0.002 0.000 ARG A 559 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 7) link_NAG-ASN : angle 2.72611 ( 21) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 0.86038 ( 6) hydrogen bonds : bond 0.16795 ( 290) hydrogen bonds : angle 5.98054 ( 821) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.32768 ( 3) metal coordination : bond 0.20377 ( 2) SS BOND : bond 0.00299 ( 7) SS BOND : angle 0.79712 ( 14) covalent geometry : bond 0.00358 ( 6744) covalent geometry : angle 0.59220 ( 9170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.6929 (tm-30) cc_final: 0.6717 (tm-30) REVERT: A 483 GLU cc_start: 0.7192 (tm-30) cc_final: 0.6992 (tm-30) REVERT: A 549 GLU cc_start: 0.7445 (mp0) cc_final: 0.7150 (mp0) REVERT: B 438 SER cc_start: 0.8205 (t) cc_final: 0.7900 (t) outliers start: 3 outliers final: 1 residues processed: 180 average time/residue: 1.0296 time to fit residues: 195.7383 Evaluate side-chains 156 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 155 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 417 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 175 GLN A 210 ASN A 374 HIS A 394 ASN A 401 HIS A 580 ASN B 417 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.138285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.113589 restraints weight = 16197.713| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.94 r_work: 0.3353 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.778 6763 Z= 0.345 Angle : 0.589 9.821 9214 Z= 0.295 Chirality : 0.043 0.199 987 Planarity : 0.004 0.037 1176 Dihedral : 6.031 53.935 1070 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.86 % Allowed : 11.67 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.30), residues: 788 helix: 1.21 (0.28), residues: 367 sheet: 0.95 (0.73), residues: 48 loop : -1.13 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 302 HIS 0.006 0.001 HIS A 241 PHE 0.017 0.001 PHE B 400 TYR 0.012 0.001 TYR A 183 ARG 0.004 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00669 ( 7) link_NAG-ASN : angle 2.97623 ( 21) link_BETA1-4 : bond 0.00565 ( 2) link_BETA1-4 : angle 1.15485 ( 6) hydrogen bonds : bond 0.05274 ( 290) hydrogen bonds : angle 4.68378 ( 821) link_BETA1-6 : bond 0.00417 ( 1) link_BETA1-6 : angle 1.21812 ( 3) metal coordination : bond 0.55039 ( 2) SS BOND : bond 0.00422 ( 7) SS BOND : angle 0.69082 ( 14) covalent geometry : bond 0.00309 ( 6744) covalent geometry : angle 0.57120 ( 9170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 164 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7386 (tm-30) cc_final: 0.7178 (tm-30) REVERT: A 549 GLU cc_start: 0.7685 (mp0) cc_final: 0.7465 (mp0) outliers start: 6 outliers final: 3 residues processed: 167 average time/residue: 1.0351 time to fit residues: 182.5104 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 402 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 chunk 39 optimal weight: 0.0570 chunk 72 optimal weight: 0.0000 chunk 19 optimal weight: 0.0060 chunk 70 optimal weight: 0.0870 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 24 optimal weight: 0.0980 chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.0496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 188 ASN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 580 ASN B 417 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.145371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.123958 restraints weight = 8992.976| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.06 r_work: 0.3485 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6763 Z= 0.097 Angle : 0.517 7.055 9214 Z= 0.256 Chirality : 0.040 0.190 987 Planarity : 0.003 0.032 1176 Dihedral : 5.539 53.674 1068 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.44 % Allowed : 14.55 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.31), residues: 788 helix: 1.46 (0.28), residues: 373 sheet: 0.84 (0.74), residues: 48 loop : -1.01 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.004 0.001 HIS A 374 PHE 0.017 0.001 PHE B 400 TYR 0.014 0.001 TYR A 516 ARG 0.003 0.000 ARG A 192 Details of bonding type rmsd link_NAG-ASN : bond 0.00557 ( 7) link_NAG-ASN : angle 2.73789 ( 21) link_BETA1-4 : bond 0.00516 ( 2) link_BETA1-4 : angle 1.00620 ( 6) hydrogen bonds : bond 0.03763 ( 290) hydrogen bonds : angle 4.31782 ( 821) link_BETA1-6 : bond 0.00463 ( 1) link_BETA1-6 : angle 1.17019 ( 3) metal coordination : bond 0.01031 ( 2) SS BOND : bond 0.00338 ( 7) SS BOND : angle 0.65128 ( 14) covalent geometry : bond 0.00191 ( 6744) covalent geometry : angle 0.49958 ( 9170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 171 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7446 (mp0) REVERT: A 228 HIS cc_start: 0.7742 (OUTLIER) cc_final: 0.7347 (m-70) REVERT: B 355 ARG cc_start: 0.7761 (mtp85) cc_final: 0.7352 (ttt-90) outliers start: 10 outliers final: 3 residues processed: 170 average time/residue: 1.0613 time to fit residues: 190.2228 Evaluate side-chains 164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 159 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 175 GLN A 188 ASN A 210 ASN A 374 HIS A 580 ASN B 417 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119166 restraints weight = 9836.592| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.16 r_work: 0.3406 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.806 6763 Z= 0.363 Angle : 0.552 7.740 9214 Z= 0.276 Chirality : 0.044 0.203 987 Planarity : 0.004 0.033 1176 Dihedral : 5.557 55.410 1068 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 1.73 % Allowed : 15.71 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 788 helix: 1.36 (0.28), residues: 373 sheet: 0.53 (0.81), residues: 38 loop : -1.10 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 PHE 0.014 0.001 PHE A 308 TYR 0.012 0.001 TYR A 183 ARG 0.006 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00514 ( 7) link_NAG-ASN : angle 2.75042 ( 21) link_BETA1-4 : bond 0.00440 ( 2) link_BETA1-4 : angle 1.07820 ( 6) hydrogen bonds : bond 0.04936 ( 290) hydrogen bonds : angle 4.25379 ( 821) link_BETA1-6 : bond 0.00450 ( 1) link_BETA1-6 : angle 1.11050 ( 3) metal coordination : bond 0.57028 ( 2) SS BOND : bond 0.00370 ( 7) SS BOND : angle 0.68792 ( 14) covalent geometry : bond 0.00368 ( 6744) covalent geometry : angle 0.53583 ( 9170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 161 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7397 (tm-30) REVERT: A 549 GLU cc_start: 0.7822 (mp0) cc_final: 0.7598 (mp0) REVERT: A 557 MET cc_start: 0.8597 (tmm) cc_final: 0.8395 (tmm) REVERT: B 355 ARG cc_start: 0.7774 (mtp85) cc_final: 0.7323 (ttt-90) REVERT: B 503 VAL cc_start: 0.8580 (p) cc_final: 0.8312 (t) outliers start: 12 outliers final: 4 residues processed: 164 average time/residue: 1.0528 time to fit residues: 182.1328 Evaluate side-chains 166 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 162 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 18 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 30 optimal weight: 0.3980 chunk 77 optimal weight: 8.9990 chunk 14 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 374 HIS A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118505 restraints weight = 12454.864| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.41 r_work: 0.3381 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.794 6763 Z= 0.351 Angle : 0.542 7.901 9214 Z= 0.270 Chirality : 0.043 0.223 987 Planarity : 0.004 0.031 1176 Dihedral : 5.244 53.827 1068 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 2.31 % Allowed : 16.86 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.30), residues: 788 helix: 1.44 (0.28), residues: 370 sheet: 0.22 (0.80), residues: 38 loop : -1.03 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 308 TYR 0.013 0.001 TYR A 385 ARG 0.004 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 7) link_NAG-ASN : angle 2.75886 ( 21) link_BETA1-4 : bond 0.00375 ( 2) link_BETA1-4 : angle 1.07971 ( 6) hydrogen bonds : bond 0.04819 ( 290) hydrogen bonds : angle 4.24927 ( 821) link_BETA1-6 : bond 0.00414 ( 1) link_BETA1-6 : angle 1.14051 ( 3) metal coordination : bond 0.56122 ( 2) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.69130 ( 14) covalent geometry : bond 0.00322 ( 6744) covalent geometry : angle 0.52549 ( 9170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7710 (tm-30) cc_final: 0.7466 (tm-30) REVERT: A 167 SER cc_start: 0.8761 (m) cc_final: 0.8042 (m) REVERT: A 171 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7545 (mp0) REVERT: A 549 GLU cc_start: 0.7863 (mp0) cc_final: 0.7636 (mp0) REVERT: B 355 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7328 (ttt-90) REVERT: B 503 VAL cc_start: 0.8610 (p) cc_final: 0.8327 (t) outliers start: 16 outliers final: 7 residues processed: 162 average time/residue: 0.9960 time to fit residues: 170.6609 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 171 GLU Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 74 optimal weight: 0.4980 chunk 17 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.0000 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 374 HIS A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.141588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.117557 restraints weight = 15136.628| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.77 r_work: 0.3373 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3376 r_free = 0.3376 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3376 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.784 6763 Z= 0.337 Angle : 0.527 7.893 9214 Z= 0.260 Chirality : 0.042 0.202 987 Planarity : 0.003 0.031 1176 Dihedral : 5.005 53.389 1068 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.16 % Allowed : 17.72 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 788 helix: 1.45 (0.28), residues: 370 sheet: 0.23 (0.81), residues: 38 loop : -0.94 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 436 HIS 0.005 0.001 HIS A 241 PHE 0.011 0.001 PHE B 400 TYR 0.011 0.001 TYR A 183 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00605 ( 7) link_NAG-ASN : angle 2.65381 ( 21) link_BETA1-4 : bond 0.00446 ( 2) link_BETA1-4 : angle 1.06822 ( 6) hydrogen bonds : bond 0.04401 ( 290) hydrogen bonds : angle 4.17932 ( 821) link_BETA1-6 : bond 0.00394 ( 1) link_BETA1-6 : angle 1.17715 ( 3) metal coordination : bond 0.55428 ( 2) SS BOND : bond 0.00342 ( 7) SS BOND : angle 0.67136 ( 14) covalent geometry : bond 0.00244 ( 6744) covalent geometry : angle 0.51063 ( 9170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7428 (tm-30) cc_final: 0.7209 (tm-30) REVERT: A 167 SER cc_start: 0.8682 (m) cc_final: 0.8435 (m) REVERT: A 549 GLU cc_start: 0.7621 (mp0) cc_final: 0.7392 (mp0) REVERT: A 557 MET cc_start: 0.8524 (tmm) cc_final: 0.8308 (tmm) REVERT: B 355 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7247 (mtt-85) REVERT: B 503 VAL cc_start: 0.8533 (p) cc_final: 0.8291 (t) outliers start: 15 outliers final: 10 residues processed: 163 average time/residue: 1.0366 time to fit residues: 178.5051 Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 228 HIS Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 63 optimal weight: 0.6980 chunk 24 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.140629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.117870 restraints weight = 11065.622| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.30 r_work: 0.3397 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3250 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6763 Z= 0.134 Angle : 0.547 8.021 9214 Z= 0.270 Chirality : 0.043 0.210 987 Planarity : 0.004 0.031 1176 Dihedral : 4.959 53.553 1068 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.30), residues: 788 helix: 1.47 (0.28), residues: 370 sheet: 0.26 (0.81), residues: 38 loop : -0.97 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 PHE 0.012 0.001 PHE A 390 TYR 0.012 0.001 TYR A 385 ARG 0.003 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00474 ( 7) link_NAG-ASN : angle 2.70309 ( 21) link_BETA1-4 : bond 0.00416 ( 2) link_BETA1-4 : angle 1.08395 ( 6) hydrogen bonds : bond 0.04721 ( 290) hydrogen bonds : angle 4.19848 ( 821) link_BETA1-6 : bond 0.00427 ( 1) link_BETA1-6 : angle 1.16967 ( 3) metal coordination : bond 0.00624 ( 2) SS BOND : bond 0.00365 ( 7) SS BOND : angle 0.70527 ( 14) covalent geometry : bond 0.00307 ( 6744) covalent geometry : angle 0.53131 ( 9170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7421 (tm-30) REVERT: A 167 SER cc_start: 0.8734 (m) cc_final: 0.8483 (m) REVERT: A 359 LEU cc_start: 0.8590 (OUTLIER) cc_final: 0.8192 (tt) REVERT: A 549 GLU cc_start: 0.7787 (mp0) cc_final: 0.7563 (mp0) REVERT: A 557 MET cc_start: 0.8616 (tmm) cc_final: 0.8414 (tmm) REVERT: B 355 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7373 (mtt-85) REVERT: B 503 VAL cc_start: 0.8597 (p) cc_final: 0.8322 (t) outliers start: 14 outliers final: 10 residues processed: 162 average time/residue: 0.9850 time to fit residues: 168.6941 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 156 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 70 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 56 optimal weight: 0.9980 chunk 37 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.140970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.116715 restraints weight = 16372.147| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.85 r_work: 0.3355 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6763 Z= 0.125 Angle : 0.542 7.976 9214 Z= 0.267 Chirality : 0.042 0.200 987 Planarity : 0.003 0.030 1176 Dihedral : 4.871 53.353 1068 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 17.87 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.31), residues: 788 helix: 1.44 (0.28), residues: 374 sheet: 0.16 (0.81), residues: 38 loop : -0.94 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 PHE 0.011 0.001 PHE A 308 TYR 0.012 0.001 TYR A 385 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 7) link_NAG-ASN : angle 2.63732 ( 21) link_BETA1-4 : bond 0.00401 ( 2) link_BETA1-4 : angle 1.09053 ( 6) hydrogen bonds : bond 0.04565 ( 290) hydrogen bonds : angle 4.17288 ( 821) link_BETA1-6 : bond 0.00407 ( 1) link_BETA1-6 : angle 1.17550 ( 3) metal coordination : bond 0.00380 ( 2) SS BOND : bond 0.00358 ( 7) SS BOND : angle 0.70690 ( 14) covalent geometry : bond 0.00283 ( 6744) covalent geometry : angle 0.52685 ( 9170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7216 (tm-30) REVERT: A 167 SER cc_start: 0.8671 (m) cc_final: 0.8408 (m) REVERT: A 359 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8113 (tt) REVERT: A 549 GLU cc_start: 0.7600 (mp0) cc_final: 0.7372 (mp0) REVERT: A 557 MET cc_start: 0.8543 (tmm) cc_final: 0.8332 (tmm) REVERT: B 355 ARG cc_start: 0.7615 (mtp85) cc_final: 0.7234 (mtt-85) REVERT: B 503 VAL cc_start: 0.8544 (p) cc_final: 0.8293 (t) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.9837 time to fit residues: 171.7243 Evaluate side-chains 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 292 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 410 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 536 GLU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 76 optimal weight: 0.0050 chunk 68 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 8 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.4980 chunk 45 optimal weight: 0.0050 chunk 32 optimal weight: 0.0020 chunk 11 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.1216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 374 HIS A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.144473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120636 restraints weight = 17765.586| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.94 r_work: 0.3387 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3387 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.769 6763 Z= 0.325 Angle : 0.513 7.667 9214 Z= 0.248 Chirality : 0.040 0.205 987 Planarity : 0.003 0.030 1176 Dihedral : 4.709 53.257 1068 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.03 % Favored : 97.84 % Rotamer: Outliers : 1.15 % Allowed : 18.73 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.31), residues: 788 helix: 1.65 (0.28), residues: 373 sheet: 0.30 (0.82), residues: 38 loop : -0.86 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 477 HIS 0.003 0.001 HIS A 241 PHE 0.010 0.001 PHE B 400 TYR 0.010 0.001 TYR A 613 ARG 0.002 0.000 ARG B 452 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 7) link_NAG-ASN : angle 2.64233 ( 21) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 1.07932 ( 6) hydrogen bonds : bond 0.03640 ( 290) hydrogen bonds : angle 4.04765 ( 821) link_BETA1-6 : bond 0.00402 ( 1) link_BETA1-6 : angle 1.19088 ( 3) metal coordination : bond 0.54342 ( 2) SS BOND : bond 0.00300 ( 7) SS BOND : angle 0.64991 ( 14) covalent geometry : bond 0.00195 ( 6744) covalent geometry : angle 0.49671 ( 9170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 156 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7222 (tm-30) REVERT: A 167 SER cc_start: 0.8659 (m) cc_final: 0.8396 (m) REVERT: A 549 GLU cc_start: 0.7574 (mp0) cc_final: 0.7353 (mp0) REVERT: B 355 ARG cc_start: 0.7625 (mtp85) cc_final: 0.7262 (mtt-85) REVERT: B 489 TYR cc_start: 0.7306 (m-80) cc_final: 0.7013 (m-80) REVERT: B 503 VAL cc_start: 0.8567 (p) cc_final: 0.8312 (t) outliers start: 8 outliers final: 5 residues processed: 158 average time/residue: 1.0166 time to fit residues: 170.0109 Evaluate side-chains 157 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 152 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 7 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.0270 chunk 13 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 12 optimal weight: 0.0040 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 374 HIS A 394 ASN A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 448 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.143247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118934 restraints weight = 17640.146| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.00 r_work: 0.3356 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.784 6763 Z= 0.340 Angle : 0.536 7.732 9214 Z= 0.264 Chirality : 0.042 0.208 987 Planarity : 0.003 0.030 1176 Dihedral : 4.723 53.315 1068 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 1.01 % Allowed : 19.60 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.31), residues: 788 helix: 1.57 (0.28), residues: 374 sheet: 0.30 (0.82), residues: 38 loop : -0.87 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 327 TYR 0.011 0.001 TYR A 613 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 7) link_NAG-ASN : angle 2.55062 ( 21) link_BETA1-4 : bond 0.00377 ( 2) link_BETA1-4 : angle 1.07309 ( 6) hydrogen bonds : bond 0.04267 ( 290) hydrogen bonds : angle 4.06676 ( 821) link_BETA1-6 : bond 0.00391 ( 1) link_BETA1-6 : angle 1.15952 ( 3) metal coordination : bond 0.55418 ( 2) SS BOND : bond 0.00344 ( 7) SS BOND : angle 0.67147 ( 14) covalent geometry : bond 0.00273 ( 6744) covalent geometry : angle 0.52133 ( 9170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1576 Ramachandran restraints generated. 788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7213 (tm-30) REVERT: A 167 SER cc_start: 0.8652 (m) cc_final: 0.8395 (m) REVERT: A 323 MET cc_start: 0.7213 (mmm) cc_final: 0.6412 (mtm) REVERT: A 549 GLU cc_start: 0.7614 (mp0) cc_final: 0.7385 (mp0) REVERT: B 355 ARG cc_start: 0.7632 (mtp85) cc_final: 0.7250 (mtt-85) REVERT: B 489 TYR cc_start: 0.7343 (m-80) cc_final: 0.6993 (m-80) REVERT: B 503 VAL cc_start: 0.8561 (p) cc_final: 0.8315 (t) outliers start: 7 outliers final: 6 residues processed: 160 average time/residue: 1.0395 time to fit residues: 175.7363 Evaluate side-chains 163 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 157 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 52 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 73 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 374 HIS A 580 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.144126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121445 restraints weight = 12941.723| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.46 r_work: 0.3398 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.755 6763 Z= 0.327 Angle : 0.536 7.686 9214 Z= 0.264 Chirality : 0.042 0.205 987 Planarity : 0.003 0.030 1176 Dihedral : 4.724 53.243 1068 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.54 % Favored : 97.33 % Rotamer: Outliers : 1.01 % Allowed : 19.45 % Favored : 79.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.31), residues: 788 helix: 1.57 (0.28), residues: 374 sheet: 0.26 (0.82), residues: 38 loop : -0.86 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.005 0.001 HIS A 241 PHE 0.010 0.001 PHE A 308 TYR 0.011 0.001 TYR A 613 ARG 0.002 0.000 ARG A 219 Details of bonding type rmsd link_NAG-ASN : bond 0.00453 ( 7) link_NAG-ASN : angle 2.56796 ( 21) link_BETA1-4 : bond 0.00412 ( 2) link_BETA1-4 : angle 1.06320 ( 6) hydrogen bonds : bond 0.04204 ( 290) hydrogen bonds : angle 4.10418 ( 821) link_BETA1-6 : bond 0.00378 ( 1) link_BETA1-6 : angle 1.16749 ( 3) metal coordination : bond 0.53359 ( 2) SS BOND : bond 0.00356 ( 7) SS BOND : angle 0.68170 ( 14) covalent geometry : bond 0.00255 ( 6744) covalent geometry : angle 0.52105 ( 9170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5905.54 seconds wall clock time: 101 minutes 58.42 seconds (6118.42 seconds total)