Starting phenix.real_space_refine on Sat Oct 11 04:21:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wdz_37468/10_2025/8wdz_37468.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wdz_37468/10_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_37468/10_2025/8wdz_37468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wdz_37468/10_2025/8wdz_37468.map" model { file = "/net/cci-nas-00/data/ceres_data/8wdz_37468/10_2025/8wdz_37468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wdz_37468/10_2025/8wdz_37468.cif" } resolution = 2.71 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 2.49, per 1000 atoms: 0.38 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: 0.45 Conformation dependent library (CDL) restraints added in 368.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.16 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: 0.68 Time building geometry restraints manager: 0.60 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.410 Find NCS groups from input model: 0.030 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:6.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG A 559 TYR 0.012 0.001 TYR A 183 PHE 0.011 0.001 PHE A 308 TRP 0.046 0.001 TRP A 302 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 6744) covalent geometry : angle 0.59220 ( 9170) SS BOND : bond 0.00299 ( 7) SS BOND : angle 0.79712 ( 14) hydrogen bonds : bond 0.16795 ( 290) hydrogen bonds : angle 5.98054 ( 821) metal coordination : bond 0.20377 ( 2) link_BETA1-4 : bond 0.00382 ( 2) link_BETA1-4 : angle 0.86038 ( 6) link_BETA1-6 : bond 0.00400 ( 1) link_BETA1-6 : angle 1.32768 ( 3) link_NAG-ASN : bond 0.00556 ( 7) link_NAG-ASN : angle 2.72611 ( 21) *********************** 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 : 0.235 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: 0.5190 time to fit residues: 98.5237 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 : 0.247 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.137617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.114381 restraints weight = 11050.145| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.38 r_work: 0.3384 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3246 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3246 r_free = 0.3246 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.781 6763 Z= 0.354 Angle : 0.602 9.762 9214 Z= 0.302 Chirality : 0.044 0.208 987 Planarity : 0.004 0.037 1176 Dihedral : 6.056 54.003 1070 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.01 % Allowed : 11.67 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.14 (0.30), residues: 788 helix: 1.18 (0.28), residues: 367 sheet: 0.91 (0.73), residues: 48 loop : -1.15 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 192 TYR 0.013 0.001 TYR A 183 PHE 0.017 0.001 PHE B 400 TRP 0.015 0.001 TRP A 302 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 6744) covalent geometry : angle 0.58409 ( 9170) SS BOND : bond 0.00444 ( 7) SS BOND : angle 0.73317 ( 14) hydrogen bonds : bond 0.05481 ( 290) hydrogen bonds : angle 4.67749 ( 821) metal coordination : bond 0.55196 ( 2) link_BETA1-4 : bond 0.00602 ( 2) link_BETA1-4 : angle 1.16178 ( 6) link_BETA1-6 : bond 0.00326 ( 1) link_BETA1-6 : angle 1.14966 ( 3) link_NAG-ASN : bond 0.00603 ( 7) link_NAG-ASN : angle 3.01560 ( 21) *********************** 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 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 165 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 549 GLU cc_start: 0.7870 (mp0) cc_final: 0.7663 (mp0) outliers start: 7 outliers final: 4 residues processed: 168 average time/residue: 0.5625 time to fit residues: 99.3473 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 163 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 500 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 32 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 36 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 374 HIS A 580 ASN B 417 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.116105 restraints weight = 17771.832| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.14 r_work: 0.3335 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3336 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.786 6763 Z= 0.343 Angle : 0.554 8.020 9214 Z= 0.276 Chirality : 0.043 0.203 987 Planarity : 0.004 0.033 1176 Dihedral : 5.786 57.492 1068 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.30 % Allowed : 14.70 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.30), residues: 788 helix: 1.25 (0.28), residues: 373 sheet: 0.60 (0.81), residues: 38 loop : -1.21 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 219 TYR 0.012 0.001 TYR A 183 PHE 0.015 0.001 PHE B 400 TRP 0.009 0.001 TRP A 478 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 6744) covalent geometry : angle 0.53690 ( 9170) SS BOND : bond 0.00379 ( 7) SS BOND : angle 0.69305 ( 14) hydrogen bonds : bond 0.04828 ( 290) hydrogen bonds : angle 4.40732 ( 821) metal coordination : bond 0.55601 ( 2) link_BETA1-4 : bond 0.00457 ( 2) link_BETA1-4 : angle 1.03559 ( 6) link_BETA1-6 : bond 0.00450 ( 1) link_BETA1-6 : angle 1.13748 ( 3) link_NAG-ASN : bond 0.00573 ( 7) link_NAG-ASN : angle 2.86185 ( 21) *********************** 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 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 549 GLU cc_start: 0.7706 (mp0) cc_final: 0.7483 (mp0) REVERT: B 503 VAL cc_start: 0.8541 (p) cc_final: 0.8303 (t) outliers start: 9 outliers final: 5 residues processed: 167 average time/residue: 0.5550 time to fit residues: 97.7140 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 163 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 334 THR Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 417 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 0.0270 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 210 ASN 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 = 0.3858 r_free = 0.3858 target = 0.142321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.117537 restraints weight = 17908.250| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.06 r_work: 0.3340 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1418 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= 0.116 Angle : 0.535 7.818 9214 Z= 0.265 Chirality : 0.042 0.201 987 Planarity : 0.004 0.031 1176 Dihedral : 5.501 53.606 1068 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 1.87 % Allowed : 15.99 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.17 (0.30), residues: 788 helix: 1.32 (0.28), residues: 373 sheet: 0.45 (0.80), residues: 38 loop : -1.19 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 219 TYR 0.011 0.001 TYR A 183 PHE 0.013 0.001 PHE B 400 TRP 0.009 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 6744) covalent geometry : angle 0.51734 ( 9170) SS BOND : bond 0.00380 ( 7) SS BOND : angle 0.69290 ( 14) hydrogen bonds : bond 0.04563 ( 290) hydrogen bonds : angle 4.27832 ( 821) metal coordination : bond 0.00528 ( 2) link_BETA1-4 : bond 0.00497 ( 2) link_BETA1-4 : angle 1.05129 ( 6) link_BETA1-6 : bond 0.00375 ( 1) link_BETA1-6 : angle 1.12396 ( 3) link_NAG-ASN : bond 0.00607 ( 7) link_NAG-ASN : angle 2.78024 ( 21) *********************** 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 171 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 549 GLU cc_start: 0.7659 (mp0) cc_final: 0.7434 (mp0) REVERT: B 355 ARG cc_start: 0.7690 (mtp85) cc_final: 0.7241 (ttt-90) outliers start: 13 outliers final: 6 residues processed: 161 average time/residue: 0.5638 time to fit residues: 95.6225 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 161 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 292 ASP Chi-restraints excluded: chain A residue 445 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 54 optimal weight: 1.9990 chunk 67 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 0.0270 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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 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 = 0.3856 r_free = 0.3856 target = 0.141409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.119562 restraints weight = 9016.486| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 2.06 r_work: 0.3430 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1507 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= 0.113 Angle : 0.535 7.889 9214 Z= 0.265 Chirality : 0.042 0.209 987 Planarity : 0.003 0.031 1176 Dihedral : 5.185 53.379 1068 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.29 % Favored : 97.59 % Rotamer: Outliers : 2.02 % Allowed : 15.99 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.22 (0.30), residues: 788 helix: 1.32 (0.27), residues: 376 sheet: 0.28 (0.81), residues: 38 loop : -1.12 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 192 TYR 0.016 0.001 TYR A 454 PHE 0.012 0.001 PHE A 327 TRP 0.008 0.001 TRP A 478 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6744) covalent geometry : angle 0.51788 ( 9170) SS BOND : bond 0.00362 ( 7) SS BOND : angle 0.68209 ( 14) hydrogen bonds : bond 0.04444 ( 290) hydrogen bonds : angle 4.20696 ( 821) metal coordination : bond 0.00321 ( 2) link_BETA1-4 : bond 0.00429 ( 2) link_BETA1-4 : angle 1.05613 ( 6) link_BETA1-6 : bond 0.00367 ( 1) link_BETA1-6 : angle 1.11512 ( 3) link_NAG-ASN : bond 0.00546 ( 7) link_NAG-ASN : angle 2.75047 ( 21) *********************** 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 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 159 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8733 (m) cc_final: 0.8483 (m) REVERT: A 228 HIS cc_start: 0.7823 (OUTLIER) cc_final: 0.7399 (m-70) REVERT: A 549 GLU cc_start: 0.7741 (mp0) cc_final: 0.7520 (mp0) REVERT: B 355 ARG cc_start: 0.7737 (mtp85) cc_final: 0.7276 (ttt-90) REVERT: B 503 VAL cc_start: 0.8561 (p) cc_final: 0.8309 (t) outliers start: 14 outliers final: 6 residues processed: 162 average time/residue: 0.5543 time to fit residues: 94.5933 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 160 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 334 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 49 optimal weight: 0.0970 chunk 52 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 210 ASN 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 = 0.3848 r_free = 0.3848 target = 0.141064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118458 restraints weight = 11547.474| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.34 r_work: 0.3382 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6763 Z= 0.138 Angle : 0.552 8.168 9214 Z= 0.272 Chirality : 0.043 0.220 987 Planarity : 0.004 0.037 1176 Dihedral : 5.004 53.532 1068 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 16.71 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.15 (0.30), residues: 788 helix: 1.28 (0.27), residues: 373 sheet: 0.23 (0.80), residues: 38 loop : -1.15 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 192 TYR 0.011 0.001 TYR A 183 PHE 0.014 0.001 PHE A 327 TRP 0.010 0.001 TRP A 478 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6744) covalent geometry : angle 0.53584 ( 9170) SS BOND : bond 0.00391 ( 7) SS BOND : angle 0.74729 ( 14) hydrogen bonds : bond 0.04755 ( 290) hydrogen bonds : angle 4.21553 ( 821) metal coordination : bond 0.00349 ( 2) link_BETA1-4 : bond 0.00397 ( 2) link_BETA1-4 : angle 1.07080 ( 6) link_BETA1-6 : bond 0.00434 ( 1) link_BETA1-6 : angle 1.14917 ( 3) link_NAG-ASN : bond 0.00599 ( 7) link_NAG-ASN : angle 2.72943 ( 21) *********************** 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: 14 poor density : 161 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8752 (m) cc_final: 0.8509 (m) REVERT: A 227 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7785 (mm-30) REVERT: A 549 GLU cc_start: 0.7846 (mp0) cc_final: 0.7620 (mp0) REVERT: B 355 ARG cc_start: 0.7779 (mtp85) cc_final: 0.7379 (mtt-85) REVERT: B 503 VAL cc_start: 0.8600 (p) cc_final: 0.8333 (t) outliers start: 14 outliers final: 9 residues processed: 164 average time/residue: 0.5289 time to fit residues: 91.4106 Evaluate side-chains 170 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 160 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN A 175 GLN 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 = 0.3848 r_free = 0.3848 target = 0.141752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.119021 restraints weight = 11440.892| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.36 r_work: 0.3373 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 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 = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6763 Z= 0.150 Angle : 0.572 8.013 9214 Z= 0.282 Chirality : 0.044 0.223 987 Planarity : 0.004 0.054 1176 Dihedral : 4.994 53.474 1068 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.41 % Favored : 97.46 % Rotamer: Outliers : 2.02 % Allowed : 17.44 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.16 (0.30), residues: 788 helix: 1.29 (0.27), residues: 373 sheet: 0.20 (0.80), residues: 38 loop : -1.14 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.013 0.001 TYR A 385 PHE 0.014 0.001 PHE A 327 TRP 0.013 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 6744) covalent geometry : angle 0.55597 ( 9170) SS BOND : bond 0.00408 ( 7) SS BOND : angle 0.76966 ( 14) hydrogen bonds : bond 0.04948 ( 290) hydrogen bonds : angle 4.24661 ( 821) metal coordination : bond 0.00408 ( 2) link_BETA1-4 : bond 0.00369 ( 2) link_BETA1-4 : angle 1.09443 ( 6) link_BETA1-6 : bond 0.00433 ( 1) link_BETA1-6 : angle 1.18287 ( 3) link_NAG-ASN : bond 0.00483 ( 7) link_NAG-ASN : angle 2.76480 ( 21) *********************** 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 175 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8735 (m) cc_final: 0.8475 (m) REVERT: A 227 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7761 (mm-30) REVERT: A 549 GLU cc_start: 0.7834 (mp0) cc_final: 0.7601 (mp0) REVERT: B 355 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7376 (mtt-85) REVERT: B 503 VAL cc_start: 0.8597 (p) cc_final: 0.8323 (t) outliers start: 14 outliers final: 10 residues processed: 165 average time/residue: 0.5417 time to fit residues: 94.2151 Evaluate side-chains 173 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 58 optimal weight: 0.0670 chunk 37 optimal weight: 0.0670 chunk 30 optimal weight: 0.6980 chunk 46 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 210 ASN A 340 GLN 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 = 0.3858 r_free = 0.3858 target = 0.141745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.118626 restraints weight = 13291.514| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.53 r_work: 0.3380 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6763 Z= 0.114 Angle : 0.547 7.951 9214 Z= 0.267 Chirality : 0.042 0.197 987 Planarity : 0.004 0.038 1176 Dihedral : 4.867 53.234 1068 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.80 % Favored : 97.08 % Rotamer: Outliers : 2.02 % Allowed : 18.01 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.24 (0.30), residues: 788 helix: 1.33 (0.27), residues: 380 sheet: 0.09 (0.80), residues: 38 loop : -1.10 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 192 TYR 0.010 0.001 TYR A 385 PHE 0.012 0.001 PHE A 327 TRP 0.011 0.001 TRP B 436 HIS 0.006 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00251 ( 6744) covalent geometry : angle 0.53120 ( 9170) SS BOND : bond 0.00371 ( 7) SS BOND : angle 0.73174 ( 14) hydrogen bonds : bond 0.04395 ( 290) hydrogen bonds : angle 4.17889 ( 821) metal coordination : bond 0.00242 ( 2) link_BETA1-4 : bond 0.00434 ( 2) link_BETA1-4 : angle 1.09460 ( 6) link_BETA1-6 : bond 0.00458 ( 1) link_BETA1-6 : angle 1.20886 ( 3) link_NAG-ASN : bond 0.00609 ( 7) link_NAG-ASN : angle 2.67184 ( 21) *********************** 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 174 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8742 (m) cc_final: 0.8498 (m) REVERT: A 340 GLN cc_start: 0.7965 (mt0) cc_final: 0.7763 (mt0) REVERT: B 355 ARG cc_start: 0.7786 (mtp85) cc_final: 0.7389 (mtt-85) REVERT: B 503 VAL cc_start: 0.8612 (p) cc_final: 0.8333 (t) outliers start: 14 outliers final: 9 residues processed: 164 average time/residue: 0.5501 time to fit residues: 95.2402 Evaluate side-chains 168 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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 74 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.116503 restraints weight = 11089.804| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.28 r_work: 0.3362 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 6763 Z= 0.204 Angle : 0.618 10.206 9214 Z= 0.303 Chirality : 0.047 0.356 987 Planarity : 0.004 0.039 1176 Dihedral : 5.045 53.797 1068 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.02 % Allowed : 18.59 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.30), residues: 788 helix: 1.18 (0.27), residues: 381 sheet: 0.17 (0.81), residues: 38 loop : -1.12 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 192 TYR 0.020 0.002 TYR A 183 PHE 0.016 0.001 PHE A 390 TRP 0.016 0.002 TRP B 436 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 6744) covalent geometry : angle 0.59399 ( 9170) SS BOND : bond 0.00466 ( 7) SS BOND : angle 0.89658 ( 14) hydrogen bonds : bond 0.05550 ( 290) hydrogen bonds : angle 4.28980 ( 821) metal coordination : bond 0.00603 ( 2) link_BETA1-4 : bond 0.00294 ( 2) link_BETA1-4 : angle 1.13081 ( 6) link_BETA1-6 : bond 0.00216 ( 1) link_BETA1-6 : angle 1.06766 ( 3) link_NAG-ASN : bond 0.00587 ( 7) link_NAG-ASN : angle 3.52451 ( 21) *********************** 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 174 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 ASN cc_start: 0.7993 (t0) cc_final: 0.7485 (m-40) REVERT: A 167 SER cc_start: 0.8716 (m) cc_final: 0.8464 (m) REVERT: A 340 GLN cc_start: 0.7972 (mt0) cc_final: 0.7770 (mt0) REVERT: B 355 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7349 (mtt-85) REVERT: B 503 VAL cc_start: 0.8601 (p) cc_final: 0.8319 (t) REVERT: B 511 VAL cc_start: 0.8096 (t) cc_final: 0.7767 (p) outliers start: 14 outliers final: 10 residues processed: 164 average time/residue: 0.5535 time to fit residues: 95.8196 Evaluate side-chains 172 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.257 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.139670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.116812 restraints weight = 12765.302| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.46 r_work: 0.3357 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3198 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3198 r_free = 0.3198 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3198 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6763 Z= 0.160 Angle : 0.599 9.054 9214 Z= 0.292 Chirality : 0.045 0.326 987 Planarity : 0.004 0.034 1176 Dihedral : 5.021 53.358 1068 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.92 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 19.45 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.11 (0.30), residues: 788 helix: 1.18 (0.27), residues: 379 sheet: 0.14 (0.81), residues: 38 loop : -1.12 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 509 TYR 0.023 0.002 TYR A 183 PHE 0.014 0.001 PHE A 390 TRP 0.017 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00372 ( 6744) covalent geometry : angle 0.57602 ( 9170) SS BOND : bond 0.00427 ( 7) SS BOND : angle 0.82793 ( 14) hydrogen bonds : bond 0.05120 ( 290) hydrogen bonds : angle 4.32216 ( 821) metal coordination : bond 0.00335 ( 2) link_BETA1-4 : bond 0.00374 ( 2) link_BETA1-4 : angle 1.13698 ( 6) link_BETA1-6 : bond 0.00404 ( 1) link_BETA1-6 : angle 1.19538 ( 3) link_NAG-ASN : bond 0.00654 ( 7) link_NAG-ASN : angle 3.37347 ( 21) ********************** 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 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 SER cc_start: 0.8726 (m) cc_final: 0.8471 (m) REVERT: A 262 LEU cc_start: 0.8787 (mp) cc_final: 0.8550 (mt) REVERT: A 340 GLN cc_start: 0.7987 (mt0) cc_final: 0.7782 (mt0) REVERT: B 355 ARG cc_start: 0.7775 (mtp85) cc_final: 0.7297 (ttt-90) REVERT: B 503 VAL cc_start: 0.8616 (p) cc_final: 0.8337 (t) REVERT: B 511 VAL cc_start: 0.8099 (t) cc_final: 0.7710 (p) outliers start: 10 outliers final: 10 residues processed: 159 average time/residue: 0.5565 time to fit residues: 93.1983 Evaluate side-chains 167 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.292 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 59 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 76 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.115917 restraints weight = 12857.309| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.50 r_work: 0.3358 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6763 Z= 0.149 Angle : 0.601 11.536 9214 Z= 0.290 Chirality : 0.046 0.459 987 Planarity : 0.004 0.037 1176 Dihedral : 5.041 53.346 1068 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 1.59 % Allowed : 19.31 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 aren not related in a simple way. whole: 0.14 (0.30), residues: 788 helix: 1.20 (0.27), residues: 380 sheet: 0.16 (0.81), residues: 38 loop : -1.10 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 192 TYR 0.017 0.001 TYR A 183 PHE 0.014 0.001 PHE A 327 TRP 0.019 0.001 TRP B 436 HIS 0.007 0.001 HIS A 241 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 6744) covalent geometry : angle 0.57111 ( 9170) SS BOND : bond 0.00425 ( 7) SS BOND : angle 0.82871 ( 14) hydrogen bonds : bond 0.04960 ( 290) hydrogen bonds : angle 4.25112 ( 821) metal coordination : bond 0.00348 ( 2) link_BETA1-4 : bond 0.00343 ( 2) link_BETA1-4 : angle 1.13409 ( 6) link_BETA1-6 : bond 0.00383 ( 1) link_BETA1-6 : angle 1.18751 ( 3) link_NAG-ASN : bond 0.00662 ( 7) link_NAG-ASN : angle 3.84807 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.13 seconds wall clock time: 57 minutes 52.28 seconds (3472.28 seconds total)