Starting phenix.real_space_refine on Fri Aug 22 16:10:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zuf_60483/08_2025/8zuf_60483.map" } resolution = 3.31 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 33 5.16 5 C 3702 2.51 5 N 989 2.21 5 O 1020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5745 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4327 Classifications: {'peptide': 585} Incomplete info: {'truncation_to_alanine': 166} Link IDs: {'PTRANS': 24, 'TRANS': 560} Unresolved non-hydrogen bonds: 482 Unresolved non-hydrogen angles: 593 Unresolved non-hydrogen dihedrals: 375 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLU:plan': 34, 'ARG:plan': 1, 'ASP:plan': 21, 'ASN:plan1': 13, 'GLN:plan1': 7, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 281 Chain: "B" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1171 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 97} Link IDs: {'PTRANS': 13, 'TRANS': 171} Chain breaks: 4 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 229 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'GLN:plan1': 4, 'ASP:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 142 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 43 Unusual residues: {' ZN': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 2.21, per 1000 atoms: 0.38 Number of scatterers: 5745 At special positions: 0 Unit cell: (76.95, 76, 115.9, 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 33 16.00 O 1020 8.00 N 989 7.00 C 3702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 142 " distance=2.16 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.08 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.01 Simple disulfide: pdb=" SG CYS B 425 " - pdb=" SG CYS B 478 " distance=2.04 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 538 " distance=2.02 Simple disulfide: pdb=" SG CYS B 506 " - pdb=" SG CYS B 520 " 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 C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 901 " - " ASN A 91 " " NAG A 902 " - " ASN A 322 " " NAG A 903 " - " ASN A 329 " " NAG B 700 " - " ASN B 550 " " NAG C 1 " - " ASN B 496 " " NAG D 1 " - " ASN A 104 " " NAG E 1 " - " ASN A 216 " " NAG F 1 " - " ASN A 280 " " NAG G 1 " - " ASN A 534 " " NAG H 1 " - " ASN A 546 " Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 494.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 904 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 374 " pdb="ZN ZN A 904 " - pdb=" NE2 HIS A 378 " 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 5 sheets defined 59.7% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 56 through 81 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 91 through 103 Processing helix chain 'A' and resid 104 through 109 removed outlier: 3.562A pdb=" N SER A 107 " --> pdb=" O ASN A 104 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 130 Processing helix chain 'A' and resid 145 through 153 Processing helix chain 'A' and resid 157 through 172 Processing helix chain 'A' and resid 172 through 193 Proline residue: A 178 - end of helix Processing helix chain 'A' and resid 198 through 204 Processing helix chain 'A' and resid 218 through 252 removed outlier: 3.826A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) Proline residue: A 235 - end of helix removed outlier: 3.611A pdb=" N GLN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' 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 300 Processing helix chain 'A' and resid 303 through 317 Processing helix chain 'A' and resid 324 through 331 Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 399 through 413 Processing helix chain 'A' and resid 414 through 421 Processing helix chain 'A' and resid 431 through 447 Processing helix chain 'A' and resid 448 through 466 removed outlier: 4.057A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 472 through 485 Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 503 through 508 Processing helix chain 'A' and resid 512 through 533 removed outlier: 4.080A pdb=" N PHE A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 542 Processing helix chain 'A' and resid 547 through 559 removed outlier: 3.562A pdb=" N MET A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 575 removed outlier: 3.732A pdb=" N ILE A 573 " --> pdb=" O ALA A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 600 Processing helix chain 'B' and resid 395 through 399 removed outlier: 3.681A pdb=" N PHE B 399 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 415 Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'B' and resid 535 through 549 removed outlier: 3.501A pdb=" N VAL B 541 " --> pdb=" O SER B 537 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLY B 549 " --> pdb=" O GLY B 545 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 135 removed outlier: 5.697A pdb=" N GLN A 141 " --> pdb=" O ASN A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.088A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA4, first strand: chain 'B' and resid 400 through 402 removed outlier: 6.768A pdb=" N TYR B 483 " --> pdb=" O VAL B 420 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N VAL B 420 " --> pdb=" O TYR B 483 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 518 through 525 removed outlier: 4.268A pdb=" N GLY B 505 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N GLU B 523 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N CYS B 503 " --> pdb=" O GLU B 523 " (cutoff:3.500A) removed outlier: 10.569A pdb=" N VAL B 525 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 12.815A pdb=" N THR B 501 " --> pdb=" O VAL B 525 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL B 574 " --> pdb=" O THR B 501 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N CYS B 503 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS B 572 " --> pdb=" O CYS B 503 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLY B 505 " --> pdb=" O TRP B 570 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N TRP B 570 " --> pdb=" O GLY B 505 " (cutoff:3.500A) 335 hydrogen bonds defined for protein. 948 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: 0.82 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1114 1.33 - 1.45: 1589 1.45 - 1.58: 3146 1.58 - 1.70: 0 1.70 - 1.83: 52 Bond restraints: 5901 Sorted by residual: bond pdb=" N ILE B 547 " pdb=" CA ILE B 547 " ideal model delta sigma weight residual 1.456 1.492 -0.036 9.50e-03 1.11e+04 1.42e+01 bond pdb=" C2 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.439 1.510 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.03e+01 bond pdb=" N GLU A 210 " pdb=" CA GLU A 210 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.40e+00 bond pdb=" C7 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.346 1.403 -0.057 2.00e-02 2.50e+03 8.16e+00 ... (remaining 5896 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.92: 7984 4.92 - 9.84: 87 9.84 - 14.75: 1 14.75 - 19.67: 1 19.67 - 24.59: 1 Bond angle restraints: 8074 Sorted by residual: angle pdb=" C2 NAG H 1 " pdb=" N2 NAG H 1 " pdb=" C7 NAG H 1 " ideal model delta sigma weight residual 124.56 99.97 24.59 3.00e+00 1.11e-01 6.72e+01 angle pdb=" C ASN B 513 " pdb=" N PRO B 514 " pdb=" CA PRO B 514 " ideal model delta sigma weight residual 119.56 127.45 -7.89 1.02e+00 9.61e-01 5.98e+01 angle pdb=" C VAL A 283 " pdb=" N PRO A 284 " pdb=" CA PRO A 284 " ideal model delta sigma weight residual 119.24 126.91 -7.67 1.04e+00 9.25e-01 5.45e+01 angle pdb=" C SER A 257 " pdb=" N PRO A 258 " pdb=" CA PRO A 258 " ideal model delta sigma weight residual 119.56 126.97 -7.41 1.02e+00 9.61e-01 5.27e+01 angle pdb=" C GLY A 537 " pdb=" N PRO A 538 " pdb=" CA PRO A 538 " ideal model delta sigma weight residual 119.76 126.86 -7.10 1.03e+00 9.43e-01 4.75e+01 ... (remaining 8069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 3512 21.36 - 42.73: 97 42.73 - 64.09: 21 64.09 - 85.45: 14 85.45 - 106.81: 9 Dihedral angle restraints: 3653 sinusoidal: 1404 harmonic: 2249 Sorted by residual: dihedral pdb=" O4 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.10 106.81 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C5 BMA H 3 " pdb=" O5 BMA H 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.17 105.88 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C3 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sinusoidal sigma weight residual 47.62 -58.18 105.80 1 3.00e+01 1.11e-03 1.36e+01 ... (remaining 3650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 845 0.134 - 0.268: 68 0.268 - 0.402: 14 0.402 - 0.537: 1 0.537 - 0.671: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.73 -0.67 2.00e-02 2.50e+03 1.12e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-02 2.50e+03 2.77e+02 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.05e+01 ... (remaining 926 not shown) Planarity restraints: 1036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.035 2.00e-02 2.50e+03 2.88e-02 1.04e+01 pdb=" C7 NAG G 2 " 0.006 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.026 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.046 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 903 " -0.034 2.00e-02 2.50e+03 2.85e-02 1.02e+01 pdb=" C7 NAG A 903 " 0.008 2.00e-02 2.50e+03 pdb=" C8 NAG A 903 " 0.009 2.00e-02 2.50e+03 pdb=" N2 NAG A 903 " 0.045 2.00e-02 2.50e+03 pdb=" O7 NAG A 903 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 204 " 0.231 9.50e-02 1.11e+02 1.04e-01 6.58e+00 pdb=" NE ARG A 204 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 204 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 204 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 204 " 0.008 2.00e-02 2.50e+03 ... (remaining 1033 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 2314 2.90 - 3.40: 5485 3.40 - 3.90: 9895 3.90 - 4.40: 11246 4.40 - 4.90: 18014 Nonbonded interactions: 46954 Sorted by model distance: nonbonded pdb=" OD1 ASN A 322 " pdb=" O5 NAG A 902 " model vdw 2.400 3.040 nonbonded pdb=" NZ LYS A 288 " pdb=" OD2 ASP B 563 " model vdw 2.431 3.120 nonbonded pdb=" O SER A 107 " pdb=" N LEU A 109 " model vdw 2.468 3.120 nonbonded pdb=" OH TYR A 207 " pdb=" OG1 THR A 517 " model vdw 2.489 3.040 nonbonded pdb=" O HIS A 345 " pdb=" NZ LYS A 359 " model vdw 2.551 3.120 ... (remaining 46949 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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=1.00 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.350 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 : 0.012 0.306 5927 Z= 0.660 Angle : 1.374 24.588 8140 Z= 0.884 Chirality : 0.086 0.671 929 Planarity : 0.007 0.104 1026 Dihedral : 13.434 106.813 2183 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 1.19 % Favored : 98.55 % Rotamer: Outliers : 0.24 % Allowed : 2.15 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.28), residues: 758 helix: 0.06 (0.23), residues: 395 sheet: 0.78 (0.59), residues: 73 loop : 0.37 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 533 TYR 0.031 0.005 TYR B 397 PHE 0.015 0.003 PHE A 230 TRP 0.030 0.004 TRP A 478 HIS 0.004 0.001 HIS A 221 Details of bonding type rmsd covalent geometry : bond 0.01101 ( 5901) covalent geometry : angle 1.32751 ( 8074) SS BOND : bond 0.05605 ( 6) SS BOND : angle 4.07652 ( 12) hydrogen bonds : bond 0.18801 ( 335) hydrogen bonds : angle 6.87948 ( 948) metal coordination : bond 0.22147 ( 2) link_BETA1-4 : bond 0.05377 ( 8) link_BETA1-4 : angle 4.26033 ( 24) link_NAG-ASN : bond 0.04549 ( 10) link_NAG-ASN : angle 4.09562 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 MET cc_start: 0.7521 (mmm) cc_final: 0.6974 (mmt) REVERT: A 280 ASN cc_start: 0.6793 (m110) cc_final: 0.6146 (t0) REVERT: B 546 HIS cc_start: 0.7920 (t70) cc_final: 0.7709 (t70) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.0792 time to fit residues: 9.1299 Evaluate side-chains 59 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 97 GLN A 373 HIS A 572 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.193093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158458 restraints weight = 6557.512| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 2.27 r_work: 0.3594 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3461 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6782 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5927 Z= 0.160 Angle : 0.591 5.124 8140 Z= 0.309 Chirality : 0.043 0.225 929 Planarity : 0.005 0.037 1026 Dihedral : 8.769 66.711 1195 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.95 % Allowed : 5.97 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.30), residues: 758 helix: 1.62 (0.26), residues: 395 sheet: 0.92 (0.56), residues: 72 loop : 0.78 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.017 0.002 TYR A 385 PHE 0.020 0.002 PHE A 369 TRP 0.015 0.001 TRP B 570 HIS 0.004 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 5901) covalent geometry : angle 0.57141 ( 8074) SS BOND : bond 0.00706 ( 6) SS BOND : angle 1.02681 ( 12) hydrogen bonds : bond 0.05699 ( 335) hydrogen bonds : angle 4.99269 ( 948) metal coordination : bond 0.00739 ( 2) link_BETA1-4 : bond 0.00620 ( 8) link_BETA1-4 : angle 1.79519 ( 24) link_NAG-ASN : bond 0.00434 ( 10) link_NAG-ASN : angle 1.98816 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.7645 (mmt-90) cc_final: 0.7195 (mmt-90) REVERT: A 280 ASN cc_start: 0.7592 (m110) cc_final: 0.7185 (t0) REVERT: A 322 ASN cc_start: 0.7198 (OUTLIER) cc_final: 0.6980 (m-40) REVERT: A 340 ARG cc_start: 0.8492 (mtp180) cc_final: 0.8207 (mtp180) REVERT: B 546 HIS cc_start: 0.7172 (t70) cc_final: 0.6529 (t70) outliers start: 4 outliers final: 0 residues processed: 76 average time/residue: 0.0762 time to fit residues: 7.8153 Evaluate side-chains 66 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 1 optimal weight: 0.9990 chunk 58 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 71 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.192336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.158924 restraints weight = 6523.063| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.18 r_work: 0.3607 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5927 Z= 0.135 Angle : 0.526 6.449 8140 Z= 0.272 Chirality : 0.042 0.166 929 Planarity : 0.005 0.043 1026 Dihedral : 6.158 47.989 1195 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.19 % Allowed : 6.68 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.02 (0.30), residues: 758 helix: 1.65 (0.26), residues: 401 sheet: 0.79 (0.53), residues: 74 loop : 1.28 (0.39), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 533 TYR 0.019 0.001 TYR A 385 PHE 0.019 0.002 PHE A 84 TRP 0.018 0.001 TRP B 570 HIS 0.004 0.001 HIS A 42 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5901) covalent geometry : angle 0.51129 ( 8074) SS BOND : bond 0.00303 ( 6) SS BOND : angle 0.76133 ( 12) hydrogen bonds : bond 0.04828 ( 335) hydrogen bonds : angle 4.61689 ( 948) metal coordination : bond 0.00102 ( 2) link_BETA1-4 : bond 0.00627 ( 8) link_BETA1-4 : angle 1.56956 ( 24) link_NAG-ASN : bond 0.00414 ( 10) link_NAG-ASN : angle 1.62270 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.135 Fit side-chains revert: symmetry clash REVERT: A 38 GLU cc_start: 0.6822 (tt0) cc_final: 0.6595 (tt0) REVERT: A 280 ASN cc_start: 0.7640 (m110) cc_final: 0.7161 (t0) REVERT: A 322 ASN cc_start: 0.6849 (OUTLIER) cc_final: 0.6608 (m-40) REVERT: B 546 HIS cc_start: 0.7289 (t70) cc_final: 0.6569 (t70) outliers start: 5 outliers final: 1 residues processed: 76 average time/residue: 0.0670 time to fit residues: 6.7531 Evaluate side-chains 65 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 63 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 322 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 63 optimal weight: 0.0370 chunk 44 optimal weight: 2.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 194 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 = 0.4059 r_free = 0.4059 target = 0.193374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.160321 restraints weight = 6461.081| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.13 r_work: 0.3629 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5927 Z= 0.124 Angle : 0.505 6.966 8140 Z= 0.257 Chirality : 0.041 0.231 929 Planarity : 0.004 0.037 1026 Dihedral : 5.168 43.734 1195 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.19 % Allowed : 8.11 % Favored : 90.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.06 (0.31), residues: 758 helix: 1.66 (0.26), residues: 404 sheet: 0.82 (0.51), residues: 74 loop : 1.33 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 533 TYR 0.018 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.017 0.001 TRP A 163 HIS 0.003 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5901) covalent geometry : angle 0.49054 ( 8074) SS BOND : bond 0.00260 ( 6) SS BOND : angle 0.70276 ( 12) hydrogen bonds : bond 0.04465 ( 335) hydrogen bonds : angle 4.47580 ( 948) metal coordination : bond 0.00047 ( 2) link_BETA1-4 : bond 0.00563 ( 8) link_BETA1-4 : angle 1.45992 ( 24) link_NAG-ASN : bond 0.00338 ( 10) link_NAG-ASN : angle 1.58387 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 82 GLN cc_start: 0.5217 (OUTLIER) cc_final: 0.4970 (mm-40) REVERT: A 280 ASN cc_start: 0.7564 (m110) cc_final: 0.7119 (t0) REVERT: B 546 HIS cc_start: 0.7291 (t70) cc_final: 0.6504 (t70) outliers start: 5 outliers final: 2 residues processed: 71 average time/residue: 0.0530 time to fit residues: 5.2068 Evaluate side-chains 67 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 43 optimal weight: 0.5980 chunk 19 optimal weight: 0.0970 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.194321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.161257 restraints weight = 6600.717| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.17 r_work: 0.3631 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6890 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5927 Z= 0.113 Angle : 0.495 7.081 8140 Z= 0.250 Chirality : 0.040 0.178 929 Planarity : 0.004 0.034 1026 Dihedral : 4.975 38.796 1195 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.43 % Allowed : 9.31 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.17 (0.31), residues: 758 helix: 1.73 (0.26), residues: 404 sheet: 0.86 (0.52), residues: 74 loop : 1.41 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 533 TYR 0.017 0.001 TYR A 385 PHE 0.015 0.001 PHE A 369 TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 5901) covalent geometry : angle 0.47964 ( 8074) SS BOND : bond 0.00227 ( 6) SS BOND : angle 0.64261 ( 12) hydrogen bonds : bond 0.04238 ( 335) hydrogen bonds : angle 4.42450 ( 948) metal coordination : bond 0.00023 ( 2) link_BETA1-4 : bond 0.00528 ( 8) link_BETA1-4 : angle 1.36699 ( 24) link_NAG-ASN : bond 0.00650 ( 10) link_NAG-ASN : angle 1.68233 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.121 Fit side-chains revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7572 (m110) cc_final: 0.7128 (t0) REVERT: B 546 HIS cc_start: 0.7166 (t-90) cc_final: 0.6394 (t70) outliers start: 6 outliers final: 3 residues processed: 65 average time/residue: 0.0599 time to fit residues: 5.3339 Evaluate side-chains 62 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 59 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 40 optimal weight: 0.4980 chunk 60 optimal weight: 20.0000 chunk 26 optimal weight: 0.0670 chunk 14 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 194 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 = 0.4060 r_free = 0.4060 target = 0.193845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.160951 restraints weight = 6532.486| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.13 r_work: 0.3635 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5927 Z= 0.112 Angle : 0.491 6.545 8140 Z= 0.248 Chirality : 0.041 0.225 929 Planarity : 0.004 0.035 1026 Dihedral : 4.492 38.390 1195 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 1.67 % Allowed : 9.79 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.24 (0.31), residues: 758 helix: 1.80 (0.26), residues: 404 sheet: 0.91 (0.54), residues: 74 loop : 1.43 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 533 TYR 0.016 0.001 TYR A 385 PHE 0.017 0.001 PHE A 369 TRP 0.016 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5901) covalent geometry : angle 0.47616 ( 8074) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.62683 ( 12) hydrogen bonds : bond 0.04060 ( 335) hydrogen bonds : angle 4.33887 ( 948) metal coordination : bond 0.00083 ( 2) link_BETA1-4 : bond 0.00494 ( 8) link_BETA1-4 : angle 1.28190 ( 24) link_NAG-ASN : bond 0.00404 ( 10) link_NAG-ASN : angle 1.74364 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7538 (m110) cc_final: 0.7094 (t0) REVERT: B 546 HIS cc_start: 0.7103 (t-90) cc_final: 0.6298 (t70) outliers start: 7 outliers final: 4 residues processed: 72 average time/residue: 0.0660 time to fit residues: 6.5516 Evaluate side-chains 68 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 64 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.2980 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 60 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 194 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 = 0.4048 r_free = 0.4048 target = 0.192604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.159836 restraints weight = 6549.495| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.13 r_work: 0.3633 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3504 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5927 Z= 0.116 Angle : 0.498 6.857 8140 Z= 0.249 Chirality : 0.041 0.199 929 Planarity : 0.004 0.035 1026 Dihedral : 4.418 39.897 1195 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.67 % Allowed : 10.02 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.29 (0.31), residues: 758 helix: 1.81 (0.26), residues: 406 sheet: 0.87 (0.53), residues: 79 loop : 1.53 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 533 TYR 0.017 0.001 TYR A 385 PHE 0.022 0.001 PHE A 568 TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5901) covalent geometry : angle 0.48383 ( 8074) SS BOND : bond 0.00213 ( 6) SS BOND : angle 0.61631 ( 12) hydrogen bonds : bond 0.04005 ( 335) hydrogen bonds : angle 4.35544 ( 948) metal coordination : bond 0.00041 ( 2) link_BETA1-4 : bond 0.00478 ( 8) link_BETA1-4 : angle 1.25293 ( 24) link_NAG-ASN : bond 0.00366 ( 10) link_NAG-ASN : angle 1.70855 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 TYR cc_start: 0.8132 (t80) cc_final: 0.7798 (t80) REVERT: A 280 ASN cc_start: 0.7537 (m110) cc_final: 0.7101 (t0) REVERT: B 546 HIS cc_start: 0.7215 (t-90) cc_final: 0.6353 (t70) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.0559 time to fit residues: 5.4164 Evaluate side-chains 67 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 102 GLN ** A 194 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 = 0.4047 r_free = 0.4047 target = 0.192292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.159618 restraints weight = 6532.910| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 2.11 r_work: 0.3613 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3483 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5927 Z= 0.127 Angle : 0.509 6.059 8140 Z= 0.257 Chirality : 0.041 0.165 929 Planarity : 0.004 0.035 1026 Dihedral : 4.386 40.138 1195 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.39 % Allowed : 10.02 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.31), residues: 758 helix: 1.74 (0.25), residues: 407 sheet: 0.86 (0.53), residues: 80 loop : 1.50 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 533 TYR 0.018 0.001 TYR A 385 PHE 0.023 0.002 PHE A 568 TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 5901) covalent geometry : angle 0.49397 ( 8074) SS BOND : bond 0.00224 ( 6) SS BOND : angle 0.65003 ( 12) hydrogen bonds : bond 0.04078 ( 335) hydrogen bonds : angle 4.38228 ( 948) metal coordination : bond 0.00053 ( 2) link_BETA1-4 : bond 0.00525 ( 8) link_BETA1-4 : angle 1.31283 ( 24) link_NAG-ASN : bond 0.00360 ( 10) link_NAG-ASN : angle 1.78575 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.6806 (t0) cc_final: 0.6448 (t0) REVERT: A 217 TYR cc_start: 0.8208 (t80) cc_final: 0.7874 (t80) REVERT: A 280 ASN cc_start: 0.7556 (m110) cc_final: 0.7118 (t0) REVERT: A 363 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7743 (mttm) REVERT: B 546 HIS cc_start: 0.7277 (t-90) cc_final: 0.6413 (t70) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 0.0630 time to fit residues: 6.1021 Evaluate side-chains 66 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 GLN Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 50 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 49 optimal weight: 0.0770 chunk 51 optimal weight: 0.9990 chunk 30 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 102 GLN ** A 194 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 = 0.4049 r_free = 0.4049 target = 0.192566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.159920 restraints weight = 6557.439| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 2.13 r_work: 0.3660 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5927 Z= 0.117 Angle : 0.503 5.964 8140 Z= 0.253 Chirality : 0.040 0.142 929 Planarity : 0.004 0.035 1026 Dihedral : 4.335 40.224 1195 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.91 % Allowed : 10.50 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.22 (0.31), residues: 758 helix: 1.76 (0.25), residues: 407 sheet: 0.83 (0.53), residues: 80 loop : 1.50 (0.41), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 533 TYR 0.017 0.001 TYR A 385 PHE 0.023 0.001 PHE A 568 TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5901) covalent geometry : angle 0.48773 ( 8074) SS BOND : bond 0.00199 ( 6) SS BOND : angle 0.62107 ( 12) hydrogen bonds : bond 0.03990 ( 335) hydrogen bonds : angle 4.40127 ( 948) metal coordination : bond 0.00037 ( 2) link_BETA1-4 : bond 0.00516 ( 8) link_BETA1-4 : angle 1.29512 ( 24) link_NAG-ASN : bond 0.00351 ( 10) link_NAG-ASN : angle 1.74708 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.6785 (t0) cc_final: 0.6427 (t0) REVERT: A 217 TYR cc_start: 0.8163 (t80) cc_final: 0.7841 (t80) REVERT: A 280 ASN cc_start: 0.7516 (m110) cc_final: 0.7097 (t0) REVERT: A 363 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7752 (mttm) REVERT: B 546 HIS cc_start: 0.7314 (t-90) cc_final: 0.6748 (t-90) outliers start: 8 outliers final: 5 residues processed: 65 average time/residue: 0.0689 time to fit residues: 6.1753 Evaluate side-chains 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 36 optimal weight: 0.4980 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 20.0000 chunk 43 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.197763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.165784 restraints weight = 6550.652| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.11 r_work: 0.3678 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5927 Z= 0.107 Angle : 0.490 6.102 8140 Z= 0.248 Chirality : 0.040 0.141 929 Planarity : 0.004 0.035 1026 Dihedral : 4.147 40.267 1195 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.43 % Allowed : 11.46 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.35 (0.31), residues: 758 helix: 1.90 (0.25), residues: 405 sheet: 0.95 (0.54), residues: 78 loop : 1.47 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 533 TYR 0.015 0.001 TYR A 385 PHE 0.022 0.001 PHE A 568 TRP 0.016 0.001 TRP A 163 HIS 0.004 0.001 HIS A 77 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 5901) covalent geometry : angle 0.47556 ( 8074) SS BOND : bond 0.00172 ( 6) SS BOND : angle 0.56295 ( 12) hydrogen bonds : bond 0.03827 ( 335) hydrogen bonds : angle 4.36268 ( 948) metal coordination : bond 0.00105 ( 2) link_BETA1-4 : bond 0.00500 ( 8) link_BETA1-4 : angle 1.19818 ( 24) link_NAG-ASN : bond 0.00362 ( 10) link_NAG-ASN : angle 1.70963 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1516 Ramachandran restraints generated. 758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.6781 (t0) cc_final: 0.6442 (t0) REVERT: A 217 TYR cc_start: 0.8141 (t80) cc_final: 0.7831 (t80) REVERT: A 280 ASN cc_start: 0.7444 (m110) cc_final: 0.7050 (t0) REVERT: A 363 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7562 (mttm) REVERT: A 424 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8206 (mp) REVERT: B 546 HIS cc_start: 0.7279 (t-90) cc_final: 0.6577 (t-90) outliers start: 6 outliers final: 4 residues processed: 69 average time/residue: 0.0639 time to fit residues: 6.0125 Evaluate side-chains 66 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 61 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 293 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 440 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 19 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.191209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.158595 restraints weight = 6465.711| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.13 r_work: 0.3628 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5927 Z= 0.145 Angle : 0.527 5.547 8140 Z= 0.270 Chirality : 0.041 0.144 929 Planarity : 0.004 0.036 1026 Dihedral : 4.227 40.459 1195 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.19 % Allowed : 11.93 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.31), residues: 758 helix: 1.80 (0.25), residues: 405 sheet: 0.74 (0.54), residues: 80 loop : 1.38 (0.40), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 533 TYR 0.019 0.002 TYR A 385 PHE 0.028 0.002 PHE A 568 TRP 0.016 0.002 TRP A 163 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5901) covalent geometry : angle 0.51280 ( 8074) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.72384 ( 12) hydrogen bonds : bond 0.04190 ( 335) hydrogen bonds : angle 4.44488 ( 948) metal coordination : bond 0.00098 ( 2) link_BETA1-4 : bond 0.00485 ( 8) link_BETA1-4 : angle 1.30491 ( 24) link_NAG-ASN : bond 0.00307 ( 10) link_NAG-ASN : angle 1.76159 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1512.93 seconds wall clock time: 26 minutes 25.10 seconds (1585.10 seconds total)