Starting phenix.real_space_refine on Sat May 10 08:05:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zuf_60483/05_2025/8zuf_60483_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zuf_60483/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zuf_60483/05_2025/8zuf_60483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zuf_60483/05_2025/8zuf_60483.map" model { file = "/net/cci-nas-00/data/ceres_data/8zuf_60483/05_2025/8zuf_60483_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zuf_60483/05_2025/8zuf_60483_neut.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.063 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 7, 'ASP:plan': 21, 'ASN:plan1': 13, 'HIS:plan': 2, 'GLU:plan': 34, 'ARG:plan': 1} 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: {'GLN:plan1': 4, 'TYR:plan': 4, 'ASN:plan1': 7, 'ASP:plan': 7, 'PHE:plan': 5, 'GLU:plan': 4, '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: 3.71, per 1000 atoms: 0.65 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: 1.69 Conformation dependent library (CDL) restraints added in 799.0 milliseconds 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: 0.61 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: 1.56 Time building geometry restraints manager: 1.86 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: 0.580 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 17.730 Find NCS groups from input model: 0.210 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:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.260 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (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 TRP 0.030 0.004 TRP A 478 HIS 0.004 0.001 HIS A 221 PHE 0.015 0.003 PHE A 230 TYR 0.031 0.005 TYR B 397 ARG 0.005 0.001 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.04549 ( 10) link_NAG-ASN : angle 4.09562 ( 30) link_BETA1-4 : bond 0.05377 ( 8) link_BETA1-4 : angle 4.26033 ( 24) hydrogen bonds : bond 0.18801 ( 335) hydrogen bonds : angle 6.87948 ( 948) metal coordination : bond 0.22147 ( 2) SS BOND : bond 0.05605 ( 6) SS BOND : angle 4.07652 ( 12) covalent geometry : bond 0.01101 ( 5901) covalent geometry : angle 1.32751 ( 8074) *********************** 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 : 0.604 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: 0.1964 time to fit residues: 22.6659 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 : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 0.0050 chunk 57 optimal weight: 0.8980 chunk 31 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 0.0170 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 0.5432 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.195513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.161309 restraints weight = 6424.776| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.21 r_work: 0.3667 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5927 Z= 0.143 Angle : 0.582 5.562 8140 Z= 0.303 Chirality : 0.043 0.210 929 Planarity : 0.005 0.031 1026 Dihedral : 8.387 62.916 1195 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.19 % Allowed : 5.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.30), residues: 758 helix: 1.69 (0.26), residues: 393 sheet: 0.93 (0.56), residues: 72 loop : 0.89 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 570 HIS 0.003 0.001 HIS A 505 PHE 0.020 0.002 PHE A 369 TYR 0.018 0.002 TYR A 385 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 10) link_NAG-ASN : angle 1.93720 ( 30) link_BETA1-4 : bond 0.00674 ( 8) link_BETA1-4 : angle 1.83376 ( 24) hydrogen bonds : bond 0.05431 ( 335) hydrogen bonds : angle 4.93222 ( 948) metal coordination : bond 0.00353 ( 2) SS BOND : bond 0.00340 ( 6) SS BOND : angle 0.90389 ( 12) covalent geometry : bond 0.00291 ( 5901) covalent geometry : angle 0.56237 ( 8074) *********************** 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 77 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.671 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7801 (mt) cc_final: 0.7520 (mm) REVERT: A 255 ARG cc_start: 0.7630 (mmt-90) cc_final: 0.7149 (mmt-90) REVERT: A 280 ASN cc_start: 0.7599 (m110) cc_final: 0.7161 (t0) REVERT: A 322 ASN cc_start: 0.7133 (OUTLIER) cc_final: 0.6867 (m-40) REVERT: A 479 GLU cc_start: 0.8035 (tt0) cc_final: 0.7735 (tt0) REVERT: B 546 HIS cc_start: 0.7142 (t70) cc_final: 0.6504 (t70) outliers start: 5 outliers final: 0 residues processed: 74 average time/residue: 0.1739 time to fit residues: 17.5659 Evaluate side-chains 68 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.597 ------------------------------------------------------------------------------- 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 67 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.185159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.151780 restraints weight = 6516.408| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 2.12 r_work: 0.3532 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5927 Z= 0.202 Angle : 0.593 5.371 8140 Z= 0.308 Chirality : 0.044 0.162 929 Planarity : 0.005 0.044 1026 Dihedral : 6.361 47.093 1195 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.95 % Allowed : 7.16 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.30), residues: 758 helix: 1.43 (0.26), residues: 405 sheet: 0.76 (0.53), residues: 74 loop : 1.02 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 570 HIS 0.005 0.001 HIS A 401 PHE 0.025 0.002 PHE A 369 TYR 0.021 0.002 TYR A 385 ARG 0.007 0.001 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 10) link_NAG-ASN : angle 1.71101 ( 30) link_BETA1-4 : bond 0.00629 ( 8) link_BETA1-4 : angle 1.67721 ( 24) hydrogen bonds : bond 0.05432 ( 335) hydrogen bonds : angle 4.78631 ( 948) metal coordination : bond 0.00045 ( 2) SS BOND : bond 0.00427 ( 6) SS BOND : angle 1.00739 ( 12) covalent geometry : bond 0.00461 ( 5901) covalent geometry : angle 0.57748 ( 8074) *********************** 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 80 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 ASN cc_start: 0.7613 (m110) cc_final: 0.7191 (t0) REVERT: A 363 LYS cc_start: 0.8268 (mtmm) cc_final: 0.7806 (mttm) REVERT: A 497 TYR cc_start: 0.8411 (m-80) cc_final: 0.8134 (m-80) REVERT: B 546 HIS cc_start: 0.7320 (t-90) cc_final: 0.6908 (t-90) outliers start: 4 outliers final: 2 residues processed: 79 average time/residue: 0.1896 time to fit residues: 19.7457 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 : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 20.0000 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.0040 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 HIS ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3986 r_free = 0.3986 target = 0.189307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.157582 restraints weight = 6488.701| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.88 r_work: 0.3556 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5927 Z= 0.124 Angle : 0.509 5.833 8140 Z= 0.263 Chirality : 0.041 0.181 929 Planarity : 0.004 0.040 1026 Dihedral : 5.258 42.669 1195 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.95 % Allowed : 9.31 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.30), residues: 758 helix: 1.54 (0.25), residues: 405 sheet: 0.75 (0.51), residues: 74 loop : 1.20 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 42 PHE 0.017 0.001 PHE A 369 TYR 0.019 0.001 TYR A 385 ARG 0.005 0.000 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00487 ( 10) link_NAG-ASN : angle 1.72099 ( 30) link_BETA1-4 : bond 0.00503 ( 8) link_BETA1-4 : angle 1.45774 ( 24) hydrogen bonds : bond 0.04544 ( 335) hydrogen bonds : angle 4.59402 ( 948) metal coordination : bond 0.00073 ( 2) SS BOND : bond 0.00270 ( 6) SS BOND : angle 0.72026 ( 12) covalent geometry : bond 0.00258 ( 5901) covalent geometry : angle 0.49318 ( 8074) *********************** 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 69 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7225 (t0) cc_final: 0.6738 (t0) REVERT: A 82 GLN cc_start: 0.5684 (OUTLIER) cc_final: 0.5268 (mm-40) REVERT: A 280 ASN cc_start: 0.7601 (m110) cc_final: 0.7103 (t0) REVERT: B 497 TYR cc_start: 0.6216 (m-80) cc_final: 0.5981 (m-80) REVERT: B 546 HIS cc_start: 0.7690 (t-90) cc_final: 0.7001 (t70) outliers start: 4 outliers final: 2 residues processed: 68 average time/residue: 0.1720 time to fit residues: 15.9725 Evaluate side-chains 65 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 18 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 50.0000 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 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3988 r_free = 0.3988 target = 0.189493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.157417 restraints weight = 6378.195| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.92 r_work: 0.3555 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.2902 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= 0.125 Angle : 0.501 6.396 8140 Z= 0.257 Chirality : 0.041 0.188 929 Planarity : 0.004 0.038 1026 Dihedral : 4.661 40.250 1195 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.72 % Allowed : 10.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.31), residues: 758 helix: 1.65 (0.26), residues: 406 sheet: 0.87 (0.51), residues: 74 loop : 1.34 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 77 PHE 0.017 0.001 PHE A 369 TYR 0.018 0.001 TYR A 385 ARG 0.003 0.000 ARG A 255 Details of bonding type rmsd link_NAG-ASN : bond 0.00344 ( 10) link_NAG-ASN : angle 1.64490 ( 30) link_BETA1-4 : bond 0.00513 ( 8) link_BETA1-4 : angle 1.29583 ( 24) hydrogen bonds : bond 0.04339 ( 335) hydrogen bonds : angle 4.46143 ( 948) metal coordination : bond 0.00154 ( 2) SS BOND : bond 0.00235 ( 6) SS BOND : angle 0.67922 ( 12) covalent geometry : bond 0.00265 ( 5901) covalent geometry : angle 0.48745 ( 8074) *********************** 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 74 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 0.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7338 (t0) cc_final: 0.6888 (t0) REVERT: A 280 ASN cc_start: 0.7629 (m110) cc_final: 0.7128 (t0) REVERT: A 532 ILE cc_start: 0.8843 (mm) cc_final: 0.8585 (mt) REVERT: B 497 TYR cc_start: 0.6218 (m-80) cc_final: 0.5961 (m-80) REVERT: B 546 HIS cc_start: 0.7666 (t-90) cc_final: 0.6947 (t70) outliers start: 3 outliers final: 2 residues processed: 73 average time/residue: 0.1609 time to fit residues: 16.1762 Evaluate side-chains 66 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Chi-restraints excluded: chain A residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 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 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 = 0.3977 r_free = 0.3977 target = 0.188232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.156257 restraints weight = 6478.043| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.93 r_work: 0.3541 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5927 Z= 0.131 Angle : 0.507 6.333 8140 Z= 0.260 Chirality : 0.041 0.182 929 Planarity : 0.004 0.038 1026 Dihedral : 4.488 40.056 1195 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.72 % Allowed : 11.93 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.30), residues: 758 helix: 1.62 (0.25), residues: 406 sheet: 0.96 (0.50), residues: 75 loop : 1.23 (0.40), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.028 0.002 PHE A 568 TYR 0.019 0.001 TYR A 385 ARG 0.006 0.000 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00489 ( 10) link_NAG-ASN : angle 1.42046 ( 30) link_BETA1-4 : bond 0.00498 ( 8) link_BETA1-4 : angle 1.30067 ( 24) hydrogen bonds : bond 0.04275 ( 335) hydrogen bonds : angle 4.47196 ( 948) metal coordination : bond 0.00031 ( 2) SS BOND : bond 0.00258 ( 6) SS BOND : angle 0.68725 ( 12) covalent geometry : bond 0.00287 ( 5901) covalent geometry : angle 0.49604 ( 8074) *********************** 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 71 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 68 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7207 (t0) cc_final: 0.6807 (t0) REVERT: A 280 ASN cc_start: 0.7637 (m110) cc_final: 0.7163 (t0) REVERT: A 363 LYS cc_start: 0.8337 (mtmm) cc_final: 0.7994 (mttm) REVERT: B 497 TYR cc_start: 0.6252 (m-80) cc_final: 0.5984 (m-80) REVERT: B 546 HIS cc_start: 0.7677 (t-90) cc_final: 0.6871 (t70) outliers start: 3 outliers final: 1 residues processed: 71 average time/residue: 0.1713 time to fit residues: 16.4152 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 : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.188209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.155258 restraints weight = 6548.693| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.12 r_work: 0.3580 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.3245 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= 0.129 Angle : 0.507 6.072 8140 Z= 0.259 Chirality : 0.041 0.186 929 Planarity : 0.004 0.037 1026 Dihedral : 4.328 41.390 1195 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.72 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.31), residues: 758 helix: 1.63 (0.26), residues: 407 sheet: 1.02 (0.53), residues: 80 loop : 1.31 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.004 0.001 HIS A 374 PHE 0.027 0.002 PHE A 568 TYR 0.018 0.001 TYR A 385 ARG 0.006 0.001 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00363 ( 10) link_NAG-ASN : angle 1.44554 ( 30) link_BETA1-4 : bond 0.00511 ( 8) link_BETA1-4 : angle 1.26922 ( 24) hydrogen bonds : bond 0.04216 ( 335) hydrogen bonds : angle 4.46513 ( 948) metal coordination : bond 0.00072 ( 2) SS BOND : bond 0.00232 ( 6) SS BOND : angle 0.68678 ( 12) covalent geometry : bond 0.00282 ( 5901) covalent geometry : angle 0.49566 ( 8074) *********************** 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 65 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 62 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.6934 (t0) cc_final: 0.6558 (t0) REVERT: A 217 TYR cc_start: 0.8249 (t80) cc_final: 0.7791 (t80) REVERT: A 280 ASN cc_start: 0.7571 (m110) cc_final: 0.7189 (t0) REVERT: A 363 LYS cc_start: 0.8197 (mtmm) cc_final: 0.7736 (mttm) REVERT: B 546 HIS cc_start: 0.7229 (t-90) cc_final: 0.6352 (t70) outliers start: 3 outliers final: 2 residues processed: 65 average time/residue: 0.1639 time to fit residues: 14.5984 Evaluate side-chains 62 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 60 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 143 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 6 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.185801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.154177 restraints weight = 6376.488| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.88 r_work: 0.3516 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3393 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5927 Z= 0.161 Angle : 0.536 5.514 8140 Z= 0.276 Chirality : 0.042 0.186 929 Planarity : 0.004 0.040 1026 Dihedral : 4.412 41.166 1195 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.30), residues: 758 helix: 1.59 (0.26), residues: 406 sheet: 0.97 (0.54), residues: 80 loop : 1.16 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 570 HIS 0.003 0.001 HIS A 378 PHE 0.028 0.002 PHE A 568 TYR 0.021 0.002 TYR A 385 ARG 0.006 0.001 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 10) link_NAG-ASN : angle 1.48161 ( 30) link_BETA1-4 : bond 0.00498 ( 8) link_BETA1-4 : angle 1.30214 ( 24) hydrogen bonds : bond 0.04436 ( 335) hydrogen bonds : angle 4.53131 ( 948) metal coordination : bond 0.00141 ( 2) SS BOND : bond 0.00287 ( 6) SS BOND : angle 0.80220 ( 12) covalent geometry : bond 0.00365 ( 5901) covalent geometry : angle 0.52528 ( 8074) *********************** 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 70 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7356 (t0) cc_final: 0.6957 (t0) REVERT: A 280 ASN cc_start: 0.7568 (m110) cc_final: 0.7184 (t0) REVERT: A 363 LYS cc_start: 0.8346 (mtmm) cc_final: 0.7818 (mttm) REVERT: B 546 HIS cc_start: 0.7734 (t-90) cc_final: 0.6771 (t70) outliers start: 6 outliers final: 4 residues processed: 68 average time/residue: 0.1667 time to fit residues: 15.3998 Evaluate side-chains 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.543 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 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 = 0.3980 r_free = 0.3980 target = 0.188148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.156891 restraints weight = 6390.776| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 1.89 r_work: 0.3551 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.3479 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= 0.123 Angle : 0.513 5.758 8140 Z= 0.262 Chirality : 0.041 0.144 929 Planarity : 0.004 0.038 1026 Dihedral : 4.375 41.462 1195 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.72 % Allowed : 12.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.31), residues: 758 helix: 1.68 (0.26), residues: 406 sheet: 0.94 (0.54), residues: 80 loop : 1.26 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.003 0.001 HIS A 374 PHE 0.025 0.002 PHE A 568 TYR 0.018 0.001 TYR A 385 ARG 0.006 0.000 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 10) link_NAG-ASN : angle 1.45901 ( 30) link_BETA1-4 : bond 0.00505 ( 8) link_BETA1-4 : angle 1.21790 ( 24) hydrogen bonds : bond 0.04139 ( 335) hydrogen bonds : angle 4.45817 ( 948) metal coordination : bond 0.00036 ( 2) SS BOND : bond 0.00228 ( 6) SS BOND : angle 0.67943 ( 12) covalent geometry : bond 0.00266 ( 5901) covalent geometry : angle 0.50218 ( 8074) *********************** 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 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7249 (t0) cc_final: 0.6917 (t0) REVERT: A 217 TYR cc_start: 0.8211 (t80) cc_final: 0.7881 (t80) REVERT: A 280 ASN cc_start: 0.7511 (m110) cc_final: 0.7143 (t0) REVERT: A 363 LYS cc_start: 0.8322 (mtmm) cc_final: 0.7795 (mttm) REVERT: B 546 HIS cc_start: 0.7620 (t-90) cc_final: 0.6752 (t70) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.1824 time to fit residues: 15.1228 Evaluate side-chains 61 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 58 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.9980 chunk 69 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.188664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.156945 restraints weight = 6565.769| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.96 r_work: 0.3548 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3424 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.3572 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= 0.127 Angle : 0.516 5.823 8140 Z= 0.263 Chirality : 0.041 0.145 929 Planarity : 0.004 0.038 1026 Dihedral : 4.314 41.333 1195 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.72 % Allowed : 12.65 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.31), residues: 758 helix: 1.67 (0.26), residues: 407 sheet: 0.91 (0.53), residues: 80 loop : 1.22 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 168 HIS 0.004 0.001 HIS A 374 PHE 0.025 0.002 PHE A 568 TYR 0.019 0.001 TYR A 385 ARG 0.007 0.001 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 10) link_NAG-ASN : angle 1.41473 ( 30) link_BETA1-4 : bond 0.00497 ( 8) link_BETA1-4 : angle 1.24180 ( 24) hydrogen bonds : bond 0.04112 ( 335) hydrogen bonds : angle 4.44188 ( 948) metal coordination : bond 0.00066 ( 2) SS BOND : bond 0.00239 ( 6) SS BOND : angle 0.66527 ( 12) covalent geometry : bond 0.00278 ( 5901) covalent geometry : angle 0.50569 ( 8074) ********************** 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 63 residues out of total 682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.7273 (t0) cc_final: 0.6973 (t0) REVERT: A 217 TYR cc_start: 0.8206 (t80) cc_final: 0.7874 (t80) REVERT: A 280 ASN cc_start: 0.7499 (m110) cc_final: 0.7143 (t0) REVERT: A 363 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7807 (mttm) REVERT: B 546 HIS cc_start: 0.7661 (t-90) cc_final: 0.6778 (t70) outliers start: 3 outliers final: 3 residues processed: 62 average time/residue: 0.1785 time to fit residues: 15.3908 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 : 0.772 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 43 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 72 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.206890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.181765 restraints weight = 6374.168| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.58 r_work: 0.3624 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.3665 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= 0.115 Angle : 0.507 5.885 8140 Z= 0.257 Chirality : 0.040 0.143 929 Planarity : 0.004 0.037 1026 Dihedral : 4.229 41.390 1195 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.95 % Allowed : 12.65 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.31), residues: 758 helix: 1.71 (0.26), residues: 407 sheet: 0.88 (0.54), residues: 80 loop : 1.26 (0.40), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 168 HIS 0.003 0.001 HIS A 374 PHE 0.024 0.001 PHE A 568 TYR 0.018 0.001 TYR A 385 ARG 0.007 0.000 ARG B 533 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 10) link_NAG-ASN : angle 1.40777 ( 30) link_BETA1-4 : bond 0.00503 ( 8) link_BETA1-4 : angle 1.21140 ( 24) hydrogen bonds : bond 0.03948 ( 335) hydrogen bonds : angle 4.40099 ( 948) metal coordination : bond 0.00072 ( 2) SS BOND : bond 0.00197 ( 6) SS BOND : angle 0.61166 ( 12) covalent geometry : bond 0.00248 ( 5901) covalent geometry : angle 0.49714 ( 8074) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.99 seconds wall clock time: 58 minutes 5.66 seconds (3485.66 seconds total)