Starting phenix.real_space_refine on Mon Jul 28 13:31:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642.map" model { file = "/net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v7v_8642/07_2025/5v7v_8642_neut_trim.cif" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.008 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 S 20 5.16 5 C 3260 2.51 5 N 852 2.21 5 O 976 1.98 5 H 4811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9919 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9799 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" 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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 5.15, per 1000 atoms: 0.52 Number of scatterers: 9919 At special positions: 0 Unit cell: (81, 94.5, 109.35, 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) S 20 16.00 O 976 8.00 N 852 7.00 C 3260 6.00 H 4811 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 908 " - " ASN A 429 " " NAG A 909 " - " ASN A 611 " " NAG B 1 " - " ASN A 123 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 3.09 Conformation dependent library (CDL) restraints added in 724.2 milliseconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 71.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.790A pdb=" N ALA A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.817A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.687A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.588A pdb=" N TYR A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 92 " --> pdb=" O HIS A 88 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.528A pdb=" N TYR A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.577A pdb=" N GLU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.617A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.634A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.710A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.750A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.655A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.864A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.581A pdb=" N GLN A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 383 removed outlier: 3.818A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 406 removed outlier: 3.582A pdb=" N ALA A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.987A pdb=" N GLN A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.821A pdb=" N LYS A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 removed outlier: 3.761A pdb=" N LEU A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 removed outlier: 4.235A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 487 " --> pdb=" O PRO A 483 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.787A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.601A pdb=" N ALA A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 547 removed outlier: 4.322A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.510A pdb=" N LYS A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.145A pdb=" N GLY A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 624 removed outlier: 3.601A pdb=" N LEU A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.628A pdb=" N LYS A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 684 removed outlier: 3.691A pdb=" N SER A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 786 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: 2.97 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4807 1.02 - 1.22: 5 1.22 - 1.41: 2259 1.41 - 1.61: 2938 1.61 - 1.81: 38 Bond restraints: 10047 Sorted by residual: bond pdb=" CA ASN A 101 " pdb=" C ASN A 101 " ideal model delta sigma weight residual 1.523 1.637 -0.114 1.34e-02 5.57e+03 7.21e+01 bond pdb=" CA TRP A 115 " pdb=" C TRP A 115 " ideal model delta sigma weight residual 1.522 1.630 -0.108 1.32e-02 5.74e+03 6.68e+01 bond pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 1.519 1.587 -0.068 9.50e-03 1.11e+04 5.10e+01 bond pdb=" CZ ARG A 646 " pdb=" NH2 ARG A 646 " ideal model delta sigma weight residual 1.330 1.420 -0.090 1.30e-02 5.92e+03 4.77e+01 bond pdb=" CZ ARG A 646 " pdb=" NH1 ARG A 646 " ideal model delta sigma weight residual 1.323 1.416 -0.093 1.40e-02 5.10e+03 4.44e+01 ... (remaining 10042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 17655 3.33 - 6.67: 279 6.67 - 10.00: 36 10.00 - 13.34: 10 13.34 - 16.67: 4 Bond angle restraints: 17984 Sorted by residual: angle pdb=" N SER A 116 " pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 111.74 95.84 15.90 1.35e+00 5.49e-01 1.39e+02 angle pdb=" N ASN A 102 " pdb=" CA ASN A 102 " pdb=" CB ASN A 102 " ideal model delta sigma weight residual 109.82 126.49 -16.67 1.52e+00 4.33e-01 1.20e+02 angle pdb=" N TRP A 115 " pdb=" CA TRP A 115 " pdb=" C TRP A 115 " ideal model delta sigma weight residual 113.50 126.40 -12.90 1.23e+00 6.61e-01 1.10e+02 angle pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" O TRP A 115 " ideal model delta sigma weight residual 119.14 129.75 -10.61 1.10e+00 8.26e-01 9.31e+01 angle pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" N SER A 116 " ideal model delta sigma weight residual 118.31 107.46 10.85 1.40e+00 5.10e-01 6.01e+01 ... (remaining 17979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 4512 21.99 - 43.98: 313 43.98 - 65.96: 62 65.96 - 87.95: 24 87.95 - 109.94: 8 Dihedral angle restraints: 4919 sinusoidal: 2668 harmonic: 2251 Sorted by residual: dihedral pdb=" N ASN A 102 " pdb=" C ASN A 102 " pdb=" CA ASN A 102 " pdb=" CB ASN A 102 " ideal model delta harmonic sigma weight residual 122.80 141.39 -18.59 0 2.50e+00 1.60e-01 5.53e+01 dihedral pdb=" CA PHE A 569 " pdb=" C PHE A 569 " pdb=" N GLU A 570 " pdb=" CA GLU A 570 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 689 0.095 - 0.191: 76 0.191 - 0.286: 9 0.286 - 0.381: 1 0.381 - 0.476: 2 Chirality restraints: 777 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.20e+00 chirality pdb=" CA TRP A 115 " pdb=" N TRP A 115 " pdb=" C TRP A 115 " pdb=" CB TRP A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 774 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 102 " -0.132 2.00e-02 2.50e+03 4.83e-01 3.51e+03 pdb=" CG ASN A 102 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 102 " 0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN A 102 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 102 " 0.824 2.00e-02 2.50e+03 pdb="HD22 ASN A 102 " -0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " 0.033 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CD GLN A 99 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 99 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN A 99 " -0.741 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 95 " 0.123 2.00e-02 2.50e+03 4.20e-01 2.64e+03 pdb=" CD GLN A 95 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN A 95 " -0.121 2.00e-02 2.50e+03 pdb=" NE2 GLN A 95 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 95 " -0.713 2.00e-02 2.50e+03 pdb="HE22 GLN A 95 " 0.719 2.00e-02 2.50e+03 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 38 1.80 - 2.50: 7443 2.50 - 3.20: 29283 3.20 - 3.90: 36037 3.90 - 4.60: 55896 Nonbonded interactions: 128697 Sorted by model distance: nonbonded pdb=" HB2 SER A 40 " pdb="HE22 GLN A 117 " model vdw 1.096 2.270 nonbonded pdb=" HD2 TYR A 612 " pdb=" HB3 LEU A 642 " model vdw 1.139 2.270 nonbonded pdb="HD22 ASN A 102 " pdb=" HG3 GLU A 104 " model vdw 1.200 2.270 nonbonded pdb="HD13 ILE A 37 " pdb=" HD1 TYR A 118 " model vdw 1.217 2.270 nonbonded pdb=" HB2 SER A 40 " pdb=" NE2 GLN A 117 " model vdw 1.238 2.770 ... (remaining 128692 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 'B' selection = chain 'C' } 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 group one per residue 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: 9.760 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: 0.140 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.110 Process input model: 24.390 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.011 0.114 5244 Z= 0.662 Angle : 1.314 35.283 7121 Z= 0.755 Chirality : 0.067 0.476 777 Planarity : 0.007 0.069 900 Dihedral : 15.676 109.939 2053 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.17 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Cbeta Deviations : 0.17 % 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: -4.92 (0.26), residues: 609 helix: -2.93 (0.19), residues: 393 sheet: None (None), residues: 0 loop : -3.66 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 541 HIS 0.009 0.002 HIS A 113 PHE 0.022 0.003 PHE A 59 TYR 0.032 0.003 TYR A 655 ARG 0.013 0.002 ARG A 574 Details of bonding type rmsd link_NAG-ASN : bond 0.01021 ( 4) link_NAG-ASN : angle 5.16032 ( 12) link_BETA1-4 : bond 0.03750 ( 4) link_BETA1-4 : angle 11.10068 ( 12) hydrogen bonds : bond 0.19184 ( 262) hydrogen bonds : angle 10.03923 ( 786) covalent geometry : bond 0.01121 ( 5236) covalent geometry : angle 1.21576 ( 7097) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.3729 (p90) cc_final: 0.3044 (p90) REVERT: A 65 TYR cc_start: 0.8512 (t80) cc_final: 0.8218 (t80) REVERT: A 87 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8581 (mtp85) REVERT: A 91 GLU cc_start: 0.8486 (tt0) cc_final: 0.7896 (tp30) REVERT: A 122 HIS cc_start: 0.8578 (p90) cc_final: 0.7864 (p90) REVERT: A 329 ASP cc_start: 0.8063 (t70) cc_final: 0.7682 (t70) REVERT: A 595 ASN cc_start: 0.7219 (t0) cc_final: 0.6814 (t0) REVERT: A 604 ASP cc_start: 0.8875 (m-30) cc_final: 0.8560 (m-30) REVERT: A 620 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 637 MET cc_start: 0.7251 (tpt) cc_final: 0.6711 (tpt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4497 time to fit residues: 94.0469 Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 355 GLN A 424 GLN A 593 GLN A 677 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102504 restraints weight = 34273.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.106484 restraints weight = 16002.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109084 restraints weight = 9718.624| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5244 Z= 0.163 Angle : 0.783 7.608 7121 Z= 0.405 Chirality : 0.040 0.155 777 Planarity : 0.006 0.063 900 Dihedral : 11.303 66.137 871 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.32 % Allowed : 16.26 % Favored : 82.42 % 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: -3.43 (0.29), residues: 609 helix: -1.62 (0.22), residues: 407 sheet: None (None), residues: 0 loop : -3.48 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS A 113 PHE 0.014 0.002 PHE A 488 TYR 0.019 0.002 TYR A 90 ARG 0.003 0.001 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00606 ( 4) link_NAG-ASN : angle 4.01258 ( 12) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 3.57725 ( 12) hydrogen bonds : bond 0.06372 ( 262) hydrogen bonds : angle 6.12515 ( 786) covalent geometry : bond 0.00330 ( 5236) covalent geometry : angle 0.75258 ( 7097) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.4060 (p90) cc_final: 0.3293 (p90) REVERT: A 87 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8204 (mtp85) REVERT: A 91 GLU cc_start: 0.7869 (tt0) cc_final: 0.7271 (tp30) REVERT: A 100 PHE cc_start: 0.7557 (m-80) cc_final: 0.7227 (m-10) REVERT: A 122 HIS cc_start: 0.8312 (p90) cc_final: 0.7933 (p90) REVERT: A 396 GLU cc_start: 0.7651 (mp0) cc_final: 0.7411 (mp0) REVERT: A 485 ILE cc_start: 0.9243 (mm) cc_final: 0.8995 (mt) REVERT: A 604 ASP cc_start: 0.8530 (m-30) cc_final: 0.8186 (m-30) REVERT: A 620 GLN cc_start: 0.8138 (tm-30) cc_final: 0.7722 (tm-30) REVERT: A 637 MET cc_start: 0.7326 (tpt) cc_final: 0.6998 (tpt) outliers start: 7 outliers final: 4 residues processed: 127 average time/residue: 0.3345 time to fit residues: 56.3269 Evaluate side-chains 114 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 645 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.116976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.097995 restraints weight = 34231.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.101951 restraints weight = 15076.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.104500 restraints weight = 8975.381| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5244 Z= 0.188 Angle : 0.702 7.099 7121 Z= 0.369 Chirality : 0.040 0.133 777 Planarity : 0.005 0.060 900 Dihedral : 7.737 40.152 871 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 3.02 % Allowed : 16.45 % Favored : 80.53 % 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: -2.46 (0.32), residues: 609 helix: -0.85 (0.23), residues: 414 sheet: None (None), residues: 0 loop : -3.23 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 541 HIS 0.003 0.001 HIS A 113 PHE 0.015 0.002 PHE A 607 TYR 0.015 0.002 TYR A 563 ARG 0.004 0.001 ARG A 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00323 ( 4) link_NAG-ASN : angle 3.40046 ( 12) link_BETA1-4 : bond 0.00495 ( 4) link_BETA1-4 : angle 3.66761 ( 12) hydrogen bonds : bond 0.05016 ( 262) hydrogen bonds : angle 5.56736 ( 786) covalent geometry : bond 0.00401 ( 5236) covalent geometry : angle 0.67265 ( 7097) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 110 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.4232 (p90) cc_final: 0.3445 (p90) REVERT: A 87 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8373 (mtp180) REVERT: A 91 GLU cc_start: 0.7646 (tt0) cc_final: 0.7207 (tp30) REVERT: A 441 MET cc_start: 0.8131 (tmm) cc_final: 0.7397 (tmm) REVERT: A 485 ILE cc_start: 0.9316 (mm) cc_final: 0.9048 (mt) REVERT: A 604 ASP cc_start: 0.8533 (m-30) cc_final: 0.8176 (m-30) REVERT: A 620 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7874 (tm-30) outliers start: 16 outliers final: 11 residues processed: 117 average time/residue: 0.3430 time to fit residues: 52.8819 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 40 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.118128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.098878 restraints weight = 33634.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102833 restraints weight = 14933.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.105433 restraints weight = 8977.914| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5244 Z= 0.132 Angle : 0.649 6.962 7121 Z= 0.337 Chirality : 0.037 0.124 777 Planarity : 0.005 0.053 900 Dihedral : 6.594 37.514 871 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.36 % Favored : 90.64 % Rotamer: Outliers : 2.08 % Allowed : 19.09 % Favored : 78.83 % 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: -1.91 (0.33), residues: 609 helix: -0.39 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -3.13 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 78 HIS 0.005 0.001 HIS A 128 PHE 0.011 0.001 PHE A 607 TYR 0.017 0.001 TYR A 368 ARG 0.002 0.000 ARG A 31 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 4) link_NAG-ASN : angle 3.32617 ( 12) link_BETA1-4 : bond 0.00347 ( 4) link_BETA1-4 : angle 3.45471 ( 12) hydrogen bonds : bond 0.04567 ( 262) hydrogen bonds : angle 5.13361 ( 786) covalent geometry : bond 0.00285 ( 5236) covalent geometry : angle 0.61900 ( 7097) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 114 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8962 (mpp) cc_final: 0.8723 (mtm) REVERT: A 49 MET cc_start: 0.7938 (pmm) cc_final: 0.7621 (ppp) REVERT: A 56 PHE cc_start: 0.4182 (p90) cc_final: 0.3406 (p90) REVERT: A 87 ARG cc_start: 0.8612 (mtp85) cc_final: 0.8289 (mtp180) REVERT: A 91 GLU cc_start: 0.7573 (tt0) cc_final: 0.7208 (tp30) REVERT: A 158 CYS cc_start: 0.4889 (m) cc_final: 0.4484 (m) REVERT: A 485 ILE cc_start: 0.9345 (mm) cc_final: 0.9060 (mt) REVERT: A 604 ASP cc_start: 0.8507 (m-30) cc_final: 0.8194 (m-30) REVERT: A 620 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7977 (tm-30) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 0.3430 time to fit residues: 49.0261 Evaluate side-chains 110 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.116040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096197 restraints weight = 34233.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.100127 restraints weight = 15535.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102745 restraints weight = 9480.209| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5244 Z= 0.155 Angle : 0.627 6.023 7121 Z= 0.332 Chirality : 0.037 0.140 777 Planarity : 0.005 0.053 900 Dihedral : 6.067 34.783 871 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.40 % Allowed : 17.58 % Favored : 79.02 % 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: -1.56 (0.34), residues: 609 helix: -0.05 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -3.17 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 27 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.002 PHE A 207 TYR 0.016 0.001 TYR A 368 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 3.22907 ( 12) link_BETA1-4 : bond 0.00360 ( 4) link_BETA1-4 : angle 2.96453 ( 12) hydrogen bonds : bond 0.04307 ( 262) hydrogen bonds : angle 4.91337 ( 786) covalent geometry : bond 0.00333 ( 5236) covalent geometry : angle 0.60211 ( 7097) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 104 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.9012 (mpp) cc_final: 0.8742 (mtm) REVERT: A 49 MET cc_start: 0.7985 (pmm) cc_final: 0.7629 (ppp) REVERT: A 87 ARG cc_start: 0.8591 (mtp85) cc_final: 0.8040 (mtp85) REVERT: A 91 GLU cc_start: 0.7623 (tt0) cc_final: 0.7158 (tp30) REVERT: A 158 CYS cc_start: 0.4692 (m) cc_final: 0.4257 (m) REVERT: A 393 MET cc_start: 0.8146 (ttp) cc_final: 0.7893 (tpp) REVERT: A 441 MET cc_start: 0.8309 (tmm) cc_final: 0.7742 (tmm) REVERT: A 485 ILE cc_start: 0.9300 (mm) cc_final: 0.9075 (mt) REVERT: A 604 ASP cc_start: 0.8463 (m-30) cc_final: 0.8115 (m-30) REVERT: A 620 GLN cc_start: 0.8158 (tm-30) cc_final: 0.7853 (tm-30) REVERT: A 658 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8728 (p) outliers start: 18 outliers final: 14 residues processed: 109 average time/residue: 0.4696 time to fit residues: 69.7355 Evaluate side-chains 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 14 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095524 restraints weight = 34486.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099420 restraints weight = 15635.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.101970 restraints weight = 9535.187| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5244 Z= 0.151 Angle : 0.633 8.865 7121 Z= 0.334 Chirality : 0.037 0.230 777 Planarity : 0.005 0.052 900 Dihedral : 5.976 32.932 871 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.97 % Allowed : 16.64 % Favored : 79.40 % 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: -1.29 (0.34), residues: 609 helix: 0.20 (0.25), residues: 412 sheet: None (None), residues: 0 loop : -3.18 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.026 0.002 PHE A 120 TYR 0.023 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00282 ( 4) link_NAG-ASN : angle 3.27377 ( 12) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 2.72723 ( 12) hydrogen bonds : bond 0.04206 ( 262) hydrogen bonds : angle 4.78481 ( 786) covalent geometry : bond 0.00327 ( 5236) covalent geometry : angle 0.60944 ( 7097) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8104 (pmm) cc_final: 0.7871 (pmm) REVERT: A 87 ARG cc_start: 0.8595 (mtp85) cc_final: 0.8191 (mtp85) REVERT: A 91 GLU cc_start: 0.7687 (tt0) cc_final: 0.7264 (tp30) REVERT: A 124 MET cc_start: 0.6761 (mpt) cc_final: 0.6529 (mmt) REVERT: A 158 CYS cc_start: 0.4862 (m) cc_final: 0.4300 (m) REVERT: A 368 TYR cc_start: 0.8631 (m-80) cc_final: 0.8375 (m-80) REVERT: A 441 MET cc_start: 0.8413 (tmm) cc_final: 0.8016 (tmm) REVERT: A 485 ILE cc_start: 0.9313 (mm) cc_final: 0.9096 (mt) REVERT: A 604 ASP cc_start: 0.8485 (m-30) cc_final: 0.8173 (m-30) REVERT: A 620 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7915 (tm-30) REVERT: A 658 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (p) outliers start: 21 outliers final: 18 residues processed: 110 average time/residue: 0.4077 time to fit residues: 60.4171 Evaluate side-chains 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.115857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096367 restraints weight = 34357.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.100270 restraints weight = 15325.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102823 restraints weight = 9252.308| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5244 Z= 0.118 Angle : 0.612 9.917 7121 Z= 0.318 Chirality : 0.037 0.211 777 Planarity : 0.004 0.050 900 Dihedral : 5.748 32.671 871 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.84 % Allowed : 19.09 % Favored : 78.07 % 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: -1.03 (0.35), residues: 609 helix: 0.50 (0.26), residues: 406 sheet: None (None), residues: 0 loop : -3.21 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.016 0.001 PHE A 120 TYR 0.017 0.001 TYR A 74 ARG 0.002 0.000 ARG A 342 Details of bonding type rmsd link_NAG-ASN : bond 0.00310 ( 4) link_NAG-ASN : angle 3.10644 ( 12) link_BETA1-4 : bond 0.00318 ( 4) link_BETA1-4 : angle 2.54623 ( 12) hydrogen bonds : bond 0.03981 ( 262) hydrogen bonds : angle 4.55292 ( 786) covalent geometry : bond 0.00257 ( 5236) covalent geometry : angle 0.59040 ( 7097) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 122 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8193 (mtp180) REVERT: A 91 GLU cc_start: 0.7731 (tt0) cc_final: 0.7274 (tp30) REVERT: A 158 CYS cc_start: 0.4891 (m) cc_final: 0.4398 (m) REVERT: A 368 TYR cc_start: 0.8650 (m-80) cc_final: 0.8408 (m-80) REVERT: A 441 MET cc_start: 0.8401 (tmm) cc_final: 0.7802 (tmm) REVERT: A 485 ILE cc_start: 0.9329 (mm) cc_final: 0.9111 (mt) REVERT: A 604 ASP cc_start: 0.8499 (m-30) cc_final: 0.8209 (m-30) REVERT: A 620 GLN cc_start: 0.8303 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 658 VAL cc_start: 0.9008 (OUTLIER) cc_final: 0.8786 (p) outliers start: 15 outliers final: 14 residues processed: 110 average time/residue: 0.5704 time to fit residues: 82.1843 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 0.2980 chunk 14 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094250 restraints weight = 34988.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097993 restraints weight = 15716.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.100475 restraints weight = 9602.539| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5244 Z= 0.165 Angle : 0.642 9.304 7121 Z= 0.340 Chirality : 0.037 0.195 777 Planarity : 0.004 0.051 900 Dihedral : 5.745 35.773 871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.40 % Allowed : 19.47 % Favored : 77.13 % 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: -1.01 (0.35), residues: 609 helix: 0.49 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -3.24 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.004 0.001 HIS A 143 PHE 0.014 0.002 PHE A 120 TYR 0.018 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 4) link_NAG-ASN : angle 3.15337 ( 12) link_BETA1-4 : bond 0.00321 ( 4) link_BETA1-4 : angle 2.41425 ( 12) hydrogen bonds : bond 0.04031 ( 262) hydrogen bonds : angle 4.68803 ( 786) covalent geometry : bond 0.00359 ( 5236) covalent geometry : angle 0.62176 ( 7097) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8225 (mtp180) REVERT: A 91 GLU cc_start: 0.7765 (tt0) cc_final: 0.7356 (tp30) REVERT: A 158 CYS cc_start: 0.5023 (m) cc_final: 0.4593 (m) REVERT: A 368 TYR cc_start: 0.8765 (m-80) cc_final: 0.8548 (m-80) REVERT: A 441 MET cc_start: 0.8492 (tmm) cc_final: 0.7831 (tmm) REVERT: A 485 ILE cc_start: 0.9346 (mm) cc_final: 0.9117 (mt) REVERT: A 604 ASP cc_start: 0.8509 (m-30) cc_final: 0.8173 (m-30) REVERT: A 620 GLN cc_start: 0.8380 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 637 MET cc_start: 0.7238 (tpt) cc_final: 0.6996 (tpt) REVERT: A 658 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8817 (p) outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 0.3404 time to fit residues: 48.3723 Evaluate side-chains 117 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 43 optimal weight: 0.0470 chunk 9 optimal weight: 1.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.113484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094409 restraints weight = 34582.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098205 restraints weight = 15442.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100712 restraints weight = 9346.223| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5244 Z= 0.147 Angle : 0.634 9.664 7121 Z= 0.334 Chirality : 0.037 0.198 777 Planarity : 0.004 0.051 900 Dihedral : 5.691 37.327 871 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.40 % Allowed : 19.66 % Favored : 76.94 % 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: -0.91 (0.35), residues: 609 helix: 0.59 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -3.26 (0.44), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 120 TYR 0.016 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00194 ( 4) link_NAG-ASN : angle 3.12604 ( 12) link_BETA1-4 : bond 0.00389 ( 4) link_BETA1-4 : angle 2.30074 ( 12) hydrogen bonds : bond 0.03999 ( 262) hydrogen bonds : angle 4.65963 ( 786) covalent geometry : bond 0.00324 ( 5236) covalent geometry : angle 0.61434 ( 7097) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 120 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8574 (mtp85) cc_final: 0.8207 (mtp180) REVERT: A 91 GLU cc_start: 0.7735 (tt0) cc_final: 0.7336 (tp30) REVERT: A 158 CYS cc_start: 0.5114 (m) cc_final: 0.4687 (m) REVERT: A 441 MET cc_start: 0.8471 (tmm) cc_final: 0.7819 (tmm) REVERT: A 485 ILE cc_start: 0.9336 (mm) cc_final: 0.9115 (mt) REVERT: A 604 ASP cc_start: 0.8512 (m-30) cc_final: 0.8209 (m-30) REVERT: A 620 GLN cc_start: 0.8359 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 637 MET cc_start: 0.7252 (tpt) cc_final: 0.6992 (tpt) REVERT: A 658 VAL cc_start: 0.9037 (OUTLIER) cc_final: 0.8825 (p) outliers start: 18 outliers final: 17 residues processed: 109 average time/residue: 0.3169 time to fit residues: 45.9187 Evaluate side-chains 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 0.0870 chunk 12 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.1962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 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 = 0.3500 r_free = 0.3500 target = 0.113116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.093546 restraints weight = 35060.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097368 restraints weight = 15879.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.099858 restraints weight = 9690.306| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.5732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5244 Z= 0.139 Angle : 0.631 9.021 7121 Z= 0.333 Chirality : 0.037 0.185 777 Planarity : 0.004 0.051 900 Dihedral : 5.587 38.544 871 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.21 % Allowed : 20.23 % Favored : 76.56 % 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: -0.77 (0.35), residues: 609 helix: 0.72 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -3.25 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.012 0.001 PHE A 120 TYR 0.014 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00218 ( 4) link_NAG-ASN : angle 3.08326 ( 12) link_BETA1-4 : bond 0.00378 ( 4) link_BETA1-4 : angle 2.18437 ( 12) hydrogen bonds : bond 0.03906 ( 262) hydrogen bonds : angle 4.58615 ( 786) covalent geometry : bond 0.00308 ( 5236) covalent geometry : angle 0.61271 ( 7097) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 ARG cc_start: 0.8576 (mtp85) cc_final: 0.8321 (mtp85) REVERT: A 91 GLU cc_start: 0.7759 (tt0) cc_final: 0.7335 (tp30) REVERT: A 158 CYS cc_start: 0.5138 (m) cc_final: 0.4701 (m) REVERT: A 441 MET cc_start: 0.8491 (tmm) cc_final: 0.7754 (tmm) REVERT: A 474 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7595 (mp0) REVERT: A 485 ILE cc_start: 0.9346 (mm) cc_final: 0.9120 (mt) REVERT: A 604 ASP cc_start: 0.8516 (m-30) cc_final: 0.8202 (m-30) REVERT: A 620 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 637 MET cc_start: 0.7395 (tpt) cc_final: 0.7120 (tpt) REVERT: A 658 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8836 (p) REVERT: A 666 TYR cc_start: 0.6526 (t80) cc_final: 0.6121 (t80) outliers start: 17 outliers final: 14 residues processed: 112 average time/residue: 0.3217 time to fit residues: 48.0632 Evaluate side-chains 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 479 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 = 0.3482 r_free = 0.3482 target = 0.111894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.092587 restraints weight = 35245.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.096379 restraints weight = 15858.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098844 restraints weight = 9653.992| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5244 Z= 0.167 Angle : 0.642 8.088 7121 Z= 0.341 Chirality : 0.037 0.160 777 Planarity : 0.004 0.051 900 Dihedral : 5.623 40.689 871 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 2.84 % Allowed : 20.79 % Favored : 76.37 % 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: -0.88 (0.35), residues: 609 helix: 0.64 (0.26), residues: 415 sheet: None (None), residues: 0 loop : -3.40 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 78 HIS 0.003 0.001 HIS A 128 PHE 0.012 0.002 PHE A 207 TYR 0.014 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 Details of bonding type rmsd link_NAG-ASN : bond 0.00166 ( 4) link_NAG-ASN : angle 3.11987 ( 12) link_BETA1-4 : bond 0.00426 ( 4) link_BETA1-4 : angle 2.09120 ( 12) hydrogen bonds : bond 0.03922 ( 262) hydrogen bonds : angle 4.69212 ( 786) covalent geometry : bond 0.00366 ( 5236) covalent geometry : angle 0.62417 ( 7097) =============================================================================== Job complete usr+sys time: 3915.35 seconds wall clock time: 71 minutes 28.80 seconds (4288.80 seconds total)