Starting phenix.real_space_refine on Tue Nov 18 02:55:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v7v_8642/11_2025/5v7v_8642_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v7v_8642/11_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 { model { file = "/net/cci-nas-00/data/ceres_data/5v7v_8642/11_2025/5v7v_8642_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v7v_8642/11_2025/5v7v_8642_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5v7v_8642/11_2025/5v7v_8642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v7v_8642/11_2025/5v7v_8642.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/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: 2.20, per 1000 atoms: 0.22 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: 1.15 Conformation dependent library (CDL) restraints added in 230.9 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: 0.24 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: 2.20 Time building geometry restraints manager: 1.53 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: 0.490 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: 0.070 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.590 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.013 0.002 ARG A 574 TYR 0.032 0.003 TYR A 655 PHE 0.022 0.003 PHE A 59 TRP 0.018 0.002 TRP A 541 HIS 0.009 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.01121 ( 5236) covalent geometry : angle 1.21576 ( 7097) hydrogen bonds : bond 0.19184 ( 262) hydrogen bonds : angle 10.03923 ( 786) link_BETA1-4 : bond 0.03750 ( 4) link_BETA1-4 : angle 11.10068 ( 12) link_NAG-ASN : bond 0.01021 ( 4) link_NAG-ASN : angle 5.16032 ( 12) *********************** 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 : 0.278 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: 0.3045 (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: 0.7895 (tp30) REVERT: A 122 HIS cc_start: 0.8578 (p90) cc_final: 0.7863 (p90) REVERT: A 329 ASP cc_start: 0.8063 (t70) cc_final: 0.7683 (t70) REVERT: A 595 ASN cc_start: 0.7219 (t0) cc_final: 0.6815 (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: 0.2259 time to fit residues: 46.7144 Evaluate side-chains 117 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 355 GLN A 424 GLN A 593 GLN A 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.120967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102156 restraints weight = 34468.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.106155 restraints weight = 16062.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108719 restraints weight = 9759.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.110301 restraints weight = 6979.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111557 restraints weight = 5574.953| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3177 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= 0.166 Angle : 0.782 7.649 7121 Z= 0.406 Chirality : 0.040 0.153 777 Planarity : 0.006 0.064 900 Dihedral : 11.538 67.572 871 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 1.13 % Allowed : 16.64 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.47 (0.29), residues: 609 helix: -1.64 (0.22), residues: 404 sheet: None (None), residues: 0 loop : -3.50 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 227 TYR 0.019 0.002 TYR A 560 PHE 0.013 0.002 PHE A 488 TRP 0.006 0.001 TRP A 78 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 5236) covalent geometry : angle 0.75127 ( 7097) hydrogen bonds : bond 0.06489 ( 262) hydrogen bonds : angle 6.20914 ( 786) link_BETA1-4 : bond 0.00681 ( 4) link_BETA1-4 : angle 3.56680 ( 12) link_NAG-ASN : bond 0.00629 ( 4) link_NAG-ASN : angle 4.08181 ( 12) *********************** 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 129 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 123 time to evaluate : 0.268 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: 0.3960 (p90) cc_final: 0.3217 (p90) REVERT: A 87 ARG cc_start: 0.8597 (mtp85) cc_final: 0.8192 (mtp85) REVERT: A 91 GLU cc_start: 0.7738 (tt0) cc_final: 0.7236 (tp30) REVERT: A 100 PHE cc_start: 0.7488 (m-80) cc_final: 0.7219 (m-10) REVERT: A 122 HIS cc_start: 0.8304 (p90) cc_final: 0.7947 (p90) REVERT: A 396 GLU cc_start: 0.7575 (mp0) cc_final: 0.7352 (mp0) REVERT: A 604 ASP cc_start: 0.8544 (m-30) cc_final: 0.8196 (m-30) REVERT: A 620 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 637 MET cc_start: 0.7260 (tpt) cc_final: 0.6953 (tpt) outliers start: 6 outliers final: 4 residues processed: 126 average time/residue: 0.1527 time to fit residues: 25.4632 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 : 0.293 ------------------------------------------------------------------------------- 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 28 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 47 optimal weight: 0.5980 chunk 45 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.119815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101181 restraints weight = 34444.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.105056 restraints weight = 15949.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107603 restraints weight = 9697.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.109270 restraints weight = 6944.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110437 restraints weight = 5518.545| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5244 Z= 0.147 Angle : 0.684 7.222 7121 Z= 0.354 Chirality : 0.038 0.131 777 Planarity : 0.005 0.058 900 Dihedral : 7.749 40.831 871 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.27 % Allowed : 17.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.32), residues: 609 helix: -0.84 (0.23), residues: 414 sheet: None (None), residues: 0 loop : -3.16 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 227 TYR 0.012 0.001 TYR A 666 PHE 0.012 0.001 PHE A 607 TRP 0.005 0.001 TRP A 78 HIS 0.003 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5236) covalent geometry : angle 0.65325 ( 7097) hydrogen bonds : bond 0.04950 ( 262) hydrogen bonds : angle 5.46561 ( 786) link_BETA1-4 : bond 0.00471 ( 4) link_BETA1-4 : angle 3.66787 ( 12) link_NAG-ASN : bond 0.00369 ( 4) link_NAG-ASN : angle 3.38921 ( 12) *********************** 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 124 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.268 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: A 49 MET cc_start: 0.7819 (pmm) cc_final: 0.7546 (ppp) REVERT: A 56 PHE cc_start: 0.4072 (p90) cc_final: 0.3376 (p90) REVERT: A 87 ARG cc_start: 0.8640 (mtp85) cc_final: 0.8353 (mtp180) REVERT: A 91 GLU cc_start: 0.7625 (tt0) cc_final: 0.7216 (tp30) REVERT: A 122 HIS cc_start: 0.8323 (p90) cc_final: 0.8106 (p90) REVERT: A 441 MET cc_start: 0.8033 (tmm) cc_final: 0.7343 (tmm) REVERT: A 604 ASP cc_start: 0.8591 (m-30) cc_final: 0.8262 (m-30) REVERT: A 620 GLN cc_start: 0.8223 (tm-30) cc_final: 0.7913 (tm-30) outliers start: 12 outliers final: 9 residues processed: 116 average time/residue: 0.1627 time to fit residues: 24.3952 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE 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 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.117423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.098561 restraints weight = 34331.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102356 restraints weight = 16051.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.104841 restraints weight = 9875.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.106477 restraints weight = 7147.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107624 restraints weight = 5717.286| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5244 Z= 0.161 Angle : 0.648 6.579 7121 Z= 0.341 Chirality : 0.037 0.167 777 Planarity : 0.005 0.055 900 Dihedral : 6.458 37.679 871 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.27 % Allowed : 17.58 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.33), residues: 609 helix: -0.37 (0.24), residues: 415 sheet: None (None), residues: 0 loop : -3.17 (0.44), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 579 TYR 0.012 0.001 TYR A 666 PHE 0.011 0.002 PHE A 607 TRP 0.008 0.001 TRP A 541 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 5236) covalent geometry : angle 0.61961 ( 7097) hydrogen bonds : bond 0.04570 ( 262) hydrogen bonds : angle 5.17599 ( 786) link_BETA1-4 : bond 0.00531 ( 4) link_BETA1-4 : angle 3.35319 ( 12) link_NAG-ASN : bond 0.00327 ( 4) link_NAG-ASN : angle 3.30495 ( 12) *********************** 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 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.248 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: A 44 MET cc_start: 0.8973 (mpp) cc_final: 0.8727 (mtm) REVERT: A 49 MET cc_start: 0.7952 (pmm) cc_final: 0.7630 (ppp) REVERT: A 87 ARG cc_start: 0.8658 (mtp85) cc_final: 0.8276 (mtp180) REVERT: A 91 GLU cc_start: 0.7669 (tt0) cc_final: 0.7356 (tp30) REVERT: A 158 CYS cc_start: 0.5123 (m) cc_final: 0.4655 (m) REVERT: A 396 GLU cc_start: 0.8002 (tp30) cc_final: 0.7761 (tp30) REVERT: A 485 ILE cc_start: 0.9222 (mm) cc_final: 0.8990 (mt) REVERT: A 604 ASP cc_start: 0.8551 (m-30) cc_final: 0.8184 (m-30) REVERT: A 620 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7958 (tm-30) REVERT: A 658 VAL cc_start: 0.8979 (OUTLIER) cc_final: 0.8755 (p) outliers start: 12 outliers final: 10 residues processed: 107 average time/residue: 0.1452 time to fit residues: 20.7754 Evaluate side-chains 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 102 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER 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 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 Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.117497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.097818 restraints weight = 34221.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.101776 restraints weight = 15318.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104409 restraints weight = 9294.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.106104 restraints weight = 6679.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107167 restraints weight = 5331.214| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.4733 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= 0.128 Angle : 0.616 6.940 7121 Z= 0.323 Chirality : 0.036 0.137 777 Planarity : 0.005 0.052 900 Dihedral : 6.009 35.317 871 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 3.59 % Allowed : 17.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.33), residues: 609 helix: -0.05 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.19 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.018 0.001 TYR A 368 PHE 0.011 0.001 PHE A 207 TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 5236) covalent geometry : angle 0.59102 ( 7097) hydrogen bonds : bond 0.04232 ( 262) hydrogen bonds : angle 4.84841 ( 786) link_BETA1-4 : bond 0.00270 ( 4) link_BETA1-4 : angle 2.95480 ( 12) link_NAG-ASN : bond 0.00322 ( 4) link_NAG-ASN : angle 3.18524 ( 12) *********************** 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 123 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.296 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 44 MET cc_start: 0.8986 (mpp) cc_final: 0.8708 (mtm) REVERT: A 49 MET cc_start: 0.7905 (pmm) cc_final: 0.7645 (ppp) REVERT: A 87 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8203 (mtp85) REVERT: A 91 GLU cc_start: 0.7614 (tt0) cc_final: 0.7212 (tp30) REVERT: A 158 CYS cc_start: 0.4635 (m) cc_final: 0.4149 (m) REVERT: A 396 GLU cc_start: 0.7765 (tp30) cc_final: 0.7562 (tp30) REVERT: A 441 MET cc_start: 0.8239 (tmm) cc_final: 0.7657 (tmm) REVERT: A 485 ILE cc_start: 0.9270 (mm) cc_final: 0.9044 (mt) REVERT: A 604 ASP cc_start: 0.8465 (m-30) cc_final: 0.8172 (m-30) REVERT: A 620 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 658 VAL cc_start: 0.8928 (OUTLIER) cc_final: 0.8692 (p) outliers start: 19 outliers final: 14 residues processed: 109 average time/residue: 0.1726 time to fit residues: 24.3194 Evaluate side-chains 117 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.114357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.094575 restraints weight = 34858.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.098506 restraints weight = 15699.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.101093 restraints weight = 9524.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.102819 restraints weight = 6866.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103840 restraints weight = 5471.947| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.5152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5244 Z= 0.177 Angle : 0.622 5.772 7121 Z= 0.333 Chirality : 0.036 0.136 777 Planarity : 0.005 0.053 900 Dihedral : 5.965 33.120 871 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 3.59 % Allowed : 18.15 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.34), residues: 609 helix: 0.10 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.29 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.011 0.001 TYR A 368 PHE 0.012 0.002 PHE A 488 TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5236) covalent geometry : angle 0.59786 ( 7097) hydrogen bonds : bond 0.04173 ( 262) hydrogen bonds : angle 4.87557 ( 786) link_BETA1-4 : bond 0.00371 ( 4) link_BETA1-4 : angle 2.72060 ( 12) link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 3.24244 ( 12) *********************** 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 125 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.267 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: 0.8138 (pmm) cc_final: 0.7925 (pmm) REVERT: A 87 ARG cc_start: 0.8567 (mtp85) cc_final: 0.8189 (mtp85) REVERT: A 158 CYS cc_start: 0.4912 (m) cc_final: 0.4399 (m) REVERT: A 368 TYR cc_start: 0.8716 (m-80) cc_final: 0.8449 (m-80) REVERT: A 441 MET cc_start: 0.8411 (tmm) cc_final: 0.8037 (tmm) REVERT: A 485 ILE cc_start: 0.9305 (mm) cc_final: 0.9090 (mt) REVERT: A 604 ASP cc_start: 0.8511 (m-30) cc_final: 0.8166 (m-30) REVERT: A 620 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7831 (tm-30) REVERT: A 637 MET cc_start: 0.7156 (tpt) cc_final: 0.6922 (tpt) REVERT: A 658 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8773 (p) outliers start: 19 outliers final: 15 residues processed: 113 average time/residue: 0.1606 time to fit residues: 23.7701 Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE 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 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 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 = 0.3517 r_free = 0.3517 target = 0.114295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.094272 restraints weight = 34906.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.098094 restraints weight = 16007.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100627 restraints weight = 9954.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.102181 restraints weight = 7237.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.103409 restraints weight = 5885.030| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.5319 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= 0.151 Angle : 0.628 9.178 7121 Z= 0.331 Chirality : 0.037 0.217 777 Planarity : 0.004 0.051 900 Dihedral : 5.866 35.212 871 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.21 % Allowed : 19.47 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.34), residues: 609 helix: 0.29 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.19 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.013 0.001 TYR A 368 PHE 0.020 0.002 PHE A 120 TRP 0.005 0.001 TRP A 681 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 5236) covalent geometry : angle 0.60605 ( 7097) hydrogen bonds : bond 0.04124 ( 262) hydrogen bonds : angle 4.73294 ( 786) link_BETA1-4 : bond 0.00364 ( 4) link_BETA1-4 : angle 2.54718 ( 12) link_NAG-ASN : bond 0.00270 ( 4) link_NAG-ASN : angle 3.21286 ( 12) *********************** 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 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.279 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: A 87 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8151 (mtp180) REVERT: A 91 GLU cc_start: 0.7698 (tt0) cc_final: 0.7267 (tp30) REVERT: A 158 CYS cc_start: 0.5098 (m) cc_final: 0.4612 (m) REVERT: A 368 TYR cc_start: 0.8721 (m-80) cc_final: 0.8507 (m-80) REVERT: A 441 MET cc_start: 0.8436 (tmm) cc_final: 0.7807 (tmm) REVERT: A 485 ILE cc_start: 0.9320 (mm) cc_final: 0.9108 (mt) REVERT: A 604 ASP cc_start: 0.8510 (m-30) cc_final: 0.8158 (m-30) REVERT: A 620 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7859 (tm-30) REVERT: A 637 MET cc_start: 0.7196 (tpt) cc_final: 0.6964 (tpt) REVERT: A 658 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8742 (p) outliers start: 17 outliers final: 16 residues processed: 105 average time/residue: 0.1514 time to fit residues: 20.9761 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE 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 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 40 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095177 restraints weight = 34421.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.099080 restraints weight = 15315.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101636 restraints weight = 9208.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.103325 restraints weight = 6612.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.104473 restraints weight = 5284.421| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.5546 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= 0.127 Angle : 0.631 10.342 7121 Z= 0.327 Chirality : 0.037 0.232 777 Planarity : 0.004 0.051 900 Dihedral : 5.697 35.366 871 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.02 % Allowed : 20.04 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.35), residues: 609 helix: 0.54 (0.26), residues: 407 sheet: None (None), residues: 0 loop : -3.20 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 321 TYR 0.022 0.001 TYR A 74 PHE 0.018 0.001 PHE A 120 TRP 0.008 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5236) covalent geometry : angle 0.61128 ( 7097) hydrogen bonds : bond 0.03933 ( 262) hydrogen bonds : angle 4.55471 ( 786) link_BETA1-4 : bond 0.00307 ( 4) link_BETA1-4 : angle 2.38110 ( 12) link_NAG-ASN : bond 0.00249 ( 4) link_NAG-ASN : angle 3.10982 ( 12) *********************** 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 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.273 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: 0.8516 (mtp85) cc_final: 0.8060 (mtp180) REVERT: A 91 GLU cc_start: 0.7638 (tt0) cc_final: 0.7226 (tp30) REVERT: A 158 CYS cc_start: 0.5068 (m) cc_final: 0.4608 (m) REVERT: A 177 TYR cc_start: 0.8504 (m-10) cc_final: 0.8274 (m-10) REVERT: A 368 TYR cc_start: 0.8698 (m-80) cc_final: 0.8488 (m-80) REVERT: A 441 MET cc_start: 0.8419 (tmm) cc_final: 0.7787 (tmm) REVERT: A 485 ILE cc_start: 0.9329 (mm) cc_final: 0.9126 (mt) REVERT: A 604 ASP cc_start: 0.8510 (m-30) cc_final: 0.8196 (m-30) REVERT: A 620 GLN cc_start: 0.8304 (tm-30) cc_final: 0.7841 (tm-30) REVERT: A 637 MET cc_start: 0.7049 (tpt) cc_final: 0.6838 (tpt) REVERT: A 658 VAL cc_start: 0.9001 (OUTLIER) cc_final: 0.8775 (p) outliers start: 16 outliers final: 15 residues processed: 105 average time/residue: 0.1552 time to fit residues: 21.5629 Evaluate side-chains 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE 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 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 35 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.0370 chunk 34 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- 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 = 0.3504 r_free = 0.3504 target = 0.113275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093504 restraints weight = 34659.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097352 restraints weight = 15839.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099870 restraints weight = 9693.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.101551 restraints weight = 7046.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.102644 restraints weight = 5665.552| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5244 Z= 0.151 Angle : 0.641 9.927 7121 Z= 0.338 Chirality : 0.037 0.220 777 Planarity : 0.004 0.050 900 Dihedral : 5.655 37.674 871 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.21 % Allowed : 20.04 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.35), residues: 609 helix: 0.59 (0.26), residues: 410 sheet: None (None), residues: 0 loop : -3.18 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 589 TYR 0.021 0.001 TYR A 90 PHE 0.017 0.002 PHE A 120 TRP 0.006 0.001 TRP A 681 HIS 0.003 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 5236) covalent geometry : angle 0.62243 ( 7097) hydrogen bonds : bond 0.03999 ( 262) hydrogen bonds : angle 4.65370 ( 786) link_BETA1-4 : bond 0.00302 ( 4) link_BETA1-4 : angle 2.25958 ( 12) link_NAG-ASN : bond 0.00198 ( 4) link_NAG-ASN : angle 3.10425 ( 12) *********************** 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 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.257 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: 0.8546 (mtp85) cc_final: 0.8119 (mtp180) REVERT: A 91 GLU cc_start: 0.7725 (tt0) cc_final: 0.7309 (tp30) REVERT: A 158 CYS cc_start: 0.5346 (m) cc_final: 0.4948 (m) REVERT: A 441 MET cc_start: 0.8477 (tmm) cc_final: 0.7702 (tmm) REVERT: A 604 ASP cc_start: 0.8512 (m-30) cc_final: 0.8208 (m-30) REVERT: A 620 GLN cc_start: 0.8357 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 637 MET cc_start: 0.7403 (tpt) cc_final: 0.7174 (tpt) REVERT: A 658 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8801 (p) outliers start: 17 outliers final: 15 residues processed: 106 average time/residue: 0.1519 time to fit residues: 21.3732 Evaluate side-chains 112 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 16 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 46 optimal weight: 0.4980 chunk 17 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 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 = 0.3515 r_free = 0.3515 target = 0.114090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.094817 restraints weight = 34421.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.098655 restraints weight = 15475.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101204 restraints weight = 9403.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.102725 restraints weight = 6743.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.103882 restraints weight = 5439.432| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.5815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 5244 Z= 0.126 Angle : 0.636 9.262 7121 Z= 0.332 Chirality : 0.037 0.191 777 Planarity : 0.004 0.050 900 Dihedral : 5.547 38.126 871 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 2.84 % Allowed : 21.55 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.35), residues: 609 helix: 0.66 (0.26), residues: 411 sheet: None (None), residues: 0 loop : -3.23 (0.43), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 227 TYR 0.014 0.001 TYR A 90 PHE 0.014 0.001 PHE A 120 TRP 0.007 0.001 TRP A 681 HIS 0.004 0.001 HIS A 128 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 5236) covalent geometry : angle 0.61839 ( 7097) hydrogen bonds : bond 0.03852 ( 262) hydrogen bonds : angle 4.56845 ( 786) link_BETA1-4 : bond 0.00376 ( 4) link_BETA1-4 : angle 2.17204 ( 12) link_NAG-ASN : bond 0.00213 ( 4) link_NAG-ASN : angle 2.99025 ( 12) ********************** 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 118 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.325 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: 0.8532 (mtp85) cc_final: 0.8093 (mtp180) REVERT: A 91 GLU cc_start: 0.7859 (tt0) cc_final: 0.7398 (tp30) REVERT: A 158 CYS cc_start: 0.5291 (m) cc_final: 0.4909 (m) REVERT: A 441 MET cc_start: 0.8363 (tmm) cc_final: 0.7753 (tmm) REVERT: A 604 ASP cc_start: 0.8516 (m-30) cc_final: 0.8223 (m-30) REVERT: A 620 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7901 (tm-30) REVERT: A 637 MET cc_start: 0.7413 (tpt) cc_final: 0.7180 (tpt) REVERT: A 666 TYR cc_start: 0.6488 (t80) cc_final: 0.6097 (t80) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.1492 time to fit residues: 21.0946 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 149 LEU 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 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 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 59 optimal weight: 0.0070 chunk 54 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.114723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.095803 restraints weight = 34860.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.099498 restraints weight = 16239.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.102020 restraints weight = 10010.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.103617 restraints weight = 7230.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.104646 restraints weight = 5786.764| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.5907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5244 Z= 0.118 Angle : 0.625 8.202 7121 Z= 0.326 Chirality : 0.036 0.180 777 Planarity : 0.004 0.049 900 Dihedral : 5.395 38.026 871 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 2.27 % Allowed : 21.74 % Favored : 75.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.35), residues: 609 helix: 0.65 (0.26), residues: 412 sheet: None (None), residues: 0 loop : -3.20 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.014 0.001 TYR A 90 PHE 0.012 0.001 PHE A 207 TRP 0.014 0.001 TRP A 632 HIS 0.004 0.001 HIS A 378 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 5236) covalent geometry : angle 0.60982 ( 7097) hydrogen bonds : bond 0.03707 ( 262) hydrogen bonds : angle 4.49090 ( 786) link_BETA1-4 : bond 0.00328 ( 4) link_BETA1-4 : angle 2.05055 ( 12) link_NAG-ASN : bond 0.00221 ( 4) link_NAG-ASN : angle 2.83254 ( 12) =============================================================================== Job complete usr+sys time: 1889.83 seconds wall clock time: 32 minutes 58.77 seconds (1978.77 seconds total)