Starting phenix.real_space_refine on Fri Feb 14 16:12:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642.map" model { file = "/net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5v7v_8642/02_2025/5v7v_8642_neut_trim.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3260 2.51 5 N 852 2.21 5 O 976 1.98 5 H 4811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9919 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9799 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.11, per 1000 atoms: 0.52 Number of scatterers: 9919 At special positions: 0 Unit cell: (81, 94.5, 109.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 976 8.00 N 852 7.00 C 3260 6.00 H 4811 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 908 " - " ASN A 429 " " NAG A 909 " - " ASN A 611 " " NAG B 1 " - " ASN A 123 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 608.3 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: 0.78 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: 3.31 Time building geometry restraints manager: 3.74 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: 0.010 Normalize map: mean=0, sd=1: 0.410 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: 0.160 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.840 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- 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 5236 Z= 0.719 Angle : 1.216 16.672 7097 Z= 0.737 Chirality : 0.067 0.476 777 Planarity : 0.007 0.069 900 Dihedral : 15.676 109.939 2053 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.17 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.26), residues: 609 helix: -2.93 (0.19), residues: 393 sheet: None (None), residues: 0 loop : -3.66 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 541 HIS 0.009 0.002 HIS A 113 PHE 0.022 0.003 PHE A 59 TYR 0.032 0.003 TYR A 655 ARG 0.013 0.002 ARG A 574 *********************** 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 : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.3729 (p90) cc_final: 0.3044 (p90) REVERT: A 65 TYR cc_start: 0.8512 (t80) cc_final: 0.8218 (t80) REVERT: A 87 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8581 (mtp85) REVERT: A 91 GLU cc_start: 0.8486 (tt0) cc_final: 0.7896 (tp30) REVERT: A 122 HIS cc_start: 0.8578 (p90) cc_final: 0.7864 (p90) REVERT: A 329 ASP cc_start: 0.8063 (t70) cc_final: 0.7682 (t70) REVERT: A 595 ASN cc_start: 0.7219 (t0) cc_final: 0.6814 (t0) REVERT: A 604 ASP cc_start: 0.8875 (m-30) cc_final: 0.8560 (m-30) REVERT: A 620 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 637 MET cc_start: 0.7251 (tpt) cc_final: 0.6711 (tpt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4581 time to fit residues: 95.1399 Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 355 GLN A 424 GLN A 593 GLN A 677 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.121292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.102504 restraints weight = 34273.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106497 restraints weight = 15995.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109083 restraints weight = 9709.827| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5236 Z= 0.215 Angle : 0.753 7.608 7097 Z= 0.399 Chirality : 0.040 0.155 777 Planarity : 0.006 0.063 900 Dihedral : 11.303 66.137 871 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 1.32 % Allowed : 16.26 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.29), residues: 609 helix: -1.62 (0.22), residues: 407 sheet: None (None), residues: 0 loop : -3.48 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS A 113 PHE 0.014 0.002 PHE A 488 TYR 0.019 0.002 TYR A 90 ARG 0.003 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 131 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.4063 (p90) cc_final: 0.3293 (p90) REVERT: A 87 ARG cc_start: 0.8657 (mtp85) cc_final: 0.8204 (mtp85) REVERT: A 91 GLU cc_start: 0.7866 (tt0) cc_final: 0.7269 (tp30) REVERT: A 100 PHE cc_start: 0.7556 (m-80) cc_final: 0.7227 (m-10) REVERT: A 122 HIS cc_start: 0.8310 (p90) cc_final: 0.7932 (p90) REVERT: A 396 GLU cc_start: 0.7652 (mp0) cc_final: 0.7411 (mp0) REVERT: A 485 ILE cc_start: 0.9243 (mm) cc_final: 0.8995 (mt) REVERT: A 604 ASP cc_start: 0.8534 (m-30) cc_final: 0.8190 (m-30) REVERT: A 620 GLN cc_start: 0.8140 (tm-30) cc_final: 0.7723 (tm-30) REVERT: A 637 MET cc_start: 0.7325 (tpt) cc_final: 0.6998 (tpt) outliers start: 7 outliers final: 4 residues processed: 127 average time/residue: 0.3298 time to fit residues: 55.6845 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 : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 645 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 22 optimal weight: 0.1980 chunk 42 optimal weight: 0.0770 chunk 59 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.118773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.100428 restraints weight = 33999.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104272 restraints weight = 15654.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.106763 restraints weight = 9440.575| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5236 Z= 0.217 Angle : 0.653 6.166 7097 Z= 0.349 Chirality : 0.038 0.128 777 Planarity : 0.005 0.057 900 Dihedral : 7.328 40.304 871 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.46 % Allowed : 17.20 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.32), residues: 609 helix: -0.77 (0.24), residues: 413 sheet: None (None), residues: 0 loop : -3.20 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 541 HIS 0.003 0.001 HIS A 113 PHE 0.013 0.002 PHE A 607 TYR 0.012 0.002 TYR A 563 ARG 0.003 0.000 ARG A 342 *********************** 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 122 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 109 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7871 (pmm) cc_final: 0.7609 (ppp) REVERT: A 56 PHE cc_start: 0.4172 (p90) cc_final: 0.3431 (p90) REVERT: A 87 ARG cc_start: 0.8648 (mtp85) cc_final: 0.8291 (mtp180) REVERT: A 91 GLU cc_start: 0.7619 (tt0) cc_final: 0.7197 (tp30) REVERT: A 122 HIS cc_start: 0.8341 (p90) cc_final: 0.8097 (p90) REVERT: A 441 MET cc_start: 0.8088 (tmm) cc_final: 0.7371 (tmm) REVERT: A 485 ILE cc_start: 0.9302 (mm) cc_final: 0.9050 (mt) REVERT: A 604 ASP cc_start: 0.8567 (m-30) cc_final: 0.8228 (m-30) REVERT: A 620 GLN cc_start: 0.8216 (tm-30) cc_final: 0.7914 (tm-30) outliers start: 13 outliers final: 9 residues processed: 114 average time/residue: 0.3680 time to fit residues: 53.8125 Evaluate side-chains 111 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.847 ------------------------------------------------------------------------------- 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 40 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 33 optimal weight: 0.1980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3580 r_free = 0.3580 target = 0.118862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100142 restraints weight = 33789.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.103998 restraints weight = 15535.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.106545 restraints weight = 9473.284| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5236 Z= 0.175 Angle : 0.603 5.944 7097 Z= 0.323 Chirality : 0.036 0.125 777 Planarity : 0.005 0.052 900 Dihedral : 6.512 38.237 871 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 2.46 % Allowed : 18.34 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.33), residues: 609 helix: -0.37 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -3.12 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 681 HIS 0.004 0.001 HIS A 128 PHE 0.010 0.001 PHE A 207 TYR 0.016 0.001 TYR A 74 ARG 0.002 0.000 ARG A 227 *********************** 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 119 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7976 (pmm) cc_final: 0.7637 (ppp) REVERT: A 87 ARG cc_start: 0.8669 (mtp85) cc_final: 0.8282 (mtp180) REVERT: A 91 GLU cc_start: 0.7711 (tt0) cc_final: 0.7369 (tp30) REVERT: A 122 HIS cc_start: 0.8367 (p90) cc_final: 0.8121 (p90) REVERT: A 158 CYS cc_start: 0.4941 (m) cc_final: 0.4533 (m) REVERT: A 485 ILE cc_start: 0.9329 (mm) cc_final: 0.9051 (mt) REVERT: A 604 ASP cc_start: 0.8540 (m-30) cc_final: 0.8225 (m-30) REVERT: A 620 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7953 (tm-30) outliers start: 13 outliers final: 11 residues processed: 109 average time/residue: 0.3067 time to fit residues: 44.5960 Evaluate side-chains 114 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 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 676 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 0.4980 chunk 31 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3562 r_free = 0.3562 target = 0.117364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.097904 restraints weight = 34249.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101876 restraints weight = 15423.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.104467 restraints weight = 9325.195| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5236 Z= 0.191 Angle : 0.599 6.855 7097 Z= 0.322 Chirality : 0.037 0.156 777 Planarity : 0.005 0.050 900 Dihedral : 5.950 36.170 871 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 3.59 % Allowed : 16.82 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.34), residues: 609 helix: 0.02 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.26 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 27 HIS 0.004 0.001 HIS A 128 PHE 0.011 0.001 PHE A 207 TYR 0.017 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 *********************** 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 125 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 1.230 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: 0.8003 (pmm) cc_final: 0.7658 (ppp) REVERT: A 87 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8190 (mtp85) REVERT: A 91 GLU cc_start: 0.7767 (tt0) cc_final: 0.7405 (tp30) REVERT: A 158 CYS cc_start: 0.4599 (m) cc_final: 0.4208 (m) REVERT: A 393 MET cc_start: 0.8119 (ttp) cc_final: 0.7878 (tpp) REVERT: A 441 MET cc_start: 0.8224 (tmm) cc_final: 0.7539 (tmm) REVERT: A 485 ILE cc_start: 0.9294 (mm) cc_final: 0.9079 (mt) REVERT: A 604 ASP cc_start: 0.8431 (m-30) cc_final: 0.8148 (m-30) REVERT: A 620 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 658 VAL cc_start: 0.8931 (OUTLIER) cc_final: 0.8685 (p) outliers start: 19 outliers final: 13 residues processed: 111 average time/residue: 0.3180 time to fit residues: 47.5487 Evaluate side-chains 116 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 ILE 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 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 14 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 HIS A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.115215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096412 restraints weight = 34573.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.100112 restraints weight = 16157.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.102545 restraints weight = 9947.072| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5236 Z= 0.234 Angle : 0.606 5.823 7097 Z= 0.332 Chirality : 0.037 0.143 777 Planarity : 0.005 0.052 900 Dihedral : 5.940 32.673 871 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.02 % Allowed : 18.53 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.34), residues: 609 helix: 0.18 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.28 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 78 HIS 0.003 0.001 HIS A 143 PHE 0.011 0.002 PHE A 607 TYR 0.016 0.001 TYR A 74 ARG 0.003 0.000 ARG A 589 *********************** 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 117 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.8087 (pmm) cc_final: 0.7818 (pmm) REVERT: A 87 ARG cc_start: 0.8616 (mtp85) cc_final: 0.8087 (mtp85) REVERT: A 91 GLU cc_start: 0.7769 (tt0) cc_final: 0.7355 (tp30) REVERT: A 158 CYS cc_start: 0.4937 (m) cc_final: 0.4489 (m) REVERT: A 368 TYR cc_start: 0.8655 (m-80) cc_final: 0.8372 (m-80) REVERT: A 441 MET cc_start: 0.8353 (tmm) cc_final: 0.7736 (tmm) REVERT: A 485 ILE cc_start: 0.9302 (mm) cc_final: 0.9086 (mt) REVERT: A 604 ASP cc_start: 0.8568 (m-30) cc_final: 0.8257 (m-30) REVERT: A 620 GLN cc_start: 0.8384 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 658 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8805 (p) outliers start: 16 outliers final: 13 residues processed: 104 average time/residue: 0.3358 time to fit residues: 45.4769 Evaluate side-chains 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 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 = 0.3514 r_free = 0.3514 target = 0.114145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094855 restraints weight = 34695.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098704 restraints weight = 15496.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.101227 restraints weight = 9384.958| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5236 Z= 0.213 Angle : 0.597 9.680 7097 Z= 0.322 Chirality : 0.037 0.255 777 Planarity : 0.004 0.051 900 Dihedral : 5.863 34.234 871 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.84 % Allowed : 19.28 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.34), residues: 609 helix: 0.45 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -3.31 (0.42), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.023 0.002 PHE A 120 TYR 0.017 0.001 TYR A 90 ARG 0.002 0.000 ARG A 589 *********************** 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 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.719 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 49 MET cc_start: 0.8177 (pmm) cc_final: 0.7928 (pmm) REVERT: A 87 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8231 (mtp180) REVERT: A 91 GLU cc_start: 0.7815 (tt0) cc_final: 0.7335 (tp30) REVERT: A 158 CYS cc_start: 0.5072 (m) cc_final: 0.4641 (m) REVERT: A 368 TYR cc_start: 0.8733 (m-80) cc_final: 0.8510 (m-80) REVERT: A 441 MET cc_start: 0.8348 (tmm) cc_final: 0.7704 (tmm) REVERT: A 485 ILE cc_start: 0.9346 (mm) cc_final: 0.9121 (mt) REVERT: A 604 ASP cc_start: 0.8510 (m-30) cc_final: 0.8164 (m-30) REVERT: A 620 GLN cc_start: 0.8346 (tm-30) cc_final: 0.7893 (tm-30) REVERT: A 658 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8778 (p) outliers start: 15 outliers final: 13 residues processed: 103 average time/residue: 0.3207 time to fit residues: 43.6456 Evaluate side-chains 108 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.728 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** A 479 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.111106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.092056 restraints weight = 35162.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095621 restraints weight = 16682.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097988 restraints weight = 10418.873| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5236 Z= 0.299 Angle : 0.648 9.978 7097 Z= 0.355 Chirality : 0.039 0.219 777 Planarity : 0.005 0.054 900 Dihedral : 6.064 40.225 871 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.40 % Allowed : 19.09 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.34), residues: 609 helix: 0.28 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -3.36 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 78 HIS 0.005 0.001 HIS A 122 PHE 0.019 0.002 PHE A 120 TYR 0.016 0.002 TYR A 563 ARG 0.003 0.000 ARG A 589 *********************** 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: 18 poor density : 100 time to evaluate : 0.806 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: A 49 MET cc_start: 0.8260 (pmm) cc_final: 0.7994 (pmm) REVERT: A 87 ARG cc_start: 0.8617 (mtp85) cc_final: 0.8237 (mtp180) REVERT: A 91 GLU cc_start: 0.7908 (tt0) cc_final: 0.7464 (tp30) REVERT: A 158 CYS cc_start: 0.5634 (m) cc_final: 0.5065 (m) REVERT: A 441 MET cc_start: 0.8460 (tmm) cc_final: 0.7790 (tmm) REVERT: A 485 ILE cc_start: 0.9337 (mm) cc_final: 0.9111 (mt) REVERT: A 604 ASP cc_start: 0.8596 (m-30) cc_final: 0.8259 (m-30) REVERT: A 620 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8206 (tm-30) REVERT: A 658 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8864 (p) outliers start: 18 outliers final: 14 residues processed: 106 average time/residue: 0.3463 time to fit residues: 48.0525 Evaluate side-chains 111 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE 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 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 53 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 34 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.092900 restraints weight = 34508.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096640 restraints weight = 15522.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099097 restraints weight = 9394.984| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.5684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5236 Z= 0.226 Angle : 0.618 9.877 7097 Z= 0.335 Chirality : 0.037 0.211 777 Planarity : 0.005 0.054 900 Dihedral : 5.913 41.289 871 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 3.02 % Allowed : 20.60 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.34), residues: 609 helix: 0.42 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -3.29 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 78 HIS 0.004 0.001 HIS A 128 PHE 0.015 0.002 PHE A 120 TYR 0.014 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 *********************** 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 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.940 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: A 49 MET cc_start: 0.8329 (pmm) cc_final: 0.8112 (pmm) REVERT: A 87 ARG cc_start: 0.8539 (mtp85) cc_final: 0.8165 (mtp180) REVERT: A 91 GLU cc_start: 0.7674 (tt0) cc_final: 0.7268 (tp30) REVERT: A 158 CYS cc_start: 0.5316 (m) cc_final: 0.4831 (m) REVERT: A 441 MET cc_start: 0.8328 (tmm) cc_final: 0.7695 (tmm) REVERT: A 485 ILE cc_start: 0.9360 (mm) cc_final: 0.9142 (mt) REVERT: A 604 ASP cc_start: 0.8462 (m-30) cc_final: 0.8143 (m-30) REVERT: A 620 GLN cc_start: 0.8404 (tm-30) cc_final: 0.8064 (tm-30) REVERT: A 658 VAL cc_start: 0.9028 (OUTLIER) cc_final: 0.8807 (p) outliers start: 16 outliers final: 15 residues processed: 104 average time/residue: 0.3292 time to fit residues: 45.3047 Evaluate side-chains 113 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.798 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 52 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 55 optimal weight: 0.2980 chunk 36 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.093344 restraints weight = 34898.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.097167 restraints weight = 15707.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.099671 restraints weight = 9633.407| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5236 Z= 0.174 Angle : 0.590 8.964 7097 Z= 0.317 Chirality : 0.036 0.191 777 Planarity : 0.004 0.051 900 Dihedral : 5.660 40.422 871 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 2.84 % Allowed : 20.98 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.35), residues: 609 helix: 0.57 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -3.29 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 681 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A 120 TYR 0.014 0.001 TYR A 177 ARG 0.002 0.000 ARG A 227 ********************** 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 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.719 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 49 MET cc_start: 0.8331 (pmm) cc_final: 0.8093 (pmm) REVERT: A 87 ARG cc_start: 0.8563 (mtp85) cc_final: 0.8279 (ttm-80) REVERT: A 91 GLU cc_start: 0.7782 (tt0) cc_final: 0.7343 (tp30) REVERT: A 158 CYS cc_start: 0.5397 (m) cc_final: 0.5048 (m) REVERT: A 441 MET cc_start: 0.8364 (tmm) cc_final: 0.7668 (tmm) REVERT: A 474 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7520 (mp0) REVERT: A 485 ILE cc_start: 0.9348 (mm) cc_final: 0.9125 (mt) REVERT: A 604 ASP cc_start: 0.8505 (m-30) cc_final: 0.8224 (m-30) REVERT: A 620 GLN cc_start: 0.8383 (tm-30) cc_final: 0.8015 (tm-30) REVERT: A 658 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8812 (p) REVERT: A 666 TYR cc_start: 0.6549 (t80) cc_final: 0.5912 (t80) outliers start: 15 outliers final: 14 residues processed: 106 average time/residue: 0.3221 time to fit residues: 44.9664 Evaluate side-chains 115 residues out of total 531 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 465 LYS Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 676 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.093413 restraints weight = 35058.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.097085 restraints weight = 16184.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.099520 restraints weight = 9923.798| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5236 Z= 0.199 Angle : 0.588 8.072 7097 Z= 0.318 Chirality : 0.036 0.167 777 Planarity : 0.004 0.051 900 Dihedral : 5.577 41.017 871 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.84 % Allowed : 21.36 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.35), residues: 609 helix: 0.68 (0.26), residues: 414 sheet: None (None), residues: 0 loop : -3.30 (0.43), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 632 HIS 0.003 0.001 HIS A 128 PHE 0.012 0.001 PHE A 207 TYR 0.011 0.001 TYR A 74 ARG 0.002 0.000 ARG A 589 =============================================================================== Job complete usr+sys time: 3262.06 seconds wall clock time: 58 minutes 33.12 seconds (3513.12 seconds total)