Starting phenix.real_space_refine on Fri Jul 3 23:05:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gep_51297/07_2026/9gep_51297.map" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Fe 1 7.16 5 P 290 5.49 5 S 44 5.16 5 C 9528 2.51 5 N 3089 2.21 5 O 3635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16587 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "M" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 837 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 10, 'TRANS': 93} Chain: "N" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3732 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 429} Chain: "N" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 71 Unusual residues: {'HEM': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.86, per 1000 atoms: 0.17 Number of scatterers: 16587 At special positions: 0 Unit cell: (112.88, 119, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 1 26.01 S 44 16.00 P 290 15.00 O 3635 8.00 N 3089 7.00 C 9528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS M 1 " - pdb=" SG CYS M 14 " distance=2.03 Simple disulfide: pdb=" SG CYS N 115 " - pdb=" SG CYS N 125 " distance=2.03 Simple disulfide: pdb=" SG CYS N 119 " - pdb=" SG CYS N 143 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 Simple disulfide: pdb=" SG CYS N 538 " - pdb=" SG CYS N 564 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 352.5 milliseconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2490 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 14 sheets defined 60.9% alpha, 3.1% beta 137 base pairs and 244 stacking pairs defined. Time for finding SS restraints: 2.08 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.605A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.536A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.558A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.705A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.622A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.544A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 4.175A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.511A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.836A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.728A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 173 through 178 Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 220 through 225 removed outlier: 3.788A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 220 through 225' Processing helix chain 'N' and resid 237 through 242 removed outlier: 4.375A pdb=" N SER N 241 " --> pdb=" O THR N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 295 Processing helix chain 'N' and resid 295 through 310 removed outlier: 3.729A pdb=" N LEU N 299 " --> pdb=" O ASP N 295 " (cutoff:3.500A) Proline residue: N 303 - end of helix Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 399 through 404 Processing helix chain 'N' and resid 416 through 429 Processing helix chain 'N' and resid 432 through 440 removed outlier: 3.512A pdb=" N TRP N 436 " --> pdb=" O GLY N 432 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS N 440 " --> pdb=" O TRP N 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 455 Processing helix chain 'N' and resid 458 through 469 Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 481 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 Processing helix chain 'N' and resid 550 through 554 removed outlier: 3.589A pdb=" N SER N 554 " --> pdb=" O ILE N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 565 through 567 No H-bonds generated for 'chain 'N' and resid 565 through 567' Processing helix chain 'N' and resid 572 through 576 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.070A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.171A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.725A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.718A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.916A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'M' and resid 27 through 28 Processing sheet with id=AB2, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.053A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AB5, first strand: chain 'N' and resid 545 through 547 559 hydrogen bonds defined for protein. 1617 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 244 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 6314 1.38 - 1.55: 10536 1.55 - 1.72: 581 1.72 - 1.88: 72 1.88 - 2.05: 4 Bond restraints: 17507 Sorted by residual: bond pdb=" C3' DG I 63 " pdb=" C2' DG I 63 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DA J 23 " pdb=" C2' DA J 23 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DC I 1 " pdb=" C2' DC I 1 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DC I 52 " pdb=" C2' DC I 52 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG J 52 " pdb=" C2' DG J 52 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.81e+00 ... (remaining 17502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 24755 2.69 - 5.37: 171 5.37 - 8.06: 6 8.06 - 10.75: 3 10.75 - 13.43: 2 Bond angle restraints: 24937 Sorted by residual: angle pdb=" O4' DC J 51 " pdb=" C4' DC J 51 " pdb=" C3' DC J 51 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" CB MET N 465 " pdb=" CG MET N 465 " pdb=" SD MET N 465 " ideal model delta sigma weight residual 112.70 126.13 -13.43 3.00e+00 1.11e-01 2.01e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J 1 " pdb=" C4 DT J 1 " pdb=" O4 DT J 1 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 24932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 8174 34.25 - 68.51: 1637 68.51 - 102.76: 42 102.76 - 137.02: 2 137.02 - 171.27: 2 Dihedral angle restraints: 9857 sinusoidal: 6006 harmonic: 3851 Sorted by residual: dihedral pdb=" CB CYS N 115 " pdb=" SG CYS N 115 " pdb=" SG CYS N 125 " pdb=" CB CYS N 125 " ideal model delta sinusoidal sigma weight residual 93.00 162.94 -69.94 1 1.00e+01 1.00e-02 6.31e+01 dihedral pdb=" CB CYS N 538 " pdb=" SG CYS N 538 " pdb=" SG CYS N 564 " pdb=" CB CYS N 564 " ideal model delta sinusoidal sigma weight residual -86.00 -142.77 56.77 1 1.00e+01 1.00e-02 4.34e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.73 171.27 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 9854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1519 0.028 - 0.057: 833 0.057 - 0.085: 271 0.085 - 0.114: 146 0.114 - 0.142: 24 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CG LEU M 22 " pdb=" CB LEU M 22 " pdb=" CD1 LEU M 22 " pdb=" CD2 LEU M 22 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CG LEU N 211 " pdb=" CB LEU N 211 " pdb=" CD1 LEU N 211 " pdb=" CD2 LEU N 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.03e-01 chirality pdb=" C3' DC I 52 " pdb=" C4' DC I 52 " pdb=" O3' DC I 52 " pdb=" C2' DC I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.60 -0.13 2.00e-01 2.50e+01 4.46e-01 ... (remaining 2790 not shown) Planarity restraints: 2187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU N 374 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C GLU N 374 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU N 374 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY N 375 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" C GLU H 110 " -0.034 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER H 109 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C SER H 109 " 0.032 2.00e-02 2.50e+03 pdb=" O SER H 109 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU H 110 " -0.011 2.00e-02 2.50e+03 ... (remaining 2184 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 540 2.69 - 3.24: 14731 3.24 - 3.80: 30742 3.80 - 4.35: 39905 4.35 - 4.90: 59204 Nonbonded interactions: 145122 Sorted by model distance: nonbonded pdb=" O ILE N 537 " pdb=" OG1 THR N 541 " model vdw 2.138 3.040 nonbonded pdb=" OG1 THR D 29 " pdb=" OP1 DC I 30 " model vdw 2.186 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR N 468 " pdb=" OD2 ASP N 475 " model vdw 2.231 3.040 nonbonded pdb=" O PHE N 147 " pdb=" NH1 ARG N 424 " model vdw 2.232 3.120 ... (remaining 145117 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 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 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 : 0.005 0.056 17514 Z= 0.436 Angle : 0.696 13.433 24949 Z= 0.577 Chirality : 0.042 0.142 2793 Planarity : 0.004 0.034 2187 Dihedral : 26.669 171.270 7349 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.37 % Allowed : 27.90 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.31 (0.23), residues: 1306 helix: 1.64 (0.19), residues: 741 sheet: None (None), residues: 0 loop : -0.10 (0.25), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.009 0.001 TYR H 37 PHE 0.023 0.001 PHE N 203 TRP 0.009 0.001 TRP M 89 HIS 0.002 0.001 HIS N 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.44 (17507) covalent geometry : angle 0.69602 / 0.58 (24937) SS BOND : bond 0.00310 / 0.19 ( 6) SS BOND : angle 1.10059 / 0.62 ( 12) hydrogen bonds : bond 0.11415 / 7.66 ( 909) hydrogen bonds : angle 4.99309 / 3.65 ( 2317) Misc. bond : bond 0.05631 / 3.75 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.286 Fit side-chains REVERT: A 52 ARG cc_start: 0.8032 (mtt-85) cc_final: 0.7796 (mtt-85) REVERT: A 53 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7346 (ttt180) REVERT: A 73 GLU cc_start: 0.7227 (tt0) cc_final: 0.6679 (pt0) REVERT: C 36 LYS cc_start: 0.8330 (mttt) cc_final: 0.7937 (mmtm) REVERT: C 99 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.6981 (mmm160) REVERT: D 30 ARG cc_start: 0.6249 (mtt180) cc_final: 0.5908 (ptm160) REVERT: D 31 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7327 (mtpp) REVERT: D 33 SER cc_start: 0.8311 (p) cc_final: 0.7851 (m) REVERT: D 75 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7635 (p) REVERT: E 56 LYS cc_start: 0.7550 (mtpt) cc_final: 0.6418 (mmtm) REVERT: E 120 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7504 (mmm) REVERT: F 63 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7783 (mt-10) REVERT: G 64 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7359 (tp30) REVERT: G 99 ARG cc_start: 0.7727 (mtp180) cc_final: 0.6919 (mtp180) REVERT: G 108 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8349 (mp) REVERT: H 31 LYS cc_start: 0.7488 (tmtm) cc_final: 0.6464 (tptm) REVERT: H 68 GLU cc_start: 0.7362 (mt-10) cc_final: 0.7053 (mp0) REVERT: N 172 ASP cc_start: 0.7514 (p0) cc_final: 0.7117 (p0) REVERT: N 338 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.5982 (mt) REVERT: N 374 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6495 (tm-30) REVERT: N 400 ASP cc_start: 0.6673 (OUTLIER) cc_final: 0.6342 (t70) REVERT: N 401 GLU cc_start: 0.5631 (mp0) cc_final: 0.5214 (mp0) REVERT: N 413 ILE cc_start: 0.7755 (tt) cc_final: 0.7179 (mt) REVERT: N 430 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7692 (mp) REVERT: N 507 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6084 (tmm-80) REVERT: N 556 SER cc_start: 0.7812 (OUTLIER) cc_final: 0.7527 (p) outliers start: 38 outliers final: 21 residues processed: 166 average time/residue: 0.5838 time to fit residues: 106.7200 Evaluate side-chains 165 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 68 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 338 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 430 LEU Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 545 THR Chi-restraints excluded: chain N residue 546 VAL Chi-restraints excluded: chain N residue 556 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 5.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 54 ASN N 201 GLN ** N 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.227276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.172250 restraints weight = 16725.871| |-----------------------------------------------------------------------------| r_work (start): 0.4061 rms_B_bonded: 1.40 r_work: 0.3867 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3749 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 17514 Z= 0.174 Angle : 0.612 9.639 24949 Z= 0.347 Chirality : 0.044 0.241 2793 Planarity : 0.004 0.035 2187 Dihedral : 28.843 170.344 4764 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.90 % Allowed : 25.95 % Favored : 70.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.39 (0.23), residues: 1306 helix: 1.80 (0.19), residues: 747 sheet: None (None), residues: 0 loop : -0.25 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.017 0.002 TYR N 309 PHE 0.013 0.002 PHE E 67 TRP 0.013 0.001 TRP M 89 HIS 0.003 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (17507) covalent geometry : angle 0.61112 / 0.35 (24937) SS BOND : bond 0.00344 / 0.21 ( 6) SS BOND : angle 1.27857 / 0.73 ( 12) hydrogen bonds : bond 0.05403 / 3.58 ( 909) hydrogen bonds : angle 3.75257 / 2.74 ( 2317) Misc. bond : bond 0.13639 / 9.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 145 time to evaluate : 0.517 Fit side-chains REVERT: A 73 GLU cc_start: 0.7626 (tt0) cc_final: 0.7140 (pt0) REVERT: C 36 LYS cc_start: 0.8222 (mttt) cc_final: 0.7991 (mmtm) REVERT: C 75 LYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6368 (mppt) REVERT: C 99 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7318 (mmm160) REVERT: D 30 ARG cc_start: 0.5883 (mtt180) cc_final: 0.5525 (ptm160) REVERT: D 31 LYS cc_start: 0.7262 (OUTLIER) cc_final: 0.6987 (mtpp) REVERT: D 33 SER cc_start: 0.8524 (p) cc_final: 0.8129 (m) REVERT: E 56 LYS cc_start: 0.7848 (mtpt) cc_final: 0.6804 (mmtm) REVERT: F 63 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7876 (mt-10) REVERT: G 99 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7445 (mtp180) REVERT: G 108 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8539 (mp) REVERT: H 31 LYS cc_start: 0.7507 (tmtm) cc_final: 0.6511 (tptp) REVERT: M 67 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.5422 (mp0) REVERT: N 172 ASP cc_start: 0.7362 (p0) cc_final: 0.6923 (p0) REVERT: N 374 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.6341 (tm-30) REVERT: N 382 ARG cc_start: 0.6318 (OUTLIER) cc_final: 0.5950 (mtt90) REVERT: N 401 GLU cc_start: 0.5569 (mp0) cc_final: 0.5125 (mp0) REVERT: N 427 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.7381 (t0) outliers start: 44 outliers final: 17 residues processed: 173 average time/residue: 0.6534 time to fit residues: 124.1431 Evaluate side-chains 160 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain N residue 227 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 439 PHE Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 73 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 81 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 147 optimal weight: 0.6980 chunk 115 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN N 351 GLN ** N 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.228220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.173461 restraints weight = 16833.885| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 1.39 r_work: 0.3888 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.095 17514 Z= 0.144 Angle : 0.576 8.549 24949 Z= 0.330 Chirality : 0.042 0.248 2793 Planarity : 0.004 0.040 2187 Dihedral : 28.871 169.241 4720 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.25 % Allowed : 25.95 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.56 (0.23), residues: 1306 helix: 1.96 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.20 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 96 TYR 0.014 0.001 TYR N 309 PHE 0.013 0.001 PHE E 67 TRP 0.011 0.001 TRP M 89 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 (17507) covalent geometry : angle 0.57600 / 0.33 (24937) SS BOND : bond 0.00256 / 0.17 ( 6) SS BOND : angle 1.03667 / 0.60 ( 12) hydrogen bonds : bond 0.04809 / 3.22 ( 909) hydrogen bonds : angle 3.49060 / 2.55 ( 2317) Misc. bond : bond 0.09514 / 6.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.491 Fit side-chains REVERT: A 53 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7618 (ttt180) REVERT: A 73 GLU cc_start: 0.7616 (tt0) cc_final: 0.7130 (pt0) REVERT: C 36 LYS cc_start: 0.8197 (mttt) cc_final: 0.7956 (mmtm) REVERT: C 75 LYS cc_start: 0.6559 (OUTLIER) cc_final: 0.6347 (mppt) REVERT: C 99 ARG cc_start: 0.7889 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: D 30 ARG cc_start: 0.5798 (mtt180) cc_final: 0.5463 (ptm160) REVERT: D 31 LYS cc_start: 0.7276 (OUTLIER) cc_final: 0.6990 (mtpp) REVERT: D 33 SER cc_start: 0.8497 (p) cc_final: 0.8106 (m) REVERT: E 56 LYS cc_start: 0.7816 (mtpt) cc_final: 0.6784 (mmtm) REVERT: F 63 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7864 (mt-10) REVERT: F 92 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7704 (ttp80) REVERT: G 99 ARG cc_start: 0.8013 (mtp180) cc_final: 0.7422 (mtp180) REVERT: H 31 LYS cc_start: 0.7564 (tmtm) cc_final: 0.6573 (tptp) REVERT: M 67 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.5301 (mp0) REVERT: N 172 ASP cc_start: 0.7400 (p0) cc_final: 0.7027 (p0) REVERT: N 187 LEU cc_start: 0.5650 (OUTLIER) cc_final: 0.5377 (mp) REVERT: N 374 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: N 382 ARG cc_start: 0.6221 (OUTLIER) cc_final: 0.5713 (mtt90) REVERT: N 401 GLU cc_start: 0.5687 (mp0) cc_final: 0.5370 (mp0) REVERT: N 530 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7111 (mp10) outliers start: 48 outliers final: 14 residues processed: 174 average time/residue: 0.6742 time to fit residues: 128.6314 Evaluate side-chains 156 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 43 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 88 GLN ** N 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.222680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166839 restraints weight = 16760.543| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 1.43 r_work: 0.3811 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.233 17514 Z= 0.251 Angle : 0.674 11.198 24949 Z= 0.370 Chirality : 0.047 0.248 2793 Planarity : 0.005 0.047 2187 Dihedral : 29.047 168.752 4716 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 5.85 % Allowed : 24.80 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 0.90 (0.23), residues: 1306 helix: 1.42 (0.19), residues: 742 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 96 TYR 0.017 0.002 TYR N 309 PHE 0.012 0.002 PHE N 512 TRP 0.016 0.002 TRP M 89 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00576 / 0.25 (17507) covalent geometry : angle 0.67334 / 0.37 (24937) SS BOND : bond 0.00327 / 0.22 ( 6) SS BOND : angle 1.52409 / 0.87 ( 12) hydrogen bonds : bond 0.06159 / 4.11 ( 909) hydrogen bonds : angle 3.75695 / 2.74 ( 2317) Misc. bond : bond 0.23309 / 15.54 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 131 time to evaluate : 0.392 Fit side-chains REVERT: A 53 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7676 (ttt180) REVERT: C 36 LYS cc_start: 0.8220 (mttt) cc_final: 0.7859 (mmtm) REVERT: C 51 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7639 (tp) REVERT: C 75 LYS cc_start: 0.6574 (OUTLIER) cc_final: 0.6355 (mppt) REVERT: C 99 ARG cc_start: 0.8039 (mmm-85) cc_final: 0.7318 (mmm160) REVERT: D 30 ARG cc_start: 0.5761 (mtt180) cc_final: 0.5466 (ptm160) REVERT: D 31 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6905 (mtpp) REVERT: D 33 SER cc_start: 0.8474 (p) cc_final: 0.8074 (m) REVERT: D 90 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7265 (mt-10) REVERT: D 105 LYS cc_start: 0.7160 (mttm) cc_final: 0.6703 (tttm) REVERT: E 56 LYS cc_start: 0.7922 (mtpt) cc_final: 0.6799 (mmtm) REVERT: F 63 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7897 (mt-10) REVERT: G 74 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7634 (mmpt) REVERT: G 92 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: G 99 ARG cc_start: 0.8012 (mtp180) cc_final: 0.7377 (mtp180) REVERT: G 108 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8480 (mp) REVERT: H 31 LYS cc_start: 0.7633 (tmtm) cc_final: 0.6591 (tptm) REVERT: N 172 ASP cc_start: 0.7603 (p0) cc_final: 0.7230 (p0) REVERT: N 187 LEU cc_start: 0.5679 (OUTLIER) cc_final: 0.5306 (mp) REVERT: N 374 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: N 382 ARG cc_start: 0.6298 (OUTLIER) cc_final: 0.5876 (mtt90) REVERT: N 427 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7387 (t0) REVERT: N 507 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6284 (tmm-80) REVERT: N 530 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: N 543 ILE cc_start: 0.6589 (OUTLIER) cc_final: 0.6036 (mp) outliers start: 66 outliers final: 33 residues processed: 179 average time/residue: 0.6301 time to fit residues: 124.1502 Evaluate side-chains 175 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 128 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 75 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain M residue 11 THR Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 223 LEU Chi-restraints excluded: chain N residue 227 SER Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 115 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 141 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 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 = 0.4538 r_free = 0.4538 target = 0.226388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.171063 restraints weight = 16740.313| |-----------------------------------------------------------------------------| r_work (start): 0.4047 rms_B_bonded: 1.34 r_work: 0.3860 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17514 Z= 0.141 Angle : 0.603 9.641 24949 Z= 0.339 Chirality : 0.043 0.250 2793 Planarity : 0.004 0.052 2187 Dihedral : 29.015 169.683 4716 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.61 % Allowed : 26.04 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.28 (0.23), residues: 1306 helix: 1.77 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.40 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.015 0.001 TYR N 309 PHE 0.016 0.001 PHE E 67 TRP 0.011 0.001 TRP N 477 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (17507) covalent geometry : angle 0.60318 / 0.34 (24937) SS BOND : bond 0.00312 / 0.21 ( 6) SS BOND : angle 0.86657 / 0.51 ( 12) hydrogen bonds : bond 0.04869 / 3.27 ( 909) hydrogen bonds : angle 3.52459 / 2.58 ( 2317) Misc. bond : bond 0.05005 / 3.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 133 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7629 (ttt180) REVERT: A 73 GLU cc_start: 0.7608 (tt0) cc_final: 0.7126 (pt0) REVERT: C 36 LYS cc_start: 0.8211 (mttt) cc_final: 0.7878 (mmtm) REVERT: C 99 ARG cc_start: 0.7963 (mmm-85) cc_final: 0.7287 (mmm160) REVERT: D 30 ARG cc_start: 0.5780 (mtt180) cc_final: 0.5507 (ptm160) REVERT: D 31 LYS cc_start: 0.7260 (OUTLIER) cc_final: 0.6924 (mtpp) REVERT: D 33 SER cc_start: 0.8471 (p) cc_final: 0.8079 (m) REVERT: D 105 LYS cc_start: 0.6986 (mttm) cc_final: 0.6597 (tttm) REVERT: E 56 LYS cc_start: 0.7815 (mtpt) cc_final: 0.6730 (mmtm) REVERT: F 63 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7843 (mt-10) REVERT: G 74 LYS cc_start: 0.8145 (mtmt) cc_final: 0.7665 (mmpt) REVERT: G 92 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7868 (mt-10) REVERT: G 99 ARG cc_start: 0.8000 (mtp180) cc_final: 0.7390 (mtp180) REVERT: G 108 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8467 (mp) REVERT: H 31 LYS cc_start: 0.7612 (tmtm) cc_final: 0.6599 (tptm) REVERT: M 67 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.5511 (mp0) REVERT: N 172 ASP cc_start: 0.7498 (p0) cc_final: 0.7156 (p0) REVERT: N 187 LEU cc_start: 0.5751 (OUTLIER) cc_final: 0.5406 (mp) REVERT: N 374 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: N 382 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5861 (mtt90) REVERT: N 427 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7324 (t0) REVERT: N 507 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6304 (tmm-80) REVERT: N 543 ILE cc_start: 0.6529 (OUTLIER) cc_final: 0.5971 (mp) outliers start: 52 outliers final: 21 residues processed: 170 average time/residue: 0.5878 time to fit residues: 109.8097 Evaluate side-chains 161 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 129 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 95 optimal weight: 9.9990 chunk 114 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 85 optimal weight: 30.0000 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 148 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 152 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 472 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 = 0.4524 r_free = 0.4524 target = 0.224875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.170034 restraints weight = 16634.313| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 1.44 r_work: 0.3840 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3720 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.173 17514 Z= 0.176 Angle : 0.611 10.117 24949 Z= 0.341 Chirality : 0.043 0.248 2793 Planarity : 0.004 0.043 2187 Dihedral : 29.021 169.368 4716 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.61 % Allowed : 25.86 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.24 (0.23), residues: 1306 helix: 1.76 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.45 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 96 TYR 0.014 0.002 TYR N 309 PHE 0.018 0.002 PHE N 203 TRP 0.014 0.001 TRP M 89 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (17507) covalent geometry : angle 0.61088 / 0.34 (24937) SS BOND : bond 0.00275 / 0.19 ( 6) SS BOND : angle 1.05739 / 0.62 ( 12) hydrogen bonds : bond 0.05140 / 3.45 ( 909) hydrogen bonds : angle 3.53358 / 2.58 ( 2317) Misc. bond : bond 0.17350 / 11.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 126 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7630 (ttt180) REVERT: A 73 GLU cc_start: 0.7621 (tt0) cc_final: 0.7127 (pt0) REVERT: C 36 LYS cc_start: 0.8230 (mttt) cc_final: 0.7892 (mmtm) REVERT: C 99 ARG cc_start: 0.7998 (mmm-85) cc_final: 0.7331 (mmm160) REVERT: D 30 ARG cc_start: 0.5850 (mtt180) cc_final: 0.5514 (ptm160) REVERT: D 31 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6977 (mtpp) REVERT: D 33 SER cc_start: 0.8477 (p) cc_final: 0.8114 (m) REVERT: D 105 LYS cc_start: 0.7050 (mttm) cc_final: 0.6660 (tttm) REVERT: E 56 LYS cc_start: 0.7885 (mtpt) cc_final: 0.6807 (mmtm) REVERT: F 63 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7876 (mt-10) REVERT: G 74 LYS cc_start: 0.8161 (mtmt) cc_final: 0.7678 (mmpt) REVERT: G 99 ARG cc_start: 0.8020 (mtp180) cc_final: 0.7422 (mtp180) REVERT: G 108 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8494 (mp) REVERT: H 31 LYS cc_start: 0.7689 (tmtm) cc_final: 0.6647 (tptm) REVERT: M 67 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.5502 (mp0) REVERT: N 172 ASP cc_start: 0.7591 (p0) cc_final: 0.7258 (p0) REVERT: N 187 LEU cc_start: 0.5789 (OUTLIER) cc_final: 0.5430 (mp) REVERT: N 374 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.6239 (tm-30) REVERT: N 382 ARG cc_start: 0.6341 (OUTLIER) cc_final: 0.5929 (mtt90) REVERT: N 427 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7369 (t0) REVERT: N 507 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6168 (tmm-80) REVERT: N 543 ILE cc_start: 0.6556 (OUTLIER) cc_final: 0.5993 (mp) outliers start: 52 outliers final: 31 residues processed: 163 average time/residue: 0.5930 time to fit residues: 106.4420 Evaluate side-chains 166 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 472 ASN Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 20.0000 chunk 125 optimal weight: 6.9990 chunk 71 optimal weight: 40.0000 chunk 145 optimal weight: 2.9990 chunk 124 optimal weight: 0.0870 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... N 421 ASN N 472 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.223012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.167124 restraints weight = 16683.032| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 1.43 r_work: 0.3815 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3693 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.218 17514 Z= 0.207 Angle : 0.648 11.000 24949 Z= 0.356 Chirality : 0.045 0.248 2793 Planarity : 0.005 0.046 2187 Dihedral : 29.127 169.668 4716 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.69 % Allowed : 25.95 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.00 (0.23), residues: 1306 helix: 1.57 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.54 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 96 TYR 0.016 0.002 TYR N 309 PHE 0.020 0.002 PHE N 203 TRP 0.015 0.002 TRP M 89 HIS 0.004 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.21 (17507) covalent geometry : angle 0.64721 / 0.36 (24937) SS BOND : bond 0.00315 / 0.22 ( 6) SS BOND : angle 1.29237 / 0.76 ( 12) hydrogen bonds : bond 0.05553 / 3.73 ( 909) hydrogen bonds : angle 3.64127 / 2.66 ( 2317) Misc. bond : bond 0.21818 / 14.55 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7629 (ttt180) REVERT: A 73 GLU cc_start: 0.7641 (tt0) cc_final: 0.7079 (pt0) REVERT: C 36 LYS cc_start: 0.8241 (mttt) cc_final: 0.7871 (mmtm) REVERT: C 99 ARG cc_start: 0.8030 (mmm-85) cc_final: 0.7343 (mmm160) REVERT: D 30 ARG cc_start: 0.5794 (mtt180) cc_final: 0.5474 (ptm160) REVERT: D 31 LYS cc_start: 0.7331 (OUTLIER) cc_final: 0.6949 (mtpp) REVERT: D 33 SER cc_start: 0.8485 (p) cc_final: 0.8091 (m) REVERT: D 90 GLU cc_start: 0.7635 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: D 105 LYS cc_start: 0.7111 (mttm) cc_final: 0.6657 (tttm) REVERT: D 113 LYS cc_start: 0.6674 (ttmt) cc_final: 0.6290 (tmtt) REVERT: E 56 LYS cc_start: 0.7890 (mtpt) cc_final: 0.6776 (mmtm) REVERT: F 63 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7901 (mt-10) REVERT: G 74 LYS cc_start: 0.8183 (mtmt) cc_final: 0.7707 (mmpt) REVERT: G 92 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7895 (mt-10) REVERT: G 99 ARG cc_start: 0.7997 (mtp180) cc_final: 0.7397 (mtp180) REVERT: G 108 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8513 (mp) REVERT: H 31 LYS cc_start: 0.7710 (tmtm) cc_final: 0.6648 (tptm) REVERT: M 67 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.5545 (mp0) REVERT: N 172 ASP cc_start: 0.7592 (p0) cc_final: 0.7317 (p0) REVERT: N 187 LEU cc_start: 0.5678 (OUTLIER) cc_final: 0.5287 (mp) REVERT: N 374 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5954 (tm-30) REVERT: N 382 ARG cc_start: 0.6390 (OUTLIER) cc_final: 0.5902 (mtt-85) REVERT: N 401 GLU cc_start: 0.5622 (mp0) cc_final: 0.5376 (mp0) REVERT: N 427 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.7370 (t0) REVERT: N 507 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.6137 (tmm-80) REVERT: N 530 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7309 (mp10) REVERT: N 543 ILE cc_start: 0.6544 (OUTLIER) cc_final: 0.5909 (mp) outliers start: 53 outliers final: 31 residues processed: 166 average time/residue: 0.7491 time to fit residues: 136.4791 Evaluate side-chains 173 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 94 ASP Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 472 ASN Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 543 ILE Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 103 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 64 optimal weight: 0.6980 chunk 120 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 87 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.220458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157969 restraints weight = 16682.240| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 1.51 r_work: 0.3683 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 17514 Z= 0.142 Angle : 0.597 10.271 24949 Z= 0.335 Chirality : 0.042 0.249 2793 Planarity : 0.004 0.041 2187 Dihedral : 29.062 169.817 4716 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.72 % Allowed : 26.75 % Favored : 69.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.37 (0.23), residues: 1306 helix: 1.89 (0.19), residues: 748 sheet: None (None), residues: 0 loop : -0.45 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 96 TYR 0.016 0.001 TYR N 309 PHE 0.021 0.001 PHE N 203 TRP 0.010 0.001 TRP N 477 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 (17507) covalent geometry : angle 0.59696 / 0.34 (24937) SS BOND : bond 0.00278 / 0.19 ( 6) SS BOND : angle 0.92056 / 0.55 ( 12) hydrogen bonds : bond 0.04715 / 3.19 ( 909) hydrogen bonds : angle 3.46390 / 2.53 ( 2317) Misc. bond : bond 0.12276 / 8.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 133 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7398 (ttt180) REVERT: A 73 GLU cc_start: 0.7430 (tt0) cc_final: 0.6849 (pt0) REVERT: C 36 LYS cc_start: 0.8151 (mttt) cc_final: 0.7648 (mmtm) REVERT: C 99 ARG cc_start: 0.7897 (mmm-85) cc_final: 0.7008 (mmm160) REVERT: D 30 ARG cc_start: 0.5624 (mtt180) cc_final: 0.5294 (ptm160) REVERT: D 31 LYS cc_start: 0.7192 (OUTLIER) cc_final: 0.6790 (mtpp) REVERT: D 33 SER cc_start: 0.8386 (p) cc_final: 0.7941 (m) REVERT: D 113 LYS cc_start: 0.6503 (ttmt) cc_final: 0.6026 (tmtt) REVERT: E 56 LYS cc_start: 0.7570 (mtpt) cc_final: 0.6314 (mmtm) REVERT: F 63 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7834 (mt-10) REVERT: G 74 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7467 (mppt) REVERT: G 99 ARG cc_start: 0.7772 (mtp180) cc_final: 0.7024 (mtp180) REVERT: G 108 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8287 (mp) REVERT: H 31 LYS cc_start: 0.7575 (tmtm) cc_final: 0.6476 (tptm) REVERT: M 67 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.5390 (mp0) REVERT: N 172 ASP cc_start: 0.7368 (p0) cc_final: 0.7030 (p0) REVERT: N 187 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.5143 (mp) REVERT: N 374 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.5790 (tm-30) REVERT: N 382 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5673 (mtt-85) REVERT: N 401 GLU cc_start: 0.5452 (mp0) cc_final: 0.5178 (mp0) REVERT: N 427 ASP cc_start: 0.7429 (OUTLIER) cc_final: 0.7200 (t0) REVERT: N 507 ARG cc_start: 0.7477 (OUTLIER) cc_final: 0.5934 (tmm-80) REVERT: N 543 ILE cc_start: 0.6425 (OUTLIER) cc_final: 0.5824 (mp) outliers start: 42 outliers final: 25 residues processed: 161 average time/residue: 0.7829 time to fit residues: 138.1269 Evaluate side-chains 164 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 129 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 543 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 540 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 = 0.4510 r_free = 0.4510 target = 0.223357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.167842 restraints weight = 16588.968| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.38 r_work: 0.3823 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.214 17514 Z= 0.200 Angle : 0.639 12.689 24949 Z= 0.352 Chirality : 0.044 0.248 2793 Planarity : 0.005 0.039 2187 Dihedral : 29.106 169.762 4715 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.16 % Allowed : 26.75 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.10 (0.23), residues: 1306 helix: 1.67 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.54 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.017 0.002 TYR N 309 PHE 0.022 0.002 PHE N 203 TRP 0.016 0.002 TRP M 89 HIS 0.003 0.001 HIS N 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (17507) covalent geometry : angle 0.63851 / 0.35 (24937) SS BOND : bond 0.00345 / 0.24 ( 6) SS BOND : angle 1.25545 / 0.75 ( 12) hydrogen bonds : bond 0.05361 / 3.61 ( 909) hydrogen bonds : angle 3.58506 / 2.62 ( 2317) Misc. bond : bond 0.21414 / 14.28 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 127 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.7314 (mtt90) cc_final: 0.7043 (mtm-85) REVERT: A 53 ARG cc_start: 0.8239 (OUTLIER) cc_final: 0.7640 (ttt180) REVERT: C 36 LYS cc_start: 0.8252 (mttt) cc_final: 0.7910 (mmtm) REVERT: C 99 ARG cc_start: 0.8031 (mmm-85) cc_final: 0.7352 (mmm160) REVERT: D 30 ARG cc_start: 0.5815 (mtt180) cc_final: 0.5536 (ptm160) REVERT: D 31 LYS cc_start: 0.7387 (OUTLIER) cc_final: 0.6979 (mtpp) REVERT: D 33 SER cc_start: 0.8492 (p) cc_final: 0.8111 (m) REVERT: D 90 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7244 (mt-10) REVERT: D 105 LYS cc_start: 0.7105 (mttm) cc_final: 0.6673 (tttm) REVERT: D 113 LYS cc_start: 0.6675 (ttmt) cc_final: 0.6321 (tmtt) REVERT: F 63 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7870 (mt-10) REVERT: G 74 LYS cc_start: 0.8203 (mtmt) cc_final: 0.7744 (mmpt) REVERT: G 99 ARG cc_start: 0.8001 (mtp180) cc_final: 0.7421 (mtp180) REVERT: G 108 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8487 (mp) REVERT: H 31 LYS cc_start: 0.7736 (tmtm) cc_final: 0.6681 (tptm) REVERT: M 67 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.5578 (mp0) REVERT: N 172 ASP cc_start: 0.7605 (p0) cc_final: 0.7330 (p0) REVERT: N 187 LEU cc_start: 0.5683 (OUTLIER) cc_final: 0.5313 (mp) REVERT: N 374 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: N 382 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5887 (mtt-85) REVERT: N 401 GLU cc_start: 0.5537 (mp0) cc_final: 0.5314 (mp0) REVERT: N 427 ASP cc_start: 0.7583 (OUTLIER) cc_final: 0.7341 (t0) REVERT: N 507 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6158 (tmm-80) REVERT: N 530 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.7306 (mp10) REVERT: N 543 ILE cc_start: 0.6470 (OUTLIER) cc_final: 0.5904 (mp) outliers start: 47 outliers final: 28 residues processed: 160 average time/residue: 0.7835 time to fit residues: 137.3867 Evaluate side-chains 165 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 456 ARG Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 543 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 71 optimal weight: 40.0000 chunk 14 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 50 optimal weight: 0.1980 chunk 7 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 86 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 540 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 = 0.4415 r_free = 0.4415 target = 0.220441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.157865 restraints weight = 16764.400| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 1.50 r_work: 0.3681 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 17514 Z= 0.141 Angle : 0.612 13.194 24949 Z= 0.340 Chirality : 0.043 0.249 2793 Planarity : 0.005 0.049 2187 Dihedral : 29.076 169.823 4715 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.81 % Allowed : 27.10 % Favored : 69.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.34 (0.23), residues: 1306 helix: 1.88 (0.19), residues: 749 sheet: None (None), residues: 0 loop : -0.47 (0.25), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.015 0.002 TYR N 309 PHE 0.024 0.002 PHE N 203 TRP 0.012 0.001 TRP N 477 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (17507) covalent geometry : angle 0.61142 / 0.34 (24937) SS BOND : bond 0.00318 / 0.22 ( 6) SS BOND : angle 0.97113 / 0.59 ( 12) hydrogen bonds : bond 0.04706 / 3.18 ( 909) hydrogen bonds : angle 3.48081 / 2.54 ( 2317) Misc. bond : bond 0.09232 / 6.15 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 127 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.6963 (mtt90) cc_final: 0.6747 (mtm-85) REVERT: A 53 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7411 (ttt180) REVERT: A 73 GLU cc_start: 0.7363 (tt0) cc_final: 0.6798 (pt0) REVERT: C 36 LYS cc_start: 0.8144 (mttt) cc_final: 0.7645 (mmtm) REVERT: C 99 ARG cc_start: 0.7915 (mmm-85) cc_final: 0.7029 (mmm160) REVERT: D 30 ARG cc_start: 0.5541 (mtt180) cc_final: 0.5284 (ptm160) REVERT: D 31 LYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6796 (mtpp) REVERT: D 33 SER cc_start: 0.8385 (p) cc_final: 0.7936 (m) REVERT: D 113 LYS cc_start: 0.6487 (ttmt) cc_final: 0.6014 (tmtt) REVERT: E 56 LYS cc_start: 0.7566 (mtpt) cc_final: 0.6307 (mmtm) REVERT: F 63 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7807 (mt-10) REVERT: G 74 LYS cc_start: 0.8079 (mtmt) cc_final: 0.7474 (mppt) REVERT: G 99 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7024 (mtp180) REVERT: G 108 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8301 (mp) REVERT: H 31 LYS cc_start: 0.7595 (tmtm) cc_final: 0.6489 (tptm) REVERT: M 67 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.5356 (mp0) REVERT: N 172 ASP cc_start: 0.7401 (p0) cc_final: 0.7069 (p0) REVERT: N 187 LEU cc_start: 0.5451 (OUTLIER) cc_final: 0.5089 (mp) REVERT: N 374 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5717 (tm-30) REVERT: N 382 ARG cc_start: 0.6142 (OUTLIER) cc_final: 0.5688 (mtt-85) REVERT: N 401 GLU cc_start: 0.5486 (mp0) cc_final: 0.5212 (mp0) REVERT: N 427 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7186 (t0) REVERT: N 507 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.5954 (tmm-80) outliers start: 43 outliers final: 29 residues processed: 156 average time/residue: 0.7708 time to fit residues: 132.2380 Evaluate side-chains 164 residues out of total 1129 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 126 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain N residue 187 LEU Chi-restraints excluded: chain N residue 254 LEU Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 374 GLU Chi-restraints excluded: chain N residue 382 ARG Chi-restraints excluded: chain N residue 395 ASN Chi-restraints excluded: chain N residue 397 ILE Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 422 MET Chi-restraints excluded: chain N residue 427 ASP Chi-restraints excluded: chain N residue 454 VAL Chi-restraints excluded: chain N residue 456 ARG Chi-restraints excluded: chain N residue 459 LYS Chi-restraints excluded: chain N residue 466 GLU Chi-restraints excluded: chain N residue 507 ARG Chi-restraints excluded: chain N residue 546 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 146 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 540 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 = 0.4422 r_free = 0.4422 target = 0.221150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.158295 restraints weight = 16704.059| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.50 r_work: 0.3691 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.129 17514 Z= 0.139 Angle : 0.600 12.998 24949 Z= 0.334 Chirality : 0.042 0.247 2793 Planarity : 0.004 0.042 2187 Dihedral : 29.038 169.671 4715 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.72 % Allowed : 27.28 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 1.47 (0.23), residues: 1306 helix: 1.98 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.41 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 96 TYR 0.018 0.001 TYR N 309 PHE 0.022 0.002 PHE N 203 TRP 0.010 0.001 TRP M 89 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (17507) covalent geometry : angle 0.59959 / 0.33 (24937) SS BOND : bond 0.00331 / 0.23 ( 6) SS BOND : angle 0.91261 / 0.56 ( 12) hydrogen bonds : bond 0.04583 / 3.10 ( 909) hydrogen bonds : angle 3.42638 / 2.50 ( 2317) Misc. bond : bond 0.12916 / 8.61 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5955.52 seconds wall clock time: 102 minutes 0.21 seconds (6120.21 seconds total)