Starting phenix.real_space_refine on Wed Mar 4 17:46:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.map" model { file = "/net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k6p_22691/03_2026/7k6p_22691.cif" } resolution = 3.2 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= 0.004 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 32 5.16 5 C 8834 2.51 5 N 2828 2.21 5 O 3461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15447 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 672 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2961 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 362} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 97 Planarities with less than four sites: {'ASN:plan1': 3, 'ARG:plan': 3, 'GLU:plan': 8, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "L" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 465 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 116 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 2, 'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 3.65, per 1000 atoms: 0.24 Number of scatterers: 15447 At special positions: 0 Unit cell: (125.235, 123.165, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 292 15.00 O 3461 8.00 N 2828 7.00 C 8834 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 368.3 milliseconds 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 60.7% alpha, 6.3% beta 139 base pairs and 265 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 44 through 56 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 132 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.562A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.720A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.444A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) 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 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 195 through 202 Processing helix chain 'K' and resid 263 through 278 Processing helix chain 'K' and resid 283 through 303 removed outlier: 3.803A pdb=" N LEU K 293 " --> pdb=" O LYS K 289 " (cutoff:3.500A) Proline residue: K 294 - end of helix Processing helix chain 'K' and resid 304 through 320 Processing helix chain 'K' and resid 323 through 334 removed outlier: 3.642A pdb=" N ILE K 327 " --> pdb=" O PRO K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 354 removed outlier: 3.914A pdb=" N HIS K 343 " --> pdb=" O ARG K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 364 removed outlier: 5.666A pdb=" N ASN K 359 " --> pdb=" O PRO K 356 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N TYR K 364 " --> pdb=" O LEU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 388 Processing helix chain 'K' and resid 403 through 414 removed outlier: 3.502A pdb=" N GLY K 414 " --> pdb=" O ALA K 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 424 through 446 Processing helix chain 'K' and resid 463 through 470 Processing helix chain 'K' and resid 471 through 473 No H-bonds generated for 'chain 'K' and resid 471 through 473' Processing helix chain 'K' and resid 484 through 496 Processing helix chain 'K' and resid 525 through 527 No H-bonds generated for 'chain 'K' and resid 525 through 527' Processing helix chain 'K' and resid 565 through 570 removed outlier: 3.839A pdb=" N ARG K 569 " --> pdb=" O SER K 565 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.489A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.092A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.623A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 186 through 188 Processing sheet with id=AB1, first strand: chain 'K' and resid 236 through 240 Processing sheet with id=AB2, first strand: chain 'K' and resid 452 through 455 removed outlier: 6.173A pdb=" N SER K 418 " --> pdb=" O GLU K 453 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER K 455 " --> pdb=" O SER K 418 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N GLY K 420 " --> pdb=" O SER K 455 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N PHE K 395 " --> pdb=" O PHE K 419 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N CYS K 421 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP K 397 " --> pdb=" O CYS K 421 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR K 394 " --> pdb=" O VAL K 475 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N LEU K 477 " --> pdb=" O THR K 394 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N MET K 396 " --> pdb=" O LEU K 477 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY K 548 " --> pdb=" O LEU K 536 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 16 removed outlier: 8.960A pdb=" N LEU L 67 " --> pdb=" O GLN L 2 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1656 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 265 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 1.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3639 1.33 - 1.45: 4489 1.45 - 1.58: 7562 1.58 - 1.70: 578 1.70 - 1.82: 51 Bond restraints: 16319 Sorted by residual: bond pdb=" O3' DA I 91 " pdb=" P DC I 92 " ideal model delta sigma weight residual 1.607 1.547 0.060 1.50e-02 4.44e+03 1.60e+01 bond pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 1.607 1.561 0.046 1.50e-02 4.44e+03 9.56e+00 bond pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.18e-02 7.18e+03 9.48e+00 bond pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.64e+00 bond pdb=" N ARG B 45 " pdb=" CA ARG B 45 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.27e-02 6.20e+03 7.07e+00 ... (remaining 16314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 22140 1.70 - 3.41: 1041 3.41 - 5.11: 139 5.11 - 6.82: 17 6.82 - 8.52: 6 Bond angle restraints: 23343 Sorted by residual: angle pdb=" O3' DA I 90 " pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 111.50 104.64 6.86 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DT I 89 " pdb=" C3' DT I 89 " pdb=" C2' DT I 89 " ideal model delta sigma weight residual 111.50 105.78 5.72 1.50e+00 4.44e-01 1.45e+01 angle pdb=" O3' DT J 15 " pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 111.50 117.00 -5.50 1.50e+00 4.44e-01 1.35e+01 angle pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 110.00 104.65 5.35 1.50e+00 4.44e-01 1.27e+01 angle pdb=" C2' DC I 111 " pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 113.50 118.27 -4.77 1.50e+00 4.44e-01 1.01e+01 ... (remaining 23338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 7423 30.08 - 60.16: 1583 60.16 - 90.24: 56 90.24 - 120.31: 0 120.31 - 150.39: 3 Dihedral angle restraints: 9065 sinusoidal: 5504 harmonic: 3561 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 -159.67 -20.33 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 69.61 150.39 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 9062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2242 0.059 - 0.118: 409 0.118 - 0.176: 32 0.176 - 0.235: 3 0.235 - 0.294: 1 Chirality restraints: 2687 Sorted by residual: chirality pdb=" C3' DT J 15 " pdb=" C4' DT J 15 " pdb=" O3' DT J 15 " pdb=" C2' DT J 15 " both_signs ideal model delta sigma weight residual False -2.66 -2.37 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' DT I 89 " pdb=" C4' DT I 89 " pdb=" O3' DT I 89 " pdb=" C2' DT I 89 " both_signs ideal model delta sigma weight residual False -2.66 -2.89 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" C3' DA I 90 " pdb=" C4' DA I 90 " pdb=" O3' DA I 90 " pdb=" C2' DA I 90 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2684 not shown) Planarity restraints: 1951 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.030 2.00e-02 2.50e+03 1.52e-02 5.79e+00 pdb=" N1 DT I 88 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.002 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 121 " -0.031 2.00e-02 2.50e+03 1.34e-02 5.37e+00 pdb=" N9 DG I 121 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 121 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 121 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 121 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 121 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 121 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 121 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 86 " 0.193 9.50e-02 1.11e+02 8.65e-02 4.93e+00 pdb=" NE ARG D 86 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG D 86 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 86 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG D 86 " 0.004 2.00e-02 2.50e+03 ... (remaining 1948 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 188 2.62 - 3.19: 12775 3.19 - 3.76: 28248 3.76 - 4.33: 38047 4.33 - 4.90: 55895 Nonbonded interactions: 135153 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.051 3.040 nonbonded pdb=" OH TYR K 247 " pdb=" OE1 GLU K 249 " model vdw 2.063 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.105 3.040 nonbonded pdb=" OH TYR K 274 " pdb=" OD2 ASP K 344 " model vdw 2.160 3.040 nonbonded pdb=" O ASN K 521 " pdb=" ND2 ASN K 527 " model vdw 2.169 3.120 ... (remaining 135148 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 16 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 16 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 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: 1.720 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.220 Find NCS groups from input model: 0.150 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 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 : 0.006 0.060 16319 Z= 0.261 Angle : 0.793 8.521 23343 Z= 0.468 Chirality : 0.044 0.294 2687 Planarity : 0.006 0.087 1951 Dihedral : 25.084 150.392 6761 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.44 (0.24), residues: 1193 helix: 1.69 (0.19), residues: 712 sheet: -0.08 (0.59), residues: 77 loop : -0.06 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 86 TYR 0.016 0.002 TYR H 40 PHE 0.020 0.002 PHE G 25 TRP 0.002 0.000 TRP K 543 HIS 0.009 0.001 HIS K 363 Details of bonding type rmsd covalent geometry : bond 0.00591 (16319) covalent geometry : angle 0.79330 (23343) hydrogen bonds : bond 0.11333 ( 920) hydrogen bonds : angle 4.79089 ( 2370) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7663 (mmm) cc_final: 0.7444 (tpt) REVERT: B 91 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8563 (ttpp) REVERT: D 85 LYS cc_start: 0.8834 (mttm) cc_final: 0.8377 (mmtt) REVERT: E 81 ASP cc_start: 0.8162 (p0) cc_final: 0.7955 (p0) REVERT: F 25 ASN cc_start: 0.8340 (m110) cc_final: 0.8067 (m110) REVERT: H 33 ARG cc_start: 0.7305 (mmt90) cc_final: 0.7087 (mtt180) REVERT: H 34 LYS cc_start: 0.8549 (tppt) cc_final: 0.7884 (tptp) REVERT: H 115 THR cc_start: 0.8982 (m) cc_final: 0.8690 (m) REVERT: K 248 MET cc_start: 0.5993 (mmt) cc_final: 0.5792 (mmt) REVERT: K 428 SER cc_start: 0.7424 (m) cc_final: 0.6806 (t) REVERT: K 431 THR cc_start: 0.8565 (m) cc_final: 0.8195 (p) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.1476 time to fit residues: 38.3939 Evaluate side-chains 149 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN B 27 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 82 HIS ** K 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 GLN K 330 HIS K 363 HIS K 521 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.117897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084819 restraints weight = 27901.654| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.01 r_work: 0.3065 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 16319 Z= 0.349 Angle : 0.669 7.934 23343 Z= 0.381 Chirality : 0.043 0.149 2687 Planarity : 0.005 0.050 1951 Dihedral : 29.773 150.081 4569 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.14 % Allowed : 7.54 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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 (0.24), residues: 1193 helix: 1.61 (0.19), residues: 727 sheet: 0.43 (0.59), residues: 83 loop : -0.23 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 116 TYR 0.019 0.002 TYR K 315 PHE 0.025 0.002 PHE C 25 TRP 0.006 0.001 TRP K 182 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00805 (16319) covalent geometry : angle 0.66914 (23343) hydrogen bonds : bond 0.04845 ( 920) hydrogen bonds : angle 3.67424 ( 2370) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 164 time to evaluate : 0.325 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8539 (pm20) cc_final: 0.8140 (pm20) REVERT: A 129 ARG cc_start: 0.8777 (tpt90) cc_final: 0.8413 (tpt90) REVERT: B 74 GLU cc_start: 0.8664 (tt0) cc_final: 0.8451 (tt0) REVERT: B 91 LYS cc_start: 0.9171 (ttmm) cc_final: 0.8707 (tttt) REVERT: D 93 GLU cc_start: 0.8559 (mp0) cc_final: 0.8260 (mp0) REVERT: D 95 GLN cc_start: 0.8803 (tt0) cc_final: 0.8475 (tt0) REVERT: D 113 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8360 (mm-30) REVERT: E 59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7863 (pm20) REVERT: H 33 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6818 (mtt180) REVERT: H 34 LYS cc_start: 0.8168 (tppt) cc_final: 0.7250 (tttp) REVERT: H 42 TYR cc_start: 0.7969 (t80) cc_final: 0.7057 (t80) REVERT: H 101 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8786 (mm) REVERT: K 326 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7161 (mmt90) REVERT: K 388 GLN cc_start: 0.8460 (tm-30) cc_final: 0.7660 (tm-30) REVERT: K 431 THR cc_start: 0.8461 (m) cc_final: 0.7992 (p) outliers start: 11 outliers final: 7 residues processed: 166 average time/residue: 0.1454 time to fit residues: 33.5385 Evaluate side-chains 156 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 421 CYS Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain L residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 75 HIS E 113 HIS F 75 HIS G 38 ASN K 246 ASN K 357 GLN L 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.089958 restraints weight = 27989.053| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.96 r_work: 0.3151 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16319 Z= 0.163 Angle : 0.542 6.712 23343 Z= 0.319 Chirality : 0.035 0.150 2687 Planarity : 0.004 0.046 1951 Dihedral : 29.147 148.078 4569 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.34 % Allowed : 10.23 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.88 (0.24), residues: 1193 helix: 2.10 (0.19), residues: 730 sheet: 0.37 (0.56), residues: 95 loop : -0.19 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.034 0.002 TYR K 315 PHE 0.010 0.001 PHE A 67 TRP 0.002 0.001 TRP K 543 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00358 (16319) covalent geometry : angle 0.54162 (23343) hydrogen bonds : bond 0.03677 ( 920) hydrogen bonds : angle 3.27187 ( 2370) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 0.432 Fit side-chains REVERT: A 59 GLU cc_start: 0.8485 (pm20) cc_final: 0.7991 (pm20) REVERT: A 129 ARG cc_start: 0.8718 (tpt90) cc_final: 0.8354 (tpt90) REVERT: B 84 MET cc_start: 0.8635 (mmm) cc_final: 0.8067 (mmm) REVERT: B 91 LYS cc_start: 0.9187 (ttmm) cc_final: 0.8693 (tttt) REVERT: C 72 ASP cc_start: 0.8753 (m-30) cc_final: 0.8496 (m-30) REVERT: D 93 GLU cc_start: 0.8475 (mp0) cc_final: 0.8212 (mp0) REVERT: D 95 GLN cc_start: 0.8692 (tt0) cc_final: 0.8408 (tt0) REVERT: D 113 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8418 (mm-30) REVERT: E 59 GLU cc_start: 0.8177 (pm20) cc_final: 0.7681 (pm20) REVERT: F 24 ASP cc_start: 0.6685 (p0) cc_final: 0.6340 (p0) REVERT: G 90 ASP cc_start: 0.8234 (t0) cc_final: 0.7997 (t0) REVERT: H 33 ARG cc_start: 0.7004 (mmt90) cc_final: 0.6767 (mtt180) REVERT: H 34 LYS cc_start: 0.8091 (tppt) cc_final: 0.7163 (tptm) REVERT: H 42 TYR cc_start: 0.7840 (t80) cc_final: 0.6841 (t80) REVERT: H 101 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8779 (mm) REVERT: H 115 THR cc_start: 0.8996 (m) cc_final: 0.8741 (m) REVERT: K 248 MET cc_start: 0.5809 (mmt) cc_final: 0.5274 (tpt) REVERT: K 326 ARG cc_start: 0.7498 (mmm-85) cc_final: 0.7163 (mmt90) outliers start: 13 outliers final: 5 residues processed: 184 average time/residue: 0.1450 time to fit residues: 37.8672 Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 159 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 27 GLN H 84 ASN ** K 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.120462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.087576 restraints weight = 27917.566| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.00 r_work: 0.3110 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16319 Z= 0.221 Angle : 0.570 6.481 23343 Z= 0.331 Chirality : 0.037 0.142 2687 Planarity : 0.004 0.047 1951 Dihedral : 29.424 146.200 4569 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.55 % Allowed : 11.57 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % 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: 1.89 (0.24), residues: 1193 helix: 2.09 (0.19), residues: 730 sheet: 0.35 (0.55), residues: 95 loop : -0.15 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.033 0.002 TYR K 315 PHE 0.014 0.002 PHE C 25 TRP 0.005 0.001 TRP K 543 HIS 0.005 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00505 (16319) covalent geometry : angle 0.56974 (23343) hydrogen bonds : bond 0.03875 ( 920) hydrogen bonds : angle 3.32411 ( 2370) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.375 Fit side-chains REVERT: A 59 GLU cc_start: 0.8520 (pm20) cc_final: 0.7974 (pm20) REVERT: A 129 ARG cc_start: 0.8759 (tpt90) cc_final: 0.8389 (tpt90) REVERT: B 74 GLU cc_start: 0.8692 (tt0) cc_final: 0.8443 (tt0) REVERT: B 84 MET cc_start: 0.8660 (mmm) cc_final: 0.8378 (mmm) REVERT: B 91 LYS cc_start: 0.9200 (ttmm) cc_final: 0.8716 (tttt) REVERT: C 72 ASP cc_start: 0.8705 (m-30) cc_final: 0.8496 (m-30) REVERT: D 95 GLN cc_start: 0.8726 (tt0) cc_final: 0.8416 (tt0) REVERT: D 113 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8456 (mm-30) REVERT: E 59 GLU cc_start: 0.8184 (pm20) cc_final: 0.7659 (pm20) REVERT: F 24 ASP cc_start: 0.6595 (p0) cc_final: 0.6164 (p0) REVERT: F 25 ASN cc_start: 0.8403 (m110) cc_final: 0.7819 (m110) REVERT: H 33 ARG cc_start: 0.7021 (mmt90) cc_final: 0.6700 (mtt180) REVERT: H 34 LYS cc_start: 0.8083 (tppt) cc_final: 0.7227 (tptm) REVERT: H 42 TYR cc_start: 0.7896 (t80) cc_final: 0.6908 (t80) REVERT: H 101 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8881 (mm) REVERT: H 115 THR cc_start: 0.9029 (m) cc_final: 0.8775 (m) REVERT: K 326 ARG cc_start: 0.7434 (mmm-85) cc_final: 0.7232 (mmt90) outliers start: 15 outliers final: 7 residues processed: 169 average time/residue: 0.1495 time to fit residues: 35.2347 Evaluate side-chains 157 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 129 optimal weight: 0.6980 chunk 101 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 104 GLN K 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.123077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.090374 restraints weight = 27770.577| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.98 r_work: 0.3159 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16319 Z= 0.153 Angle : 0.532 10.426 23343 Z= 0.312 Chirality : 0.035 0.146 2687 Planarity : 0.004 0.042 1951 Dihedral : 29.131 146.472 4569 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.65 % Allowed : 12.09 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.24), residues: 1193 helix: 2.24 (0.19), residues: 735 sheet: 0.33 (0.55), residues: 97 loop : -0.06 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.016 0.001 TYR D 40 PHE 0.010 0.001 PHE A 67 TRP 0.002 0.001 TRP K 182 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00336 (16319) covalent geometry : angle 0.53193 (23343) hydrogen bonds : bond 0.03488 ( 920) hydrogen bonds : angle 3.17718 ( 2370) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 167 time to evaluate : 0.433 Fit side-chains REVERT: A 59 GLU cc_start: 0.8478 (pm20) cc_final: 0.7914 (pm20) REVERT: A 129 ARG cc_start: 0.8670 (tpt90) cc_final: 0.8226 (tpt90) REVERT: B 91 LYS cc_start: 0.9186 (ttmm) cc_final: 0.8684 (tttt) REVERT: C 72 ASP cc_start: 0.8714 (m-30) cc_final: 0.8422 (m-30) REVERT: D 93 GLU cc_start: 0.8528 (mp0) cc_final: 0.8283 (mp0) REVERT: D 95 GLN cc_start: 0.8651 (tt0) cc_final: 0.8367 (tt0) REVERT: D 113 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8421 (mm-30) REVERT: E 59 GLU cc_start: 0.8153 (pm20) cc_final: 0.7517 (pm20) REVERT: E 73 GLU cc_start: 0.8231 (tp30) cc_final: 0.7720 (tp30) REVERT: F 24 ASP cc_start: 0.6682 (p0) cc_final: 0.6476 (p0) REVERT: F 25 ASN cc_start: 0.8510 (m110) cc_final: 0.8058 (m110) REVERT: H 33 ARG cc_start: 0.6900 (mmt90) cc_final: 0.6648 (mtt180) REVERT: H 101 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8840 (mm) REVERT: H 115 THR cc_start: 0.9050 (m) cc_final: 0.8791 (m) REVERT: H 121 TYR cc_start: 0.8474 (t80) cc_final: 0.8219 (t80) REVERT: K 248 MET cc_start: 0.5852 (mmt) cc_final: 0.5400 (tpt) REVERT: K 357 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7400 (mp10) outliers start: 16 outliers final: 8 residues processed: 174 average time/residue: 0.1538 time to fit residues: 37.6671 Evaluate side-chains 167 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 357 GLN Chi-restraints excluded: chain K residue 380 LEU Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN K 357 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.120796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087927 restraints weight = 28173.121| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.89 r_work: 0.3136 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16319 Z= 0.187 Angle : 0.554 10.179 23343 Z= 0.321 Chirality : 0.036 0.168 2687 Planarity : 0.004 0.043 1951 Dihedral : 29.255 146.398 4569 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 12.40 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.24), residues: 1193 helix: 2.25 (0.19), residues: 731 sheet: 0.35 (0.55), residues: 97 loop : -0.08 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 67 TYR 0.015 0.001 TYR D 121 PHE 0.011 0.001 PHE C 25 TRP 0.003 0.001 TRP K 182 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00424 (16319) covalent geometry : angle 0.55425 (23343) hydrogen bonds : bond 0.03625 ( 920) hydrogen bonds : angle 3.20546 ( 2370) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.451 Fit side-chains REVERT: A 59 GLU cc_start: 0.8532 (pm20) cc_final: 0.7955 (pm20) REVERT: A 129 ARG cc_start: 0.8638 (tpt90) cc_final: 0.8204 (tpt90) REVERT: B 84 MET cc_start: 0.8661 (mmm) cc_final: 0.8253 (mmm) REVERT: B 91 LYS cc_start: 0.9212 (ttmm) cc_final: 0.8745 (tttt) REVERT: C 72 ASP cc_start: 0.8710 (m-30) cc_final: 0.8465 (m-30) REVERT: D 95 GLN cc_start: 0.8679 (tt0) cc_final: 0.8381 (tt0) REVERT: D 113 GLU cc_start: 0.8771 (mm-30) cc_final: 0.8382 (mm-30) REVERT: E 59 GLU cc_start: 0.8164 (pm20) cc_final: 0.7589 (pm20) REVERT: F 24 ASP cc_start: 0.6717 (p0) cc_final: 0.6440 (p0) REVERT: F 25 ASN cc_start: 0.8601 (m110) cc_final: 0.8174 (m110) REVERT: F 93 GLN cc_start: 0.8746 (mt0) cc_final: 0.8436 (mt0) REVERT: H 33 ARG cc_start: 0.6973 (mmt90) cc_final: 0.6722 (mtt180) REVERT: H 42 TYR cc_start: 0.7927 (t80) cc_final: 0.6858 (t80) REVERT: H 101 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8878 (mm) REVERT: H 115 THR cc_start: 0.9130 (m) cc_final: 0.8877 (m) REVERT: K 240 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7338 (tm-30) REVERT: K 248 MET cc_start: 0.5778 (mmt) cc_final: 0.5276 (tpt) outliers start: 17 outliers final: 12 residues processed: 168 average time/residue: 0.1522 time to fit residues: 36.0010 Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 142 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 116 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.120306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.087386 restraints weight = 28105.839| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.88 r_work: 0.3126 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16319 Z= 0.199 Angle : 0.562 11.569 23343 Z= 0.324 Chirality : 0.037 0.164 2687 Planarity : 0.004 0.042 1951 Dihedral : 29.321 146.044 4569 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.38 % Allowed : 12.71 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.24), residues: 1193 helix: 2.20 (0.19), residues: 731 sheet: 0.37 (0.56), residues: 97 loop : -0.08 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.019 0.002 TYR K 315 PHE 0.011 0.001 PHE C 25 TRP 0.003 0.001 TRP K 182 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00454 (16319) covalent geometry : angle 0.56242 (23343) hydrogen bonds : bond 0.03678 ( 920) hydrogen bonds : angle 3.25418 ( 2370) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.442 Fit side-chains REVERT: A 59 GLU cc_start: 0.8523 (pm20) cc_final: 0.7935 (pm20) REVERT: A 129 ARG cc_start: 0.8680 (tpt90) cc_final: 0.8313 (tpt90) REVERT: B 84 MET cc_start: 0.8683 (mmm) cc_final: 0.8234 (mmm) REVERT: B 91 LYS cc_start: 0.9215 (ttmm) cc_final: 0.8750 (tttt) REVERT: D 95 GLN cc_start: 0.8750 (tt0) cc_final: 0.8481 (tt0) REVERT: D 113 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8353 (mm-30) REVERT: E 59 GLU cc_start: 0.8229 (pm20) cc_final: 0.7577 (pm20) REVERT: F 24 ASP cc_start: 0.6719 (p0) cc_final: 0.6434 (p0) REVERT: F 25 ASN cc_start: 0.8537 (m110) cc_final: 0.8045 (m110) REVERT: F 93 GLN cc_start: 0.8723 (mt0) cc_final: 0.8402 (mt0) REVERT: G 90 ASP cc_start: 0.8242 (t0) cc_final: 0.8028 (t0) REVERT: H 33 ARG cc_start: 0.7012 (mmt90) cc_final: 0.6741 (mtt180) REVERT: H 42 TYR cc_start: 0.8000 (t80) cc_final: 0.6978 (t80) REVERT: H 101 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8844 (mm) REVERT: H 115 THR cc_start: 0.9136 (m) cc_final: 0.8885 (m) REVERT: K 240 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7352 (tm-30) REVERT: K 248 MET cc_start: 0.5800 (mmt) cc_final: 0.5314 (tpt) REVERT: K 325 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7010 (mp10) outliers start: 23 outliers final: 14 residues processed: 174 average time/residue: 0.1458 time to fit residues: 36.2251 Evaluate side-chains 168 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 152 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 325 GLN Chi-restraints excluded: chain K residue 355 HIS Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain L residue 67 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 46 optimal weight: 0.0170 chunk 50 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 117 optimal weight: 0.8980 chunk 101 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 138 optimal weight: 0.0570 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS C 110 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.124201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091451 restraints weight = 28679.786| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.86 r_work: 0.3211 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3217 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16319 Z= 0.141 Angle : 0.531 12.673 23343 Z= 0.308 Chirality : 0.034 0.159 2687 Planarity : 0.004 0.041 1951 Dihedral : 28.863 145.566 4569 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 13.02 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1193 helix: 2.39 (0.19), residues: 734 sheet: 1.04 (0.60), residues: 83 loop : -0.01 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.015 0.001 TYR H 121 PHE 0.018 0.001 PHE K 367 TRP 0.003 0.001 TRP K 543 HIS 0.003 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00308 (16319) covalent geometry : angle 0.53084 (23343) hydrogen bonds : bond 0.03395 ( 920) hydrogen bonds : angle 3.08945 ( 2370) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.432 Fit side-chains REVERT: A 59 GLU cc_start: 0.8487 (pm20) cc_final: 0.7776 (pm20) REVERT: A 129 ARG cc_start: 0.8561 (tpt90) cc_final: 0.8189 (tpt90) REVERT: B 84 MET cc_start: 0.8477 (mmm) cc_final: 0.8162 (mmm) REVERT: B 91 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8709 (tttt) REVERT: E 53 ARG cc_start: 0.8405 (ttp80) cc_final: 0.8115 (ttm170) REVERT: E 59 GLU cc_start: 0.8153 (pm20) cc_final: 0.7567 (pm20) REVERT: E 73 GLU cc_start: 0.7975 (tp30) cc_final: 0.7446 (mm-30) REVERT: F 24 ASP cc_start: 0.6775 (p0) cc_final: 0.6508 (p0) REVERT: F 25 ASN cc_start: 0.8563 (m110) cc_final: 0.7968 (m110) REVERT: F 93 GLN cc_start: 0.8652 (mt0) cc_final: 0.8280 (mt0) REVERT: H 33 ARG cc_start: 0.7044 (mmt90) cc_final: 0.6799 (mtt180) REVERT: H 42 TYR cc_start: 0.7903 (t80) cc_final: 0.6856 (t80) REVERT: H 115 THR cc_start: 0.9175 (m) cc_final: 0.8927 (m) REVERT: H 121 TYR cc_start: 0.8377 (t80) cc_final: 0.8167 (t80) REVERT: K 240 GLN cc_start: 0.7474 (tm-30) cc_final: 0.6992 (tm-30) REVERT: K 248 MET cc_start: 0.5710 (mmt) cc_final: 0.5239 (tpt) outliers start: 17 outliers final: 12 residues processed: 170 average time/residue: 0.1575 time to fit residues: 37.4934 Evaluate side-chains 162 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 46 optimal weight: 0.1980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 25 ASN C 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.123629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.091060 restraints weight = 27653.076| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.94 r_work: 0.3178 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16319 Z= 0.149 Angle : 0.543 12.576 23343 Z= 0.314 Chirality : 0.035 0.151 2687 Planarity : 0.004 0.041 1951 Dihedral : 28.912 145.402 4569 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.45 % Allowed : 13.74 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.24), residues: 1193 helix: 2.40 (0.19), residues: 734 sheet: 1.13 (0.60), residues: 83 loop : -0.03 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.016 0.001 TYR D 40 PHE 0.016 0.001 PHE K 367 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00329 (16319) covalent geometry : angle 0.54301 (23343) hydrogen bonds : bond 0.03375 ( 920) hydrogen bonds : angle 3.11668 ( 2370) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 161 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8429 (pm20) cc_final: 0.7665 (pm20) REVERT: A 129 ARG cc_start: 0.8626 (tpt90) cc_final: 0.8240 (tpt90) REVERT: B 84 MET cc_start: 0.8553 (mmm) cc_final: 0.8171 (mmm) REVERT: B 91 LYS cc_start: 0.9196 (ttmm) cc_final: 0.8689 (tttt) REVERT: E 59 GLU cc_start: 0.8144 (pm20) cc_final: 0.7526 (pm20) REVERT: E 73 GLU cc_start: 0.8004 (tp30) cc_final: 0.7524 (tp30) REVERT: F 25 ASN cc_start: 0.8521 (m110) cc_final: 0.8024 (m110) REVERT: F 93 GLN cc_start: 0.8656 (mt0) cc_final: 0.8274 (mt0) REVERT: H 33 ARG cc_start: 0.7015 (mmt90) cc_final: 0.6776 (mtt180) REVERT: H 42 TYR cc_start: 0.7874 (t80) cc_final: 0.6836 (t80) REVERT: H 115 THR cc_start: 0.9118 (m) cc_final: 0.8874 (m) REVERT: K 240 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7109 (tm-30) REVERT: K 248 MET cc_start: 0.5712 (mmt) cc_final: 0.5243 (tpt) outliers start: 14 outliers final: 11 residues processed: 167 average time/residue: 0.1545 time to fit residues: 36.4337 Evaluate side-chains 164 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 532 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.9990 chunk 14 optimal weight: 0.0770 chunk 102 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.123279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.090651 restraints weight = 27849.426| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16319 Z= 0.154 Angle : 0.540 12.425 23343 Z= 0.311 Chirality : 0.035 0.174 2687 Planarity : 0.004 0.041 1951 Dihedral : 28.925 144.975 4569 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.55 % Allowed : 13.43 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.24), residues: 1193 helix: 2.36 (0.19), residues: 734 sheet: 0.59 (0.54), residues: 96 loop : -0.11 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 67 TYR 0.017 0.001 TYR D 40 PHE 0.016 0.001 PHE K 367 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00343 (16319) covalent geometry : angle 0.54043 (23343) hydrogen bonds : bond 0.03427 ( 920) hydrogen bonds : angle 3.15085 ( 2370) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2386 Ramachandran restraints generated. 1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 156 time to evaluate : 0.416 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8432 (pm20) cc_final: 0.7663 (pm20) REVERT: A 129 ARG cc_start: 0.8632 (tpt90) cc_final: 0.8243 (tpt90) REVERT: B 25 ASN cc_start: 0.8554 (t0) cc_final: 0.8025 (t0) REVERT: B 84 MET cc_start: 0.8564 (mmm) cc_final: 0.8191 (mmm) REVERT: B 91 LYS cc_start: 0.9198 (ttmm) cc_final: 0.8686 (tttt) REVERT: E 59 GLU cc_start: 0.8123 (pm20) cc_final: 0.7488 (pm20) REVERT: E 73 GLU cc_start: 0.8031 (tp30) cc_final: 0.7596 (tp30) REVERT: F 93 GLN cc_start: 0.8666 (mt0) cc_final: 0.8271 (mt0) REVERT: H 33 ARG cc_start: 0.6998 (mmt90) cc_final: 0.6760 (mtt180) REVERT: H 42 TYR cc_start: 0.7877 (t80) cc_final: 0.6835 (t80) REVERT: H 115 THR cc_start: 0.9127 (m) cc_final: 0.8883 (m) REVERT: K 240 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7150 (tm-30) REVERT: K 248 MET cc_start: 0.5705 (mmt) cc_final: 0.5262 (tpt) outliers start: 15 outliers final: 14 residues processed: 162 average time/residue: 0.1549 time to fit residues: 35.1258 Evaluate side-chains 169 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 532 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 131 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.121900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.088993 restraints weight = 28688.110| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3172 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16319 Z= 0.196 Angle : 0.563 12.385 23343 Z= 0.323 Chirality : 0.037 0.228 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.082 144.552 4569 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.96 % Allowed : 12.50 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.24), residues: 1193 helix: 2.29 (0.19), residues: 731 sheet: 0.42 (0.53), residues: 96 loop : -0.17 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.019 0.001 TYR D 40 PHE 0.019 0.001 PHE A 84 TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd covalent geometry : bond 0.00447 (16319) covalent geometry : angle 0.56307 (23343) hydrogen bonds : bond 0.03658 ( 920) hydrogen bonds : angle 3.23929 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3671.03 seconds wall clock time: 63 minutes 26.62 seconds (3806.62 seconds total)