Starting phenix.real_space_refine on Sat Sep 12 10:24:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k6p_22691/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_2026/7k6p_22691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k6p_22691/09_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-2.2.1-6174/lib/python3.11/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: 2.92, per 1000 atoms: 0.19 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: 1.26 Conformation dependent library (CDL) restraints added in 399.0 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: 2.11 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: 3.95 Time building geometry restraints manager: 1.68 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=" C1' DC J 98 " pdb=" N1 DC J 98 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.43e+01 bond pdb=" C1' DC J 134 " pdb=" N1 DC J 134 " ideal model delta sigma weight residual 1.468 1.547 -0.079 1.40e-02 5.10e+03 3.20e+01 bond pdb=" C1' DC I 12 " pdb=" N1 DC I 12 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.13e+01 bond pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.01e+01 bond pdb=" C1' DC J 46 " pdb=" N1 DC J 46 " ideal model delta sigma weight residual 1.468 1.545 -0.077 1.40e-02 5.10e+03 3.00e+01 ... (remaining 16314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 21814 1.70 - 3.41: 1328 3.41 - 5.11: 180 5.11 - 6.82: 15 6.82 - 8.52: 6 Bond angle restraints: 23343 Sorted by residual: angle pdb=" O5' DA I 137 " pdb=" C5' DA I 137 " pdb=" C4' DA I 137 " ideal model delta sigma weight residual 109.40 113.12 -3.72 8.00e-01 1.56e+00 2.16e+01 angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.59 -2.69 6.00e-01 2.78e+00 2.01e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 23338 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.08: 7403 30.08 - 60.16: 1571 60.16 - 90.24: 56 90.24 - 120.31: 0 120.31 - 150.39: 3 Dihedral angle restraints: 9033 sinusoidal: 5472 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 9030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2259 0.073 - 0.146: 307 0.146 - 0.219: 120 0.219 - 0.292: 0 0.292 - 0.364: 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 -2.73 -2.37 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C2' SAM K 601 " pdb=" C1' SAM K 601 " pdb=" C3' SAM K 601 " pdb=" O2' SAM K 601 " both_signs ideal model delta sigma weight residual False -2.76 -2.54 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" C3' DT J 50 " pdb=" C4' DT J 50 " pdb=" O3' DT J 50 " pdb=" C2' DT J 50 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.16e-01 ... (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: 2.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 16.320 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 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 : 0.008 0.082 16319 Z= 0.592 Angle : 0.879 8.521 23343 Z= 0.677 Chirality : 0.058 0.364 2687 Planarity : 0.006 0.087 1951 Dihedral : 25.067 150.392 6729 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/Z covalent geometry : bond 0.00756 / 0.59 (16319) covalent geometry : angle 0.87930 / 0.68 (23343) hydrogen bonds : bond 0.11333 / 8.04 ( 920) hydrogen bonds : angle 4.79089 / 3.47 ( 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 : 0.684 Fit side-chains revert: symmetry clash REVERT: B 84 MET cc_start: 0.7663 (mmm) cc_final: 0.7448 (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: 0.8378 (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: 0.7090 (mtt180) REVERT: H 34 LYS cc_start: 0.8549 (tppt) cc_final: 0.7881 (tptp) REVERT: H 115 THR cc_start: 0.8982 (m) cc_final: 0.8690 (m) REVERT: K 428 SER cc_start: 0.7424 (m) cc_final: 0.6805 (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: 0.1407 time to fit residues: 36.9715 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 : 0.432 ------------------------------------------------------------------------------- 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: 9.9990 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: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 GLN B 25 ASN 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 325 GLN K 330 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.119065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.085942 restraints weight = 27781.482| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.98 r_work: 0.3078 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 16319 Z= 0.339 Angle : 0.796 9.163 23343 Z= 0.430 Chirality : 0.051 0.280 2687 Planarity : 0.006 0.052 1951 Dihedral : 29.448 148.515 4537 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.85 % Favored : 97.07 % Rotamer: Outliers : 0.93 % Allowed : 7.75 % 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: 1.39 (0.24), residues: 1193 helix: 1.62 (0.19), residues: 718 sheet: 0.26 (0.60), residues: 75 loop : -0.11 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 86 TYR 0.023 0.003 TYR K 315 PHE 0.025 0.002 PHE K 279 TRP 0.006 0.002 TRP K 182 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.34 (16319) covalent geometry : angle 0.79588 / 0.43 (23343) hydrogen bonds : bond 0.05631 / 3.82 ( 920) hydrogen bonds : angle 3.81455 / 2.75 ( 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 163 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 154 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8562 (pm20) cc_final: 0.8137 (pm20) REVERT: B 84 MET cc_start: 0.8542 (mmm) cc_final: 0.7833 (mmm) REVERT: B 91 LYS cc_start: 0.9131 (ttmm) cc_final: 0.8657 (tttt) REVERT: C 72 ASP cc_start: 0.8646 (m-30) cc_final: 0.8379 (m-30) REVERT: D 113 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8483 (mm-30) REVERT: F 24 ASP cc_start: 0.6827 (p0) cc_final: 0.6606 (p0) REVERT: H 33 ARG cc_start: 0.7110 (mmt90) cc_final: 0.6866 (mtt180) REVERT: H 34 LYS cc_start: 0.8174 (tppt) cc_final: 0.7290 (tttp) REVERT: H 42 TYR cc_start: 0.7988 (t80) cc_final: 0.7189 (t80) REVERT: H 101 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8729 (mm) REVERT: H 115 THR cc_start: 0.9062 (m) cc_final: 0.8807 (m) REVERT: H 121 TYR cc_start: 0.8632 (t80) cc_final: 0.8137 (t80) REVERT: K 431 THR cc_start: 0.8436 (m) cc_final: 0.7991 (p) outliers start: 9 outliers final: 7 residues processed: 157 average time/residue: 0.1488 time to fit residues: 33.2735 Evaluate side-chains 152 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 144 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 436 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 73 optimal weight: 20.0000 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 75 HIS F 25 ASN F 75 HIS K 246 ASN K 363 HIS K 521 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.089315 restraints weight = 27990.189| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.97 r_work: 0.3142 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16319 Z= 0.150 Angle : 0.619 7.020 23343 Z= 0.356 Chirality : 0.043 0.312 2687 Planarity : 0.004 0.047 1951 Dihedral : 29.604 150.015 4537 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.03 % Allowed : 9.09 % Favored : 89.88 % 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: 1.84 (0.24), residues: 1193 helix: 2.03 (0.19), residues: 723 sheet: 0.40 (0.58), residues: 85 loop : -0.07 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.017 0.002 TYR H 40 PHE 0.011 0.001 PHE A 67 TRP 0.003 0.001 TRP K 182 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (16319) covalent geometry : angle 0.61859 / 0.36 (23343) hydrogen bonds : bond 0.04378 / 2.98 ( 920) hydrogen bonds : angle 3.46392 / 2.50 ( 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 174 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 164 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8533 (pm20) cc_final: 0.8026 (pm20) REVERT: A 125 GLN cc_start: 0.8700 (OUTLIER) cc_final: 0.8487 (mp10) REVERT: B 79 LYS cc_start: 0.8038 (ttpp) cc_final: 0.7813 (ttpp) REVERT: B 84 MET cc_start: 0.8481 (mmm) cc_final: 0.8199 (mmm) REVERT: B 91 LYS cc_start: 0.9142 (ttmm) cc_final: 0.8674 (tttt) REVERT: C 72 ASP cc_start: 0.8680 (m-30) cc_final: 0.8379 (m-30) REVERT: D 93 GLU cc_start: 0.8455 (mp0) cc_final: 0.8159 (mp0) REVERT: D 95 GLN cc_start: 0.8768 (tt0) cc_final: 0.8434 (tt0) REVERT: D 113 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8329 (mm-30) REVERT: E 59 GLU cc_start: 0.8040 (pm20) cc_final: 0.7482 (pm20) REVERT: E 81 ASP cc_start: 0.8498 (p0) cc_final: 0.8296 (p0) REVERT: H 33 ARG cc_start: 0.6999 (mmt90) cc_final: 0.6738 (mtt180) REVERT: H 42 TYR cc_start: 0.7929 (t80) cc_final: 0.7030 (t80) REVERT: H 101 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8798 (mm) REVERT: H 115 THR cc_start: 0.9011 (m) cc_final: 0.8746 (m) REVERT: H 121 TYR cc_start: 0.8578 (t80) cc_final: 0.8273 (t80) REVERT: K 482 LEU cc_start: 0.7557 (mt) cc_final: 0.7338 (mt) outliers start: 10 outliers final: 5 residues processed: 170 average time/residue: 0.1276 time to fit residues: 31.7831 Evaluate side-chains 154 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 425 ASP 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: 0.7980 chunk 58 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN G 104 GLN H 84 ASN K 357 GLN K 532 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.122200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.089331 restraints weight = 27870.683| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.96 r_work: 0.3145 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16319 Z= 0.151 Angle : 0.595 7.170 23343 Z= 0.344 Chirality : 0.042 0.310 2687 Planarity : 0.004 0.046 1951 Dihedral : 29.560 148.573 4537 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 10.33 % Favored : 87.91 % 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: 2.00 (0.24), residues: 1193 helix: 2.15 (0.19), residues: 723 sheet: 0.49 (0.57), residues: 85 loop : -0.01 (0.31), residues: 385 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 0.001 PHE K 345 TRP 0.006 0.001 TRP K 543 HIS 0.005 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.15 (16319) covalent geometry : angle 0.59498 / 0.34 (23343) hydrogen bonds : bond 0.04200 / 2.85 ( 920) hydrogen bonds : angle 3.37565 / 2.43 ( 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 168 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.446 Fit side-chains REVERT: A 59 GLU cc_start: 0.8536 (pm20) cc_final: 0.7960 (pm20) REVERT: A 129 ARG cc_start: 0.8697 (tpt90) cc_final: 0.8272 (tpt90) REVERT: B 91 LYS cc_start: 0.9155 (ttmm) cc_final: 0.8692 (tttt) REVERT: C 72 ASP cc_start: 0.8728 (m-30) cc_final: 0.8421 (m-30) REVERT: D 95 GLN cc_start: 0.8738 (tt0) cc_final: 0.8437 (tt0) REVERT: D 113 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8520 (mm-30) REVERT: E 59 GLU cc_start: 0.8032 (pm20) cc_final: 0.7580 (pm20) REVERT: E 81 ASP cc_start: 0.8498 (p0) cc_final: 0.8294 (p0) REVERT: F 24 ASP cc_start: 0.6797 (p0) cc_final: 0.6578 (p0) REVERT: F 25 ASN cc_start: 0.8245 (m-40) cc_final: 0.8021 (m110) REVERT: F 88 TYR cc_start: 0.8621 (m-10) cc_final: 0.8384 (m-10) REVERT: H 33 ARG cc_start: 0.6963 (mmt90) cc_final: 0.6697 (mtt180) REVERT: H 34 LYS cc_start: 0.8152 (tppt) cc_final: 0.7179 (tttp) REVERT: H 42 TYR cc_start: 0.7923 (t80) cc_final: 0.6957 (t80) REVERT: H 101 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8796 (mm) REVERT: H 115 THR cc_start: 0.9016 (m) cc_final: 0.8754 (m) outliers start: 17 outliers final: 8 residues processed: 162 average time/residue: 0.1322 time to fit residues: 30.8189 Evaluate side-chains 151 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 G residue 92 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 52 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 121 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 129 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN B 27 GLN E 113 HIS G 38 ASN K 357 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.121954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.088851 restraints weight = 28588.189| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3172 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16319 Z= 0.157 Angle : 0.591 6.709 23343 Z= 0.340 Chirality : 0.042 0.313 2687 Planarity : 0.004 0.043 1951 Dihedral : 29.618 147.345 4537 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.65 % Allowed : 11.26 % Favored : 87.09 % 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: 2.00 (0.24), residues: 1193 helix: 2.14 (0.19), residues: 730 sheet: 0.46 (0.57), residues: 85 loop : -0.04 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.016 0.001 TYR H 121 PHE 0.011 0.001 PHE A 67 TRP 0.004 0.001 TRP K 543 HIS 0.005 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.16 (16319) covalent geometry : angle 0.59067 / 0.34 (23343) hydrogen bonds : bond 0.04120 / 2.81 ( 920) hydrogen bonds : angle 3.34227 / 2.41 ( 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 170 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 0.438 Fit side-chains REVERT: A 59 GLU cc_start: 0.8549 (pm20) cc_final: 0.8000 (pm20) REVERT: A 129 ARG cc_start: 0.8617 (tpt90) cc_final: 0.8208 (tpt90) REVERT: B 91 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8749 (tttt) REVERT: C 72 ASP cc_start: 0.8760 (m-30) cc_final: 0.8470 (m-30) REVERT: D 93 GLU cc_start: 0.8397 (mp0) cc_final: 0.8099 (mp0) REVERT: D 95 GLN cc_start: 0.8730 (tt0) cc_final: 0.8438 (tt0) REVERT: E 59 GLU cc_start: 0.8071 (pm20) cc_final: 0.7555 (pm20) REVERT: F 24 ASP cc_start: 0.6786 (p0) cc_final: 0.6504 (p0) REVERT: H 33 ARG cc_start: 0.7008 (mmt90) cc_final: 0.6742 (mtt180) REVERT: H 34 LYS cc_start: 0.8229 (tppt) cc_final: 0.7300 (tttp) REVERT: H 42 TYR cc_start: 0.7948 (t80) cc_final: 0.6996 (t80) REVERT: H 101 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8850 (mm) REVERT: H 115 THR cc_start: 0.9086 (m) cc_final: 0.8832 (m) REVERT: K 388 GLN cc_start: 0.8387 (tm-30) cc_final: 0.8018 (tm-30) outliers start: 16 outliers final: 11 residues processed: 163 average time/residue: 0.1291 time to fit residues: 30.4975 Evaluate side-chains 153 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 49 LEU 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 K residue 425 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain K residue 522 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 16 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.122335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089190 restraints weight = 28499.797| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3176 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (17 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16319 Z= 0.150 Angle : 0.591 8.237 23343 Z= 0.339 Chirality : 0.042 0.312 2687 Planarity : 0.004 0.043 1951 Dihedral : 29.631 146.674 4537 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.76 % Allowed : 11.98 % 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: 1.94 (0.24), residues: 1193 helix: 2.13 (0.19), residues: 730 sheet: 0.35 (0.55), residues: 95 loop : -0.13 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.020 0.001 TYR H 121 PHE 0.016 0.001 PHE K 345 TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (16319) covalent geometry : angle 0.59097 / 0.34 (23343) hydrogen bonds : bond 0.04045 / 2.76 ( 920) hydrogen bonds : angle 3.32365 / 2.39 ( 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 175 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.408 Fit side-chains REVERT: A 59 GLU cc_start: 0.8534 (pm20) cc_final: 0.7967 (pm20) REVERT: A 129 ARG cc_start: 0.8614 (tpt90) cc_final: 0.8203 (tpt90) REVERT: B 84 MET cc_start: 0.8481 (mmm) cc_final: 0.8185 (mmm) REVERT: B 91 LYS cc_start: 0.9183 (ttmm) cc_final: 0.8726 (tttt) REVERT: C 72 ASP cc_start: 0.8743 (m-30) cc_final: 0.8441 (m-30) REVERT: D 95 GLN cc_start: 0.8729 (tt0) cc_final: 0.8437 (tt0) REVERT: D 113 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8130 (mm-30) REVERT: E 59 GLU cc_start: 0.8089 (pm20) cc_final: 0.7499 (pm20) REVERT: E 73 GLU cc_start: 0.8200 (tp30) cc_final: 0.7760 (tp30) REVERT: H 33 ARG cc_start: 0.7009 (mmt90) cc_final: 0.6744 (mtt180) REVERT: H 34 LYS cc_start: 0.8299 (tppt) cc_final: 0.7338 (tttp) REVERT: H 42 TYR cc_start: 0.7933 (t80) cc_final: 0.6960 (t80) REVERT: H 101 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8841 (mm) REVERT: H 115 THR cc_start: 0.9092 (m) cc_final: 0.8837 (m) REVERT: K 388 GLN cc_start: 0.8414 (tm-30) cc_final: 0.8062 (tm-30) outliers start: 17 outliers final: 13 residues processed: 167 average time/residue: 0.1356 time to fit residues: 32.3452 Evaluate side-chains 162 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR 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 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 K residue 425 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Chi-restraints excluded: chain K residue 522 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 100 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 142 optimal weight: 0.0370 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 0.1980 chunk 127 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.5980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS G 38 ASN L 49 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 = 0.122936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.090480 restraints weight = 27951.667| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.86 r_work: 0.3185 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 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 = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16319 Z= 0.129 Angle : 0.569 8.830 23343 Z= 0.330 Chirality : 0.041 0.308 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.516 146.315 4537 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.34 % Allowed : 12.40 % 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: 2.10 (0.24), residues: 1193 helix: 2.25 (0.19), residues: 732 sheet: 0.39 (0.55), residues: 97 loop : -0.05 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 86 TYR 0.024 0.001 TYR D 121 PHE 0.014 0.001 PHE K 345 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (16319) covalent geometry : angle 0.56944 / 0.33 (23343) hydrogen bonds : bond 0.03920 / 2.68 ( 920) hydrogen bonds : angle 3.23974 / 2.34 ( 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 177 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 0.426 Fit side-chains REVERT: A 59 GLU cc_start: 0.8516 (pm20) cc_final: 0.7921 (pm20) REVERT: A 129 ARG cc_start: 0.8574 (tpt90) cc_final: 0.8150 (tpt90) REVERT: B 91 LYS cc_start: 0.9174 (ttmm) cc_final: 0.8701 (tttt) REVERT: C 72 ASP cc_start: 0.8723 (m-30) cc_final: 0.8389 (m-30) REVERT: D 93 GLU cc_start: 0.8377 (mp0) cc_final: 0.8153 (mp0) REVERT: D 95 GLN cc_start: 0.8666 (tt0) cc_final: 0.8370 (tt0) REVERT: D 113 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8441 (mm-30) REVERT: E 59 GLU cc_start: 0.8094 (pm20) cc_final: 0.7631 (pm20) REVERT: E 73 GLU cc_start: 0.8071 (tp30) cc_final: 0.7648 (tp30) REVERT: H 33 ARG cc_start: 0.7044 (mmt90) cc_final: 0.6767 (mtt180) REVERT: H 34 LYS cc_start: 0.8270 (tppt) cc_final: 0.7270 (tptm) REVERT: H 101 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8893 (mm) REVERT: H 115 THR cc_start: 0.9081 (m) cc_final: 0.8826 (m) REVERT: K 388 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8080 (tm-30) outliers start: 13 outliers final: 8 residues processed: 171 average time/residue: 0.1330 time to fit residues: 32.4538 Evaluate side-chains 157 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR 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 27 VAL Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 93 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 103 optimal weight: 0.1980 chunk 117 optimal weight: 0.6980 chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 138 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 25 ASN G 38 ASN 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 = 0.122867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.090150 restraints weight = 28336.200| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.89 r_work: 0.3177 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2274 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= 0.138 Angle : 0.586 11.898 23343 Z= 0.334 Chirality : 0.041 0.301 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.524 145.748 4537 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.76 % Allowed : 11.98 % 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: 2.07 (0.24), residues: 1193 helix: 2.20 (0.19), residues: 732 sheet: 0.69 (0.56), residues: 93 loop : -0.09 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.018 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (16319) covalent geometry : angle 0.58560 / 0.33 (23343) hydrogen bonds : bond 0.03960 / 2.70 ( 920) hydrogen bonds : angle 3.24543 / 2.34 ( 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 173 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.424 Fit side-chains REVERT: A 59 GLU cc_start: 0.8552 (pm20) cc_final: 0.7945 (pm20) REVERT: A 129 ARG cc_start: 0.8564 (tpt90) cc_final: 0.8185 (tpt90) REVERT: B 84 MET cc_start: 0.8494 (mmm) cc_final: 0.8161 (mmm) REVERT: B 91 LYS cc_start: 0.9180 (ttmm) cc_final: 0.8706 (tttt) REVERT: C 72 ASP cc_start: 0.8726 (m-30) cc_final: 0.8400 (m-30) REVERT: D 95 GLN cc_start: 0.8657 (tt0) cc_final: 0.8378 (tt0) REVERT: D 113 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8449 (mm-30) REVERT: E 59 GLU cc_start: 0.8121 (pm20) cc_final: 0.7640 (pm20) REVERT: E 73 GLU cc_start: 0.8106 (tp30) cc_final: 0.7683 (tp30) REVERT: F 71 THR cc_start: 0.8572 (OUTLIER) cc_final: 0.8355 (p) REVERT: F 93 GLN cc_start: 0.8663 (mt0) cc_final: 0.8267 (mt0) REVERT: H 33 ARG cc_start: 0.7065 (mmt90) cc_final: 0.6787 (mtt180) REVERT: H 34 LYS cc_start: 0.8250 (tppt) cc_final: 0.7274 (tptm) REVERT: H 42 TYR cc_start: 0.7928 (t80) cc_final: 0.6990 (t80) REVERT: H 115 THR cc_start: 0.9092 (m) cc_final: 0.8831 (m) REVERT: H 121 TYR cc_start: 0.8418 (t80) cc_final: 0.8183 (t80) REVERT: K 388 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8122 (tm-30) outliers start: 17 outliers final: 12 residues processed: 164 average time/residue: 0.1343 time to fit residues: 31.3864 Evaluate side-chains 162 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 149 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR 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 71 THR 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 K residue 425 ASP Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.122396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.089874 restraints weight = 28047.434| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.86 r_work: 0.3175 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16319 Z= 0.143 Angle : 0.585 13.693 23343 Z= 0.333 Chirality : 0.041 0.299 2687 Planarity : 0.004 0.040 1951 Dihedral : 29.548 145.609 4537 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.34 % Allowed : 12.60 % Favored : 86.05 % 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: 2.20 (0.19), residues: 732 sheet: 0.77 (0.56), residues: 93 loop : -0.09 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.019 0.001 TYR D 40 PHE 0.010 0.001 PHE A 67 TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (16319) covalent geometry : angle 0.58512 / 0.33 (23343) hydrogen bonds : bond 0.03926 / 2.68 ( 920) hydrogen bonds : angle 3.26771 / 2.36 ( 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 171 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 158 time to evaluate : 0.415 Fit side-chains REVERT: A 59 GLU cc_start: 0.8544 (pm20) cc_final: 0.7928 (pm20) REVERT: A 129 ARG cc_start: 0.8579 (tpt90) cc_final: 0.8202 (tpt90) REVERT: B 84 MET cc_start: 0.8547 (mmm) cc_final: 0.8163 (mmm) REVERT: B 91 LYS cc_start: 0.9173 (ttmm) cc_final: 0.8698 (tttt) REVERT: C 72 ASP cc_start: 0.8720 (m-30) cc_final: 0.8395 (m-30) REVERT: D 93 GLU cc_start: 0.8437 (mp0) cc_final: 0.8233 (mp0) REVERT: D 113 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8423 (mm-30) REVERT: E 59 GLU cc_start: 0.8128 (pm20) cc_final: 0.7574 (pm20) REVERT: E 73 GLU cc_start: 0.8115 (tp30) cc_final: 0.7687 (tp30) REVERT: F 93 GLN cc_start: 0.8666 (mt0) cc_final: 0.8246 (mt0) REVERT: H 33 ARG cc_start: 0.7066 (mmt90) cc_final: 0.6822 (mtt180) REVERT: H 34 LYS cc_start: 0.8250 (tppt) cc_final: 0.7285 (tptm) REVERT: H 42 TYR cc_start: 0.7902 (t80) cc_final: 0.6967 (t80) REVERT: H 115 THR cc_start: 0.9131 (m) cc_final: 0.8877 (m) REVERT: H 121 TYR cc_start: 0.8424 (t80) cc_final: 0.8189 (t80) REVERT: K 326 ARG cc_start: 0.7481 (mmm-85) cc_final: 0.7235 (mmt90) REVERT: K 388 GLN cc_start: 0.8508 (tm-30) cc_final: 0.8124 (tm-30) outliers start: 13 outliers final: 10 residues processed: 165 average time/residue: 0.1377 time to fit residues: 32.2266 Evaluate side-chains 164 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 154 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 107 optimal weight: 0.0370 chunk 14 optimal weight: 0.7980 chunk 102 optimal weight: 0.0270 chunk 8 optimal weight: 0.4980 chunk 55 optimal weight: 0.9980 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.123901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.091754 restraints weight = 28300.293| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.86 r_work: 0.3203 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16319 Z= 0.126 Angle : 0.575 14.529 23343 Z= 0.329 Chirality : 0.041 0.291 2687 Planarity : 0.004 0.040 1951 Dihedral : 29.441 145.985 4537 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.83 % Allowed : 13.43 % Favored : 85.74 % 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: 2.13 (0.24), residues: 1193 helix: 2.25 (0.19), residues: 732 sheet: 0.63 (0.54), residues: 96 loop : -0.07 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.019 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.13 (16319) covalent geometry : angle 0.57482 / 0.33 (23343) hydrogen bonds : bond 0.03816 / 2.60 ( 920) hydrogen bonds : angle 3.25331 / 2.35 ( 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 166 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.448 Fit side-chains REVERT: A 59 GLU cc_start: 0.8524 (pm20) cc_final: 0.7895 (pm20) REVERT: A 129 ARG cc_start: 0.8558 (tpt90) cc_final: 0.8186 (tpt90) REVERT: B 84 MET cc_start: 0.8519 (mmm) cc_final: 0.8158 (mmm) REVERT: B 91 LYS cc_start: 0.9162 (ttmm) cc_final: 0.8688 (tttt) REVERT: C 72 ASP cc_start: 0.8724 (m-30) cc_final: 0.8382 (m-30) REVERT: D 85 LYS cc_start: 0.8929 (mttp) cc_final: 0.8233 (mmtt) REVERT: D 93 GLU cc_start: 0.8421 (mp0) cc_final: 0.8198 (mp0) REVERT: D 113 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8393 (mm-30) REVERT: E 59 GLU cc_start: 0.8124 (pm20) cc_final: 0.7597 (pm20) REVERT: E 73 GLU cc_start: 0.8073 (tp30) cc_final: 0.7650 (tp30) REVERT: F 24 ASP cc_start: 0.6722 (p0) cc_final: 0.6511 (p0) REVERT: F 25 ASN cc_start: 0.8330 (m-40) cc_final: 0.8009 (m110) REVERT: F 93 GLN cc_start: 0.8652 (mt0) cc_final: 0.8246 (mt0) REVERT: H 33 ARG cc_start: 0.7089 (mmt90) cc_final: 0.6806 (mtt180) REVERT: H 42 TYR cc_start: 0.7882 (t80) cc_final: 0.6962 (t80) REVERT: H 115 THR cc_start: 0.9110 (m) cc_final: 0.8853 (m) REVERT: K 388 GLN cc_start: 0.8461 (tm-30) cc_final: 0.8112 (tm-30) outliers start: 8 outliers final: 6 residues processed: 162 average time/residue: 0.1383 time to fit residues: 31.7646 Evaluate side-chains 156 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 478 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 26 optimal weight: 0.3980 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.0980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 104 GLN G 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.121631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089208 restraints weight = 28075.347| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.85 r_work: 0.3157 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 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 = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16319 Z= 0.171 Angle : 0.610 13.565 23343 Z= 0.342 Chirality : 0.042 0.286 2687 Planarity : 0.004 0.042 1951 Dihedral : 29.610 145.201 4537 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.24 % Allowed : 13.02 % Favored : 85.74 % 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: 2.02 (0.24), residues: 1193 helix: 2.18 (0.19), residues: 732 sheet: 0.61 (0.54), residues: 96 loop : -0.15 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.023 0.002 TYR H 121 PHE 0.013 0.001 PHE C 25 TRP 0.003 0.001 TRP K 182 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (16319) covalent geometry : angle 0.60963 / 0.34 (23343) hydrogen bonds : bond 0.04106 / 2.80 ( 920) hydrogen bonds : angle 3.32243 / 2.40 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3430.78 seconds wall clock time: 59 minutes 27.51 seconds (3567.51 seconds total)