Starting phenix.real_space_refine on Fri Jul 3 17:20:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k6p_22691/07_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_22691/07_2026/7k6p_22691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k6p_22691/07_2026/7k6p_22691.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 1.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 32 5.16 5 C 8834 2.51 5 N 2828 2.21 5 O 3461 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 3.10, per 1000 atoms: 0.20 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: 1.32 Conformation dependent library (CDL) restraints added in 448.2 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: 1.81 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: 3.28 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: 21828 1.70 - 3.41: 1314 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: 2.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.910 Find NCS groups from input model: 0.180 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.000 ------------------------------------------------------------------------------- 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= 0.589 Angle : 0.874 8.521 23343 Z= 0.672 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 0.87443 / 0.67 (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 : 0.428 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: 0.8379 (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: 0.7089 (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: 0.1480 time to fit residues: 38.5720 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 : 0.390 ------------------------------------------------------------------------------- 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: 9.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 82 HIS ** K 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 GLN K 330 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.118865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085721 restraints weight = 27802.522| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.03 r_work: 0.3075 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 16319 Z= 0.339 Angle : 0.771 8.808 23343 Z= 0.423 Chirality : 0.050 0.262 2687 Planarity : 0.005 0.052 1951 Dihedral : 29.650 149.684 4537 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.70 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: 1.37 (0.24), residues: 1193 helix: 1.59 (0.19), residues: 718 sheet: 0.27 (0.60), residues: 75 loop : -0.11 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.040 0.003 TYR K 315 PHE 0.026 0.002 PHE K 279 TRP 0.006 0.001 TRP K 182 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00734 / 0.34 (16319) covalent geometry : angle 0.77097 / 0.42 (23343) hydrogen bonds : bond 0.05656 / 3.83 ( 920) hydrogen bonds : angle 3.80670 / 2.74 ( 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 161 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8565 (pm20) cc_final: 0.8137 (pm20) REVERT: B 84 MET cc_start: 0.8554 (mmm) cc_final: 0.7843 (mmm) REVERT: B 91 LYS cc_start: 0.9134 (ttmm) cc_final: 0.8662 (tttt) REVERT: C 72 ASP cc_start: 0.8665 (m-30) cc_final: 0.8420 (m-30) REVERT: D 113 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8508 (mm-30) REVERT: E 59 GLU cc_start: 0.7984 (pm20) cc_final: 0.7733 (pm20) REVERT: F 24 ASP cc_start: 0.6831 (p0) cc_final: 0.6614 (p0) REVERT: H 33 ARG cc_start: 0.7079 (mmt90) cc_final: 0.6831 (mtt180) REVERT: H 34 LYS cc_start: 0.8174 (tppt) cc_final: 0.7287 (tttp) REVERT: H 101 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8781 (mm) REVERT: H 121 TYR cc_start: 0.8615 (t80) cc_final: 0.8131 (t80) REVERT: K 431 THR cc_start: 0.8484 (m) cc_final: 0.8053 (p) REVERT: K 556 MET cc_start: 0.6683 (mmt) cc_final: 0.6467 (mmm) outliers start: 9 outliers final: 6 residues processed: 156 average time/residue: 0.1334 time to fit residues: 29.6951 Evaluate side-chains 150 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 143 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 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: 0.6980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 105 optimal weight: 8.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 357 GLN K 363 HIS K 521 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.122073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089247 restraints weight = 27993.398| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.95 r_work: 0.3141 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 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: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16319 Z= 0.150 Angle : 0.607 6.859 23343 Z= 0.353 Chirality : 0.043 0.299 2687 Planarity : 0.004 0.046 1951 Dihedral : 29.695 150.310 4537 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 1.03 % Allowed : 8.99 % Favored : 89.98 % 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: 1.81 (0.24), residues: 1193 helix: 1.99 (0.19), residues: 723 sheet: 0.36 (0.58), residues: 85 loop : -0.05 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.022 0.002 TYR K 315 PHE 0.011 0.001 PHE A 67 TRP 0.005 0.001 TRP K 543 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.15 (16319) covalent geometry : angle 0.60679 / 0.35 (23343) hydrogen bonds : bond 0.04386 / 2.98 ( 920) hydrogen bonds : angle 3.47044 / 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 175 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8532 (pm20) cc_final: 0.8025 (pm20) REVERT: A 125 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8482 (mp10) REVERT: B 84 MET cc_start: 0.8479 (mmm) cc_final: 0.8195 (mmm) REVERT: B 91 LYS cc_start: 0.9145 (ttmm) cc_final: 0.8678 (tttt) REVERT: C 72 ASP cc_start: 0.8677 (m-30) cc_final: 0.8405 (m-30) REVERT: D 93 GLU cc_start: 0.8440 (mp0) cc_final: 0.8143 (mp0) REVERT: D 95 GLN cc_start: 0.8763 (tt0) cc_final: 0.8440 (tt0) REVERT: D 113 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8330 (mm-30) REVERT: E 59 GLU cc_start: 0.8122 (pm20) cc_final: 0.7709 (pm20) REVERT: E 81 ASP cc_start: 0.8491 (p0) cc_final: 0.8289 (p0) REVERT: H 33 ARG cc_start: 0.6983 (mmt90) cc_final: 0.6738 (mtt180) REVERT: H 42 TYR cc_start: 0.7921 (t80) cc_final: 0.7035 (t80) REVERT: H 101 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8829 (mm) REVERT: H 115 THR cc_start: 0.9012 (m) cc_final: 0.8748 (m) REVERT: H 121 TYR cc_start: 0.8567 (t80) cc_final: 0.8249 (t80) REVERT: K 248 MET cc_start: 0.5867 (mmt) cc_final: 0.4890 (mmt) REVERT: K 388 GLN cc_start: 0.8438 (tm-30) cc_final: 0.7626 (tm-30) outliers start: 10 outliers final: 4 residues processed: 171 average time/residue: 0.1296 time to fit residues: 32.3291 Evaluate side-chains 152 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 146 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 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: 0.9980 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: 8.9990 chunk 50 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 80 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN G 104 GLN H 84 ASN K 357 GLN K 532 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.121634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088786 restraints weight = 27921.638| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.96 r_work: 0.3134 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 16319 Z= 0.160 Angle : 0.589 7.314 23343 Z= 0.343 Chirality : 0.042 0.298 2687 Planarity : 0.004 0.046 1951 Dihedral : 29.690 149.377 4537 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.86 % Allowed : 10.23 % 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: 1.96 (0.24), residues: 1193 helix: 2.08 (0.19), residues: 724 sheet: 0.47 (0.58), residues: 85 loop : 0.04 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.034 0.002 TYR K 315 PHE 0.011 0.001 PHE C 25 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 0.00317 / 0.16 (16319) covalent geometry : angle 0.58886 / 0.34 (23343) hydrogen bonds : bond 0.04244 / 2.89 ( 920) hydrogen bonds : angle 3.38813 / 2.44 ( 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 171 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.511 Fit side-chains REVERT: A 59 GLU cc_start: 0.8540 (pm20) cc_final: 0.7974 (pm20) REVERT: A 129 ARG cc_start: 0.8704 (tpt90) cc_final: 0.8272 (tpt90) REVERT: B 91 LYS cc_start: 0.9135 (ttmm) cc_final: 0.8677 (tttt) REVERT: C 72 ASP cc_start: 0.8725 (m-30) cc_final: 0.8410 (m-30) REVERT: D 95 GLN cc_start: 0.8755 (tt0) cc_final: 0.8463 (tt0) REVERT: D 113 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8520 (mm-30) REVERT: E 59 GLU cc_start: 0.8133 (pm20) cc_final: 0.7756 (pm20) REVERT: F 24 ASP cc_start: 0.6802 (p0) cc_final: 0.6547 (p0) REVERT: F 25 ASN cc_start: 0.8277 (m-40) cc_final: 0.8053 (m110) REVERT: H 33 ARG cc_start: 0.6993 (mmt90) cc_final: 0.6723 (mtt180) REVERT: H 42 TYR cc_start: 0.7940 (t80) cc_final: 0.7014 (t80) REVERT: H 101 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8829 (mm) REVERT: H 115 THR cc_start: 0.9027 (m) cc_final: 0.8765 (m) outliers start: 18 outliers final: 11 residues processed: 164 average time/residue: 0.1275 time to fit residues: 30.1624 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 : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE 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 59 THR 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 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: 0.5980 chunk 17 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.121196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.088005 restraints weight = 28566.094| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 1.87 r_work: 0.3159 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16319 Z= 0.171 Angle : 0.593 7.386 23343 Z= 0.342 Chirality : 0.042 0.304 2687 Planarity : 0.004 0.043 1951 Dihedral : 29.771 148.003 4537 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.76 % Allowed : 11.26 % Favored : 86.98 % 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: 1.91 (0.24), residues: 1193 helix: 2.06 (0.19), residues: 730 sheet: 0.43 (0.57), residues: 85 loop : -0.04 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.019 0.002 TYR K 315 PHE 0.013 0.001 PHE K 345 TRP 0.003 0.001 TRP K 182 HIS 0.005 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (16319) covalent geometry : angle 0.59295 / 0.34 (23343) hydrogen bonds : bond 0.04204 / 2.86 ( 920) hydrogen bonds : angle 3.36613 / 2.43 ( 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 175 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 158 time to evaluate : 0.382 Fit side-chains REVERT: A 59 GLU cc_start: 0.8549 (pm20) cc_final: 0.8003 (pm20) REVERT: A 129 ARG cc_start: 0.8619 (tpt90) cc_final: 0.8214 (tpt90) REVERT: B 84 MET cc_start: 0.8488 (mmm) cc_final: 0.8194 (mmm) REVERT: B 91 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8732 (tttt) REVERT: C 72 ASP cc_start: 0.8727 (m-30) cc_final: 0.8445 (m-30) REVERT: D 95 GLN cc_start: 0.8750 (tt0) cc_final: 0.8459 (tt0) REVERT: E 59 GLU cc_start: 0.8189 (pm20) cc_final: 0.7737 (pm20) REVERT: F 24 ASP cc_start: 0.6786 (p0) cc_final: 0.6329 (p0) REVERT: H 33 ARG cc_start: 0.7020 (mmt90) cc_final: 0.6746 (mtt180) REVERT: H 42 TYR cc_start: 0.7993 (t80) cc_final: 0.7059 (t80) REVERT: H 101 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8853 (mm) REVERT: H 115 THR cc_start: 0.9087 (m) cc_final: 0.8834 (m) REVERT: K 326 ARG cc_start: 0.7537 (mmm-85) cc_final: 0.7194 (mmt90) REVERT: K 388 GLN cc_start: 0.8394 (tm-30) cc_final: 0.8026 (tm-30) outliers start: 17 outliers final: 12 residues processed: 167 average time/residue: 0.1200 time to fit residues: 28.9186 Evaluate side-chains 161 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 59 THR 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: 0.6980 chunk 76 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.122123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.088969 restraints weight = 28411.072| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.86 r_work: 0.3173 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16319 Z= 0.148 Angle : 0.582 9.036 23343 Z= 0.336 Chirality : 0.041 0.305 2687 Planarity : 0.004 0.042 1951 Dihedral : 29.755 147.487 4537 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.86 % Allowed : 12.09 % 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: 1.90 (0.24), residues: 1193 helix: 2.09 (0.19), residues: 730 sheet: 0.34 (0.55), residues: 95 loop : -0.13 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.034 0.001 TYR K 315 PHE 0.011 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 0.00281 / 0.15 (16319) covalent geometry : angle 0.58162 / 0.34 (23343) hydrogen bonds : bond 0.04042 / 2.75 ( 920) hydrogen bonds : angle 3.31867 / 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 177 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.444 Fit side-chains REVERT: A 59 GLU cc_start: 0.8516 (pm20) cc_final: 0.7986 (pm20) REVERT: A 129 ARG cc_start: 0.8601 (tpt90) cc_final: 0.8226 (tpt90) REVERT: B 91 LYS cc_start: 0.9160 (ttmm) cc_final: 0.8704 (tttt) REVERT: C 72 ASP cc_start: 0.8731 (m-30) cc_final: 0.8452 (m-30) REVERT: D 93 GLU cc_start: 0.8359 (mp0) cc_final: 0.8099 (mp0) REVERT: D 95 GLN cc_start: 0.8739 (tt0) cc_final: 0.8415 (tt0) REVERT: D 113 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8138 (mm-30) REVERT: E 59 GLU cc_start: 0.8192 (pm20) cc_final: 0.7727 (pm20) REVERT: E 73 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7597 (mm-30) REVERT: F 25 ASN cc_start: 0.8273 (m-40) cc_final: 0.7816 (m110) REVERT: H 33 ARG cc_start: 0.7014 (mmt90) cc_final: 0.6741 (mtt180) REVERT: H 34 LYS cc_start: 0.8244 (tppt) cc_final: 0.7310 (tttp) REVERT: H 42 TYR cc_start: 0.7968 (t80) cc_final: 0.7012 (t80) REVERT: H 101 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8847 (mm) REVERT: H 115 THR cc_start: 0.9090 (m) cc_final: 0.8845 (m) outliers start: 18 outliers final: 14 residues processed: 170 average time/residue: 0.1368 time to fit residues: 33.2444 Evaluate side-chains 164 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.406 ------------------------------------------------------------------------------- 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 73 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 59 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 444 LEU 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: 10.0000 chunk 12 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 116 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 113 HIS K 388 GLN L 49 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.122093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.089337 restraints weight = 28090.903| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.88 r_work: 0.3166 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16319 Z= 0.140 Angle : 0.574 11.116 23343 Z= 0.333 Chirality : 0.041 0.302 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.696 146.955 4537 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 11.78 % 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: 1.99 (0.24), residues: 1193 helix: 2.16 (0.19), residues: 733 sheet: 0.37 (0.55), residues: 95 loop : -0.09 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 67 TYR 0.024 0.001 TYR D 121 PHE 0.011 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 0.00261 / 0.14 (16319) covalent geometry : angle 0.57443 / 0.33 (23343) hydrogen bonds : bond 0.03980 / 2.72 ( 920) hydrogen bonds : angle 3.26661 / 2.36 ( 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 182 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.422 Fit side-chains REVERT: A 59 GLU cc_start: 0.8535 (pm20) cc_final: 0.7945 (pm20) REVERT: A 129 ARG cc_start: 0.8582 (tpt90) cc_final: 0.8197 (tpt90) REVERT: B 84 MET cc_start: 0.8496 (mmm) cc_final: 0.8178 (mmm) REVERT: B 91 LYS cc_start: 0.9164 (ttmm) cc_final: 0.8711 (tttt) REVERT: C 72 ASP cc_start: 0.8709 (m-30) cc_final: 0.8398 (m-30) REVERT: D 95 GLN cc_start: 0.8694 (tt0) cc_final: 0.8394 (tt0) REVERT: D 113 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8468 (mm-30) REVERT: E 59 GLU cc_start: 0.8177 (pm20) cc_final: 0.7749 (pm20) REVERT: E 73 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7507 (mm-30) REVERT: F 24 ASP cc_start: 0.6642 (p0) cc_final: 0.6416 (p0) REVERT: F 25 ASN cc_start: 0.8379 (m-40) cc_final: 0.7964 (m110) REVERT: H 33 ARG cc_start: 0.7074 (mmt90) cc_final: 0.6791 (mtt180) REVERT: H 34 LYS cc_start: 0.8269 (tppt) cc_final: 0.7337 (tttp) REVERT: H 42 TYR cc_start: 0.7927 (t80) cc_final: 0.7000 (t80) REVERT: H 115 THR cc_start: 0.9089 (m) cc_final: 0.8842 (m) REVERT: K 326 ARG cc_start: 0.7518 (mmm-85) cc_final: 0.7242 (mmt90) outliers start: 21 outliers final: 12 residues processed: 173 average time/residue: 0.1356 time to fit residues: 33.2063 Evaluate side-chains 164 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 502 CYS 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: 4.9990 chunk 87 optimal weight: 20.0000 chunk 46 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 117 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 6.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 388 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.121846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.089093 restraints weight = 28263.547| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 1.89 r_work: 0.3161 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (22 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16319 Z= 0.149 Angle : 0.588 12.906 23343 Z= 0.336 Chirality : 0.041 0.299 2687 Planarity : 0.004 0.054 1951 Dihedral : 29.709 146.573 4537 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.86 % Allowed : 12.40 % 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: 1.97 (0.24), residues: 1193 helix: 2.15 (0.19), residues: 733 sheet: 0.39 (0.55), residues: 95 loop : -0.13 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 20 TYR 0.018 0.001 TYR D 40 PHE 0.011 0.001 PHE A 67 TRP 0.007 0.001 TRP K 543 HIS 0.004 0.001 HIS K 545 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (16319) covalent geometry : angle 0.58765 / 0.34 (23343) hydrogen bonds : bond 0.04000 / 2.73 ( 920) hydrogen bonds : angle 3.27380 / 2.36 ( 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 176 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 158 time to evaluate : 0.425 Fit side-chains REVERT: A 59 GLU cc_start: 0.8542 (pm20) cc_final: 0.7940 (pm20) REVERT: A 129 ARG cc_start: 0.8585 (tpt90) cc_final: 0.8191 (tpt90) REVERT: B 91 LYS cc_start: 0.9165 (ttmm) cc_final: 0.8710 (tttt) REVERT: C 72 ASP cc_start: 0.8709 (m-30) cc_final: 0.8401 (m-30) REVERT: D 93 GLU cc_start: 0.8417 (mp0) cc_final: 0.8200 (mp0) REVERT: D 95 GLN cc_start: 0.8698 (tt0) cc_final: 0.8425 (tt0) REVERT: D 113 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8449 (mm-30) REVERT: E 59 GLU cc_start: 0.8299 (pm20) cc_final: 0.7816 (pm20) REVERT: E 73 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7557 (mm-30) REVERT: F 88 TYR cc_start: 0.8562 (m-10) cc_final: 0.8185 (m-10) REVERT: F 93 GLN cc_start: 0.8669 (mt0) cc_final: 0.8261 (mt0) REVERT: H 33 ARG cc_start: 0.7080 (mmt90) cc_final: 0.6730 (mtt180) REVERT: H 34 LYS cc_start: 0.8283 (tppt) cc_final: 0.7331 (tttp) REVERT: H 42 TYR cc_start: 0.7935 (t80) cc_final: 0.6992 (t80) REVERT: H 115 THR cc_start: 0.9128 (m) cc_final: 0.8874 (m) outliers start: 18 outliers final: 14 residues processed: 168 average time/residue: 0.1443 time to fit residues: 34.2761 Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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 73 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain 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 Chi-restraints excluded: chain K residue 495 LEU Chi-restraints excluded: chain K residue 502 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN G 89 ASN K 388 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.121423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.088625 restraints weight = 28106.525| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.88 r_work: 0.3150 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 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 = 0.3155 r_free = 0.3155 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: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16319 Z= 0.160 Angle : 0.598 12.564 23343 Z= 0.339 Chirality : 0.042 0.299 2687 Planarity : 0.004 0.041 1951 Dihedral : 29.766 146.233 4537 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.86 % Allowed : 13.12 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.24), residues: 1193 helix: 2.11 (0.19), residues: 732 sheet: 0.51 (0.56), residues: 95 loop : -0.20 (0.32), residues: 366 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 0.010 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 0.00318 / 0.16 (16319) covalent geometry : angle 0.59847 / 0.34 (23343) hydrogen bonds : bond 0.04037 / 2.75 ( 920) hydrogen bonds : angle 3.31214 / 2.38 ( 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 173 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.422 Fit side-chains REVERT: A 59 GLU cc_start: 0.8550 (pm20) cc_final: 0.8001 (pm20) REVERT: A 129 ARG cc_start: 0.8582 (tpt90) cc_final: 0.8217 (tpt90) REVERT: B 84 MET cc_start: 0.8543 (mmm) cc_final: 0.8236 (mmm) REVERT: B 91 LYS cc_start: 0.9169 (ttmm) cc_final: 0.8705 (tttt) REVERT: C 72 ASP cc_start: 0.8719 (m-30) cc_final: 0.8435 (m-30) REVERT: D 95 GLN cc_start: 0.8682 (tt0) cc_final: 0.8393 (tt0) REVERT: D 113 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8442 (mm-30) REVERT: E 59 GLU cc_start: 0.8253 (pm20) cc_final: 0.7786 (pm20) REVERT: E 73 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7491 (mm-30) REVERT: F 88 TYR cc_start: 0.8540 (m-10) cc_final: 0.8259 (m-10) REVERT: F 93 GLN cc_start: 0.8681 (mt0) cc_final: 0.8258 (mt0) REVERT: H 33 ARG cc_start: 0.6922 (mmt90) cc_final: 0.6654 (mtt180) REVERT: H 34 LYS cc_start: 0.8262 (tppt) cc_final: 0.7309 (tttp) REVERT: H 42 TYR cc_start: 0.7957 (t80) cc_final: 0.7018 (t80) REVERT: H 115 THR cc_start: 0.9123 (m) cc_final: 0.8879 (m) outliers start: 18 outliers final: 13 residues processed: 166 average time/residue: 0.1430 time to fit residues: 33.5371 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 : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 425 ASP Chi-restraints excluded: chain K residue 436 GLU Chi-restraints excluded: chain K residue 444 LEU Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU 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: 0.9980 chunk 14 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 109 optimal weight: 0.6980 chunk 65 optimal weight: 0.0770 chunk 86 optimal weight: 20.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN K 388 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.122214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.089764 restraints weight = 28151.289| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.86 r_work: 0.3171 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 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 = 0.3177 r_free = 0.3177 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: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 16319 Z= 0.133 Angle : 0.584 12.667 23343 Z= 0.333 Chirality : 0.041 0.295 2687 Planarity : 0.004 0.039 1951 Dihedral : 29.678 146.607 4537 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.45 % Allowed : 13.22 % Favored : 85.33 % 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: 2.04 (0.24), residues: 1193 helix: 2.20 (0.19), residues: 733 sheet: 0.73 (0.56), residues: 93 loop : -0.18 (0.32), residues: 367 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 0.012 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 0.00241 / 0.13 (16319) covalent geometry : angle 0.58361 / 0.33 (23343) hydrogen bonds : bond 0.03866 / 2.64 ( 920) hydrogen bonds : angle 3.27070 / 2.36 ( 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 169 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 0.403 Fit side-chains REVERT: A 59 GLU cc_start: 0.8521 (pm20) cc_final: 0.7932 (pm20) REVERT: A 129 ARG cc_start: 0.8559 (tpt90) cc_final: 0.8177 (tpt90) REVERT: B 84 MET cc_start: 0.8537 (mmm) cc_final: 0.8193 (mmm) REVERT: B 91 LYS cc_start: 0.9166 (ttmm) cc_final: 0.8693 (tttt) REVERT: C 72 ASP cc_start: 0.8716 (m-30) cc_final: 0.8406 (m-30) REVERT: D 93 GLU cc_start: 0.8434 (mp0) cc_final: 0.8231 (mp0) REVERT: D 95 GLN cc_start: 0.8654 (tt0) cc_final: 0.8367 (tt0) REVERT: D 113 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8419 (mm-30) REVERT: E 59 GLU cc_start: 0.8263 (pm20) cc_final: 0.7812 (pm20) REVERT: E 73 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: F 93 GLN cc_start: 0.8665 (mt0) cc_final: 0.8258 (mt0) REVERT: H 33 ARG cc_start: 0.6911 (mmt90) cc_final: 0.6654 (mtt180) REVERT: H 34 LYS cc_start: 0.8238 (tppt) cc_final: 0.7237 (tptm) REVERT: H 42 TYR cc_start: 0.7888 (t80) cc_final: 0.6956 (t80) REVERT: H 115 THR cc_start: 0.9123 (m) cc_final: 0.8873 (m) REVERT: K 388 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7753 (tm-30) outliers start: 14 outliers final: 11 residues processed: 161 average time/residue: 0.1496 time to fit residues: 34.1187 Evaluate side-chains 165 residues out of total 1055 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 388 GLN Chi-restraints excluded: chain K residue 478 VAL Chi-restraints excluded: chain K residue 495 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 74 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 115 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 overall best weight: 1.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.122098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089679 restraints weight = 27989.935| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.85 r_work: 0.3169 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 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 = 0.3175 r_free = 0.3175 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 (17 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.289 16319 Z= 0.243 Angle : 0.768 65.893 23343 Z= 0.461 Chirality : 0.042 0.352 2687 Planarity : 0.007 0.271 1951 Dihedral : 29.676 146.606 4537 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.60 % Favored : 97.32 % Rotamer: Outliers : 1.45 % Allowed : 13.53 % Favored : 85.02 % Cbeta Deviations : 0.09 % 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: 2.04 (0.24), residues: 1193 helix: 2.20 (0.19), residues: 733 sheet: 0.72 (0.56), residues: 93 loop : -0.18 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.018 0.001 TYR D 40 PHE 0.011 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 0.00482 / 0.24 (16319) covalent geometry : angle 0.76814 / 0.46 (23343) hydrogen bonds : bond 0.03880 / 2.65 ( 920) hydrogen bonds : angle 3.28343 / 2.37 ( 2370) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3428.03 seconds wall clock time: 59 minutes 30.81 seconds (3570.81 seconds total)