Starting phenix.real_space_refine on Sat Sep 12 11:16:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.map" model { file = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k6q_22692/09_2026/7k6q_22692.cif" } resolution = 3.1 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= 1.007 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 34 5.16 5 C 8919 2.51 5 N 2846 2.21 5 O 3487 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15578 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: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 719 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ALY:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 690 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ALY:plan-2': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 11 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: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 3029 Classifications: {'peptide': 383} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 368} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 6, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 49 Chain: "L" Number of atoms: 485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 485 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 3, 'TRANS': 71} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 78 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 LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " 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: 3.56, per 1000 atoms: 0.23 Number of scatterers: 15578 At special positions: 0 Unit cell: (110.745, 113.85, 124.2, 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 34 16.00 P 292 15.00 O 3487 8.00 N 2846 7.00 C 8919 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: 1.12 Conformation dependent library (CDL) restraints added in 547.1 milliseconds 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2318 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 12 sheets defined 60.4% alpha, 6.0% beta 142 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 2.37 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 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.463A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.666A 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 131 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: 4.533A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.550A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) 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 removed outlier: 3.518A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 124 Processing helix chain 'K' and resid 195 through 202 Processing helix chain 'K' and resid 211 through 215 Processing helix chain 'K' and resid 263 through 278 Processing helix chain 'K' and resid 283 through 303 removed outlier: 3.557A pdb=" N ILE K 292 " --> pdb=" O LEU K 288 " (cutoff:3.500A) removed outlier: 3.624A 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 321 removed outlier: 3.683A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 323 through 334 removed outlier: 3.646A pdb=" N ILE K 327 " --> pdb=" O PRO K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 354 removed outlier: 3.830A pdb=" N HIS K 343 " --> pdb=" O ARG K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 355 through 364 removed outlier: 5.886A pdb=" N ASN K 359 " --> pdb=" O PRO K 356 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N HIS K 363 " --> pdb=" O LYS K 360 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N TYR K 364 " --> pdb=" O LEU K 361 " (cutoff:3.500A) Processing helix chain 'K' and resid 376 through 387 Processing helix chain 'K' and resid 403 through 413 Processing helix chain 'K' and resid 424 through 446 Processing helix chain 'K' and resid 463 through 470 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: 3.771A 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 removed outlier: 3.582A pdb=" N TYR L 59 " --> pdb=" O THR L 55 " (cutoff:3.500A) 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 96 through 98 removed outlier: 6.306A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.670A 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: 6.887A 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: 7.601A 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 237 through 240 Processing sheet with id=AB2, first strand: chain 'K' and resid 452 through 455 removed outlier: 6.198A pdb=" N SER K 418 " --> pdb=" O GLU K 453 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N SER K 455 " --> pdb=" O SER K 418 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLY K 420 " --> pdb=" O SER K 455 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N PHE K 395 " --> pdb=" O PHE K 419 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N CYS K 421 " --> pdb=" O PHE K 395 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP K 397 " --> pdb=" O CYS K 421 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N THR K 394 " --> pdb=" O VAL K 475 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N LEU K 477 " --> pdb=" O THR K 394 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N MET K 396 " --> pdb=" O LEU K 477 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 12 through 15 removed outlier: 6.588A pdb=" N PHE L 4 " --> pdb=" O LEU L 67 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU L 69 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS L 6 " --> pdb=" O LEU L 69 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N LEU L 71 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 558 hydrogen bonds defined for protein. 1641 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 3.76 Time building geometry restraints manager: 1.53 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: 2978 1.33 - 1.45: 5034 1.45 - 1.57: 7807 1.57 - 1.69: 580 1.69 - 1.81: 55 Bond restraints: 16454 Sorted by residual: bond pdb=" C1' DC J 98 " pdb=" N1 DC J 98 " ideal model delta sigma weight residual 1.468 1.551 -0.083 1.40e-02 5.10e+03 3.51e+01 bond pdb=" C1' DC J 46 " pdb=" N1 DC J 46 " ideal model delta sigma weight residual 1.468 1.550 -0.082 1.40e-02 5.10e+03 3.44e+01 bond pdb=" C1' DC I 111 " pdb=" N1 DC I 111 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.34e+01 bond pdb=" C1' DC I 12 " pdb=" N1 DC I 12 " 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 J 134 " pdb=" N1 DC J 134 " ideal model delta sigma weight residual 1.468 1.546 -0.078 1.40e-02 5.10e+03 3.14e+01 ... (remaining 16449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 22151 1.75 - 3.50: 1214 3.50 - 5.25: 132 5.25 - 7.00: 17 7.00 - 8.75: 7 Bond angle restraints: 23521 Sorted by residual: angle pdb=" N3 DT I 112 " pdb=" C4 DT I 112 " pdb=" O4 DT I 112 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT J 51 " pdb=" C4 DT J 51 " pdb=" O4 DT J 51 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" O5' DC I 116 " pdb=" C5' DC I 116 " pdb=" C4' DC I 116 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" N3 DT I 32 " pdb=" C4 DT I 32 " pdb=" O4 DT I 32 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I 77 " pdb=" C4 DT I 77 " pdb=" O4 DT I 77 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 7450 29.40 - 58.81: 1563 58.81 - 88.21: 93 88.21 - 117.62: 1 117.62 - 147.02: 3 Dihedral angle restraints: 9110 sinusoidal: 5523 harmonic: 3587 Sorted by residual: 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 72.98 147.02 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 73.40 146.60 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 86.16 133.84 1 3.50e+01 8.16e-04 1.33e+01 ... (remaining 9107 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2325 0.078 - 0.156: 353 0.156 - 0.234: 26 0.234 - 0.312: 0 0.312 - 0.390: 1 Chirality restraints: 2705 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 -2.34 -0.39 2.00e-01 2.50e+01 3.81e+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 -2.53 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.33e-01 ... (remaining 2702 not shown) Planarity restraints: 1971 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 86 " -0.219 9.50e-02 1.11e+02 9.83e-02 6.51e+00 pdb=" NE ARG H 86 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG H 86 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 86 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 86 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 42 " -0.203 9.50e-02 1.11e+02 9.15e-02 6.12e+00 pdb=" NE ARG E 42 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG E 42 " -0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG E 42 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG E 42 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.036 5.00e-02 4.00e+02 5.46e-02 4.77e+00 pdb=" N PRO H 103 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.031 5.00e-02 4.00e+02 ... (remaining 1968 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 439 2.67 - 3.23: 13564 3.23 - 3.78: 29161 3.78 - 4.34: 37776 4.34 - 4.90: 55653 Nonbonded interactions: 136593 Sorted by model distance: nonbonded pdb=" OE2 GLU K 422 " pdb=" O2' SAM K 601 " model vdw 2.108 3.040 nonbonded pdb=" OG1 THR H 32 " pdb=" OP1 DC J 104 " model vdw 2.114 3.040 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.166 3.040 nonbonded pdb=" OH TYR K 274 " pdb=" OD2 ASP K 344 " model vdw 2.183 3.040 nonbonded pdb=" NH2 ARG A 40 " pdb=" O2 DT J 83 " model vdw 2.214 3.120 ... (remaining 136588 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 or (resid 17 and (name N or name CA or name C or name O \ or name CB )) or resid 18 through 19 or (resid 20 and (name N or name CA or nam \ e C or name O or name CB )) or resid 21 through 22 or (resid 23 and (name N or n \ ame CA or name C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and (resid 16 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 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: 2.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.600 Find NCS groups from input model: 0.160 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.007 0.083 16454 Z= 0.573 Angle : 0.861 8.745 23521 Z= 0.663 Chirality : 0.056 0.390 2705 Planarity : 0.006 0.098 1971 Dihedral : 24.787 147.020 6792 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 1201 helix: 1.64 (0.19), residues: 717 sheet: -0.22 (0.56), residues: 85 loop : -0.07 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 42 TYR 0.011 0.001 TYR D 40 PHE 0.014 0.001 PHE G 25 TRP 0.007 0.001 TRP K 543 HIS 0.010 0.001 HIS K 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00732 / 0.57 (16454) covalent geometry : angle 0.86135 / 0.66 (23521) hydrogen bonds : bond 0.11176 / 7.75 ( 922) hydrogen bonds : angle 4.63218 / 3.31 ( 2369) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.460 Fit side-chains REVERT: B 20 LYS cc_start: 0.8441 (tttm) cc_final: 0.7987 (ttmt) REVERT: B 25 ASN cc_start: 0.8207 (m-40) cc_final: 0.7936 (m-40) REVERT: D 119 THR cc_start: 0.8678 (m) cc_final: 0.8443 (p) REVERT: E 42 ARG cc_start: 0.7577 (mtm110) cc_final: 0.7336 (mtt180) REVERT: E 59 GLU cc_start: 0.8132 (pm20) cc_final: 0.7785 (pm20) REVERT: E 74 ILE cc_start: 0.9059 (mm) cc_final: 0.8830 (mt) REVERT: F 77 LYS cc_start: 0.8813 (mttt) cc_final: 0.8419 (mtmt) REVERT: F 84 MET cc_start: 0.8239 (mmm) cc_final: 0.8010 (mmm) REVERT: H 51 ASP cc_start: 0.7563 (p0) cc_final: 0.7319 (p0) REVERT: K 424 MET cc_start: 0.8287 (mmm) cc_final: 0.8087 (mmm) REVERT: K 493 LYS cc_start: 0.8665 (tttt) cc_final: 0.8427 (ttmm) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.1523 time to fit residues: 36.9415 Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.0570 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS K 355 HIS K 521 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.119876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086240 restraints weight = 30476.372| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 2.00 r_work: 0.3213 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16454 Z= 0.152 Angle : 0.634 6.890 23521 Z= 0.368 Chirality : 0.045 0.298 2705 Planarity : 0.005 0.054 1971 Dihedral : 28.781 141.689 4558 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.81 % Allowed : 5.35 % Favored : 93.84 % 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: 1.72 (0.24), residues: 1201 helix: 1.90 (0.19), residues: 726 sheet: 0.06 (0.57), residues: 85 loop : 0.02 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.014 0.001 TYR C 57 PHE 0.012 0.001 PHE K 460 TRP 0.005 0.001 TRP K 543 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (16454) covalent geometry : angle 0.63394 / 0.37 (23521) hydrogen bonds : bond 0.04896 / 3.35 ( 922) hydrogen bonds : angle 3.52626 / 2.58 ( 2369) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.451 Fit side-chains revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8794 (m-30) cc_final: 0.8505 (m-30) REVERT: B 20 LYS cc_start: 0.8632 (tttm) cc_final: 0.8237 (ttmt) REVERT: B 25 ASN cc_start: 0.8492 (m-40) cc_final: 0.8208 (m-40) REVERT: E 59 GLU cc_start: 0.8374 (pm20) cc_final: 0.7963 (pm20) REVERT: E 74 ILE cc_start: 0.9185 (mm) cc_final: 0.8979 (mt) REVERT: F 77 LYS cc_start: 0.8957 (mttt) cc_final: 0.8623 (mtmt) REVERT: F 92 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8018 (ttp80) REVERT: H 51 ASP cc_start: 0.7816 (p0) cc_final: 0.7591 (p0) REVERT: K 493 LYS cc_start: 0.8701 (tttt) cc_final: 0.8472 (ttmm) REVERT: L 72 ARG cc_start: 0.7250 (mmm-85) cc_final: 0.7023 (mmm-85) outliers start: 8 outliers final: 7 residues processed: 151 average time/residue: 0.1229 time to fit residues: 26.4403 Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 9 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 10 optimal weight: 0.0370 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 0.0670 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 23 optimal weight: 0.8980 chunk 137 optimal weight: 0.2980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN F 75 HIS K 202 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.114022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.081329 restraints weight = 27708.676| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.13 r_work: 0.3059 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16454 Z= 0.131 Angle : 0.565 6.605 23521 Z= 0.336 Chirality : 0.042 0.328 2705 Planarity : 0.004 0.049 1971 Dihedral : 29.055 140.220 4558 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.81 % Allowed : 6.86 % Favored : 92.33 % 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: 1201 helix: 2.18 (0.19), residues: 726 sheet: 0.29 (0.59), residues: 84 loop : 0.09 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.015 0.001 TYR C 57 PHE 0.013 0.001 PHE K 519 TRP 0.005 0.001 TRP K 543 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.13 (16454) covalent geometry : angle 0.56476 / 0.34 (23521) hydrogen bonds : bond 0.04357 / 3.00 ( 922) hydrogen bonds : angle 3.29760 / 2.40 ( 2369) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 0.398 Fit side-chains REVERT: A 59 GLU cc_start: 0.7768 (pm20) cc_final: 0.7357 (pm20) REVERT: A 123 ASP cc_start: 0.9025 (m-30) cc_final: 0.8767 (m-30) REVERT: B 20 LYS cc_start: 0.8545 (tttm) cc_final: 0.8057 (ttmt) REVERT: C 90 ASP cc_start: 0.8582 (t0) cc_final: 0.8304 (t0) REVERT: E 59 GLU cc_start: 0.8144 (pm20) cc_final: 0.7558 (pm20) REVERT: F 92 ARG cc_start: 0.8615 (ttp80) cc_final: 0.8177 (ttp80) REVERT: H 51 ASP cc_start: 0.7819 (p0) cc_final: 0.7586 (p0) REVERT: H 59 MET cc_start: 0.8667 (tpp) cc_final: 0.8460 (tpp) REVERT: K 493 LYS cc_start: 0.8645 (tttt) cc_final: 0.8393 (ttmm) REVERT: K 540 SER cc_start: 0.8945 (t) cc_final: 0.8536 (m) outliers start: 8 outliers final: 6 residues processed: 157 average time/residue: 0.1312 time to fit residues: 29.8772 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 132 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 134 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS A 93 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.111737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.079144 restraints weight = 27207.081| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.06 r_work: 0.3026 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16454 Z= 0.161 Angle : 0.583 10.842 23521 Z= 0.336 Chirality : 0.042 0.316 2705 Planarity : 0.004 0.045 1971 Dihedral : 29.236 140.784 4558 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.91 % Allowed : 9.89 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.24), residues: 1201 helix: 2.20 (0.19), residues: 726 sheet: 0.34 (0.59), residues: 84 loop : 0.17 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.013 0.001 TYR D 83 PHE 0.015 0.001 PHE G 25 TRP 0.004 0.001 TRP K 543 HIS 0.005 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (16454) covalent geometry : angle 0.58310 / 0.34 (23521) hydrogen bonds : bond 0.04289 / 2.96 ( 922) hydrogen bonds : angle 3.25563 / 2.36 ( 2369) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.299 Fit side-chains REVERT: A 59 GLU cc_start: 0.7756 (pm20) cc_final: 0.7471 (pm20) REVERT: A 123 ASP cc_start: 0.9002 (m-30) cc_final: 0.8758 (m-30) REVERT: B 20 LYS cc_start: 0.8548 (tttm) cc_final: 0.8029 (ttmt) REVERT: C 90 ASP cc_start: 0.8673 (t0) cc_final: 0.8344 (t0) REVERT: E 59 GLU cc_start: 0.8216 (pm20) cc_final: 0.7612 (pm20) REVERT: F 92 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8208 (ttp80) REVERT: K 318 MET cc_start: 0.8897 (ptm) cc_final: 0.8617 (ppp) REVERT: K 397 ASP cc_start: 0.8530 (t0) cc_final: 0.8299 (t0) REVERT: K 493 LYS cc_start: 0.8662 (tttt) cc_final: 0.8395 (ttmm) outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 0.1369 time to fit residues: 28.1109 Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 10 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 30 optimal weight: 4.9990 chunk 97 optimal weight: 10.9990 chunk 100 optimal weight: 20.0000 chunk 102 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 128 optimal weight: 0.0370 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 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 = 0.3755 r_free = 0.3755 target = 0.112778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.080276 restraints weight = 27027.810| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.07 r_work: 0.3045 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16454 Z= 0.130 Angle : 0.552 7.549 23521 Z= 0.324 Chirality : 0.040 0.323 2705 Planarity : 0.004 0.046 1971 Dihedral : 29.218 141.220 4558 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.31 % Allowed : 9.79 % Favored : 88.90 % 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: 2.17 (0.24), residues: 1201 helix: 2.25 (0.19), residues: 726 sheet: 0.33 (0.60), residues: 85 loop : 0.21 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 72 TYR 0.013 0.001 TYR F 72 PHE 0.009 0.001 PHE K 519 TRP 0.004 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (16454) covalent geometry : angle 0.55234 / 0.32 (23521) hydrogen bonds : bond 0.04022 / 2.77 ( 922) hydrogen bonds : angle 3.15936 / 2.29 ( 2369) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.429 Fit side-chains REVERT: A 59 GLU cc_start: 0.7768 (pm20) cc_final: 0.7461 (pm20) REVERT: A 123 ASP cc_start: 0.8984 (m-30) cc_final: 0.8761 (m-30) REVERT: B 20 LYS cc_start: 0.8581 (tttm) cc_final: 0.8084 (ttmt) REVERT: C 90 ASP cc_start: 0.8720 (t0) cc_final: 0.8454 (t0) REVERT: C 94 ASN cc_start: 0.8980 (t0) cc_final: 0.8691 (t0) REVERT: E 42 ARG cc_start: 0.7636 (mtm110) cc_final: 0.7231 (mtm-85) REVERT: E 59 GLU cc_start: 0.8130 (pm20) cc_final: 0.7544 (pm20) REVERT: G 104 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8548 (mm-40) REVERT: K 318 MET cc_start: 0.8946 (ptm) cc_final: 0.8730 (ppp) REVERT: K 397 ASP cc_start: 0.8570 (t0) cc_final: 0.8319 (t0) REVERT: K 493 LYS cc_start: 0.8654 (tttt) cc_final: 0.8401 (ttmm) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.1318 time to fit residues: 28.6816 Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 81 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 117 optimal weight: 0.0070 chunk 120 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 86 optimal weight: 20.0000 chunk 128 optimal weight: 0.1980 chunk 36 optimal weight: 0.9990 overall best weight: 0.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 84 GLN K 316 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.114050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.081643 restraints weight = 27934.110| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.03 r_work: 0.3093 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16454 Z= 0.128 Angle : 0.547 8.318 23521 Z= 0.322 Chirality : 0.040 0.318 2705 Planarity : 0.004 0.042 1971 Dihedral : 29.202 141.223 4558 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.31 % Allowed : 10.70 % Favored : 87.99 % 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: 2.26 (0.24), residues: 1201 helix: 2.32 (0.19), residues: 726 sheet: 0.41 (0.60), residues: 85 loop : 0.25 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 86 TYR 0.012 0.001 TYR C 57 PHE 0.009 0.001 PHE G 25 TRP 0.004 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.13 (16454) covalent geometry : angle 0.54687 / 0.32 (23521) hydrogen bonds : bond 0.03963 / 2.73 ( 922) hydrogen bonds : angle 3.13278 / 2.27 ( 2369) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.449 Fit side-chains REVERT: A 59 GLU cc_start: 0.7759 (pm20) cc_final: 0.7450 (pm20) REVERT: A 123 ASP cc_start: 0.8924 (m-30) cc_final: 0.8714 (m-30) REVERT: C 90 ASP cc_start: 0.8735 (t0) cc_final: 0.8482 (t0) REVERT: C 94 ASN cc_start: 0.9079 (t0) cc_final: 0.8776 (t0) REVERT: E 59 GLU cc_start: 0.8107 (pm20) cc_final: 0.7545 (pm20) REVERT: G 104 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8570 (mm-40) REVERT: H 42 TYR cc_start: 0.8067 (t80) cc_final: 0.7829 (t80) REVERT: K 318 MET cc_start: 0.8943 (ptm) cc_final: 0.8707 (ppp) REVERT: K 397 ASP cc_start: 0.8514 (t0) cc_final: 0.8290 (t0) REVERT: K 493 LYS cc_start: 0.8685 (tttt) cc_final: 0.8448 (ttmm) REVERT: K 540 SER cc_start: 0.8877 (t) cc_final: 0.8579 (m) outliers start: 13 outliers final: 9 residues processed: 145 average time/residue: 0.1390 time to fit residues: 28.7431 Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 139 optimal weight: 20.0000 chunk 16 optimal weight: 0.6980 chunk 46 optimal weight: 20.0000 chunk 84 optimal weight: 9.9990 chunk 110 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 60 optimal weight: 0.3980 chunk 133 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 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 = 0.3799 r_free = 0.3799 target = 0.113531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.081145 restraints weight = 27840.451| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 2.02 r_work: 0.3085 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16454 Z= 0.138 Angle : 0.556 8.688 23521 Z= 0.322 Chirality : 0.040 0.315 2705 Planarity : 0.004 0.045 1971 Dihedral : 29.270 140.820 4558 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.31 % Allowed : 11.00 % Favored : 87.69 % 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: 2.29 (0.24), residues: 1201 helix: 2.34 (0.19), residues: 727 sheet: 0.39 (0.60), residues: 85 loop : 0.26 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.012 0.001 TYR C 57 PHE 0.011 0.001 PHE G 25 TRP 0.003 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.14 (16454) covalent geometry : angle 0.55574 / 0.32 (23521) hydrogen bonds : bond 0.03938 / 2.72 ( 922) hydrogen bonds : angle 3.13060 / 2.27 ( 2369) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.468 Fit side-chains REVERT: A 59 GLU cc_start: 0.7703 (pm20) cc_final: 0.7373 (pm20) REVERT: A 123 ASP cc_start: 0.8925 (m-30) cc_final: 0.8713 (m-30) REVERT: B 20 LYS cc_start: 0.8650 (tttm) cc_final: 0.8144 (ttmt) REVERT: C 90 ASP cc_start: 0.8757 (t0) cc_final: 0.8500 (t0) REVERT: C 94 ASN cc_start: 0.9087 (t0) cc_final: 0.8779 (t0) REVERT: E 42 ARG cc_start: 0.7796 (mtm110) cc_final: 0.7424 (mtt90) REVERT: E 59 GLU cc_start: 0.8134 (pm20) cc_final: 0.7593 (pm20) REVERT: E 120 MET cc_start: 0.8362 (mtp) cc_final: 0.8011 (mtt) REVERT: G 104 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8631 (mm-40) REVERT: H 42 TYR cc_start: 0.8096 (t80) cc_final: 0.7873 (t80) REVERT: K 397 ASP cc_start: 0.8520 (t0) cc_final: 0.8276 (t0) REVERT: K 493 LYS cc_start: 0.8691 (tttt) cc_final: 0.8453 (ttmm) REVERT: L 7 THR cc_start: 0.7987 (OUTLIER) cc_final: 0.7454 (t) outliers start: 13 outliers final: 11 residues processed: 146 average time/residue: 0.1441 time to fit residues: 30.0026 Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 7 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.111982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079854 restraints weight = 27621.120| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 1.97 r_work: 0.3072 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16454 Z= 0.159 Angle : 0.578 9.200 23521 Z= 0.329 Chirality : 0.041 0.316 2705 Planarity : 0.004 0.043 1971 Dihedral : 29.365 140.349 4558 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.11 % Allowed : 11.40 % Favored : 87.49 % 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: 2.28 (0.24), residues: 1201 helix: 2.33 (0.19), residues: 727 sheet: 0.41 (0.60), residues: 85 loop : 0.26 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.014 0.001 TYR D 83 PHE 0.013 0.001 PHE G 25 TRP 0.003 0.001 TRP K 543 HIS 0.005 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (16454) covalent geometry : angle 0.57776 / 0.33 (23521) hydrogen bonds : bond 0.03981 / 2.74 ( 922) hydrogen bonds : angle 3.17390 / 2.29 ( 2369) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.463 Fit side-chains REVERT: A 59 GLU cc_start: 0.7683 (pm20) cc_final: 0.7343 (pm20) REVERT: A 123 ASP cc_start: 0.8956 (m-30) cc_final: 0.8706 (m-30) REVERT: B 20 LYS cc_start: 0.8641 (tttm) cc_final: 0.8144 (ttmt) REVERT: C 90 ASP cc_start: 0.8771 (t0) cc_final: 0.8519 (t0) REVERT: C 94 ASN cc_start: 0.9088 (t0) cc_final: 0.8774 (t0) REVERT: E 59 GLU cc_start: 0.8209 (pm20) cc_final: 0.7648 (pm20) REVERT: E 120 MET cc_start: 0.8352 (mtp) cc_final: 0.7970 (mtt) REVERT: G 90 ASP cc_start: 0.8473 (t0) cc_final: 0.8105 (t0) REVERT: G 104 GLN cc_start: 0.8857 (mm-40) cc_final: 0.8631 (mm-40) REVERT: H 42 TYR cc_start: 0.8084 (t80) cc_final: 0.7851 (t80) REVERT: K 397 ASP cc_start: 0.8541 (t0) cc_final: 0.8276 (t0) REVERT: K 493 LYS cc_start: 0.8720 (tttt) cc_final: 0.8477 (ttmm) REVERT: L 7 THR cc_start: 0.7948 (OUTLIER) cc_final: 0.7409 (t) outliers start: 11 outliers final: 10 residues processed: 147 average time/residue: 0.1511 time to fit residues: 31.6003 Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 7 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 126 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 chunk 136 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 91 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.111326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.078764 restraints weight = 27926.172| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.01 r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16454 Z= 0.186 Angle : 0.609 9.697 23521 Z= 0.340 Chirality : 0.042 0.322 2705 Planarity : 0.004 0.045 1971 Dihedral : 29.571 139.297 4558 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.31 % Allowed : 11.40 % Favored : 87.29 % 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: 2.15 (0.24), residues: 1201 helix: 2.23 (0.19), residues: 726 sheet: 0.52 (0.61), residues: 83 loop : 0.15 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.027 0.002 TYR D 83 PHE 0.018 0.002 PHE G 25 TRP 0.004 0.001 TRP K 543 HIS 0.006 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.19 (16454) covalent geometry : angle 0.60949 / 0.34 (23521) hydrogen bonds : bond 0.04111 / 2.83 ( 922) hydrogen bonds : angle 3.27250 / 2.36 ( 2369) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.410 Fit side-chains REVERT: A 59 GLU cc_start: 0.7706 (pm20) cc_final: 0.7343 (pm20) REVERT: B 20 LYS cc_start: 0.8644 (tttm) cc_final: 0.8144 (ttmt) REVERT: C 90 ASP cc_start: 0.8811 (t0) cc_final: 0.8567 (t0) REVERT: C 94 ASN cc_start: 0.9097 (t0) cc_final: 0.8780 (t0) REVERT: E 59 GLU cc_start: 0.8268 (pm20) cc_final: 0.7691 (pm20) REVERT: E 120 MET cc_start: 0.8422 (mtp) cc_final: 0.7922 (mtt) REVERT: G 90 ASP cc_start: 0.8468 (t0) cc_final: 0.8106 (t0) REVERT: G 104 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8647 (mm-40) REVERT: H 42 TYR cc_start: 0.8090 (t80) cc_final: 0.7850 (t80) REVERT: K 318 MET cc_start: 0.8528 (ppp) cc_final: 0.8291 (ppp) REVERT: K 397 ASP cc_start: 0.8593 (t0) cc_final: 0.8315 (t0) REVERT: K 493 LYS cc_start: 0.8738 (tttt) cc_final: 0.8471 (ttmm) REVERT: L 7 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7402 (t) outliers start: 13 outliers final: 11 residues processed: 148 average time/residue: 0.1500 time to fit residues: 31.4085 Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain L residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 115 optimal weight: 0.0070 chunk 88 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.080717 restraints weight = 27519.774| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.96 r_work: 0.3088 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 16454 Z= 0.124 Angle : 0.566 9.424 23521 Z= 0.325 Chirality : 0.040 0.334 2705 Planarity : 0.004 0.046 1971 Dihedral : 29.355 139.800 4558 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.01 % Allowed : 12.01 % 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: 2.25 (0.24), residues: 1201 helix: 2.34 (0.19), residues: 726 sheet: 0.48 (0.60), residues: 85 loop : 0.14 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.021 0.001 TYR D 83 PHE 0.007 0.001 PHE K 395 TRP 0.005 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.12 (16454) covalent geometry : angle 0.56612 / 0.32 (23521) hydrogen bonds : bond 0.03791 / 2.61 ( 922) hydrogen bonds : angle 3.16802 / 2.30 ( 2369) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2402 Ramachandran restraints generated. 1201 Oldfield, 0 Emsley, 1201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 142 time to evaluate : 0.382 Fit side-chains REVERT: A 59 GLU cc_start: 0.7623 (pm20) cc_final: 0.7257 (pm20) REVERT: B 20 LYS cc_start: 0.8638 (tttm) cc_final: 0.8129 (ttmt) REVERT: C 90 ASP cc_start: 0.8792 (t0) cc_final: 0.8570 (t0) REVERT: C 94 ASN cc_start: 0.9097 (t0) cc_final: 0.8783 (t0) REVERT: E 59 GLU cc_start: 0.8185 (pm20) cc_final: 0.7643 (pm20) REVERT: E 120 MET cc_start: 0.8308 (mtp) cc_final: 0.7934 (mtt) REVERT: G 90 ASP cc_start: 0.8447 (t0) cc_final: 0.8089 (t0) REVERT: G 104 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8640 (mm-40) REVERT: H 42 TYR cc_start: 0.8053 (t80) cc_final: 0.7763 (t80) REVERT: K 318 MET cc_start: 0.8551 (ppp) cc_final: 0.8299 (ppp) REVERT: K 397 ASP cc_start: 0.8499 (t0) cc_final: 0.8254 (t0) REVERT: K 493 LYS cc_start: 0.8716 (tttt) cc_final: 0.8461 (ttmm) REVERT: L 7 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7427 (t) outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.1506 time to fit residues: 31.5055 Evaluate side-chains 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 141 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain L residue 7 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 135 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 145 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 117 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 68 GLN E 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.107915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.075522 restraints weight = 27609.960| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.94 r_work: 0.2991 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16454 Z= 0.332 Angle : 0.715 9.622 23521 Z= 0.384 Chirality : 0.047 0.331 2705 Planarity : 0.005 0.049 1971 Dihedral : 29.820 138.638 4558 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.21 % Allowed : 11.60 % Favored : 87.18 % 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: 1.75 (0.24), residues: 1201 helix: 1.96 (0.19), residues: 725 sheet: 0.37 (0.62), residues: 83 loop : -0.09 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.028 0.002 TYR D 83 PHE 0.031 0.003 PHE G 25 TRP 0.003 0.001 TRP K 543 HIS 0.010 0.002 HIS K 347 Details of bonding type rmsd/Z covalent geometry : bond 0.00740 / 0.33 (16454) covalent geometry : angle 0.71475 / 0.38 (23521) hydrogen bonds : bond 0.04730 / 3.25 ( 922) hydrogen bonds : angle 3.45755 / 2.48 ( 2369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3135.66 seconds wall clock time: 54 minutes 31.12 seconds (3271.12 seconds total)