Starting phenix.real_space_refine on Wed Mar 4 18:25:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k6q_22692/03_2026/7k6q_22692.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k6q_22692/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7k6q_22692/03_2026/7k6q_22692.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k6q_22692/03_2026/7k6q_22692.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7k6q_22692/03_2026/7k6q_22692.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k6q_22692/03_2026/7k6q_22692.map" } 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-dev-5986/lib/python3.9/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: 3.37, per 1000 atoms: 0.22 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: 1.57 Conformation dependent library (CDL) restraints added in 435.9 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: 2.47 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: 2.94 Time building geometry restraints manager: 2.08 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=" O3' DA I 91 " pdb=" P DC I 92 " ideal model delta sigma weight residual 1.607 1.549 0.058 1.50e-02 4.44e+03 1.48e+01 bond pdb=" N ASP D 51 " pdb=" CA ASP D 51 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.18e-02 7.18e+03 1.04e+01 bond pdb=" O3' DA I 90 " pdb=" P DA I 91 " ideal model delta sigma weight residual 1.607 1.559 0.048 1.50e-02 4.44e+03 1.04e+01 bond pdb=" O3' DA I 131 " pdb=" P DG I 132 " ideal model delta sigma weight residual 1.607 1.566 0.041 1.50e-02 4.44e+03 7.53e+00 bond pdb=" N ASP C 90 " pdb=" CA ASP C 90 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.23e-02 6.61e+03 7.24e+00 ... (remaining 16449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 22466 1.75 - 3.50: 911 3.50 - 5.25: 118 5.25 - 7.00: 21 7.00 - 8.75: 5 Bond angle restraints: 23521 Sorted by residual: angle pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " pdb=" O3' DA I 91 " ideal model delta sigma weight residual 110.00 103.65 6.35 1.50e+00 4.44e-01 1.79e+01 angle pdb=" O3' DT J 15 " pdb=" C3' DT J 15 " pdb=" C2' DT J 15 " ideal model delta sigma weight residual 111.50 117.75 -6.25 1.50e+00 4.44e-01 1.74e+01 angle pdb=" O3' DA I 90 " pdb=" C3' DA I 90 " pdb=" C2' DA I 90 " ideal model delta sigma weight residual 111.50 105.33 6.17 1.50e+00 4.44e-01 1.69e+01 angle pdb=" O3' DT I 89 " pdb=" C3' DT I 89 " pdb=" C2' DT I 89 " ideal model delta sigma weight residual 111.50 106.14 5.36 1.50e+00 4.44e-01 1.28e+01 angle pdb=" C4' DT I 89 " pdb=" C3' DT I 89 " pdb=" O3' DT I 89 " ideal model delta sigma weight residual 110.00 104.64 5.36 1.50e+00 4.44e-01 1.28e+01 ... (remaining 23516 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.40: 7471 29.40 - 58.81: 1574 58.81 - 88.21: 93 88.21 - 117.62: 1 117.62 - 147.02: 3 Dihedral angle restraints: 9142 sinusoidal: 5555 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 9139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2363 0.064 - 0.128: 319 0.128 - 0.192: 19 0.192 - 0.256: 3 0.256 - 0.320: 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 -2.66 -2.34 -0.32 2.00e-01 2.50e+01 2.56e+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' DT I 89 " pdb=" C4' DT I 89 " pdb=" O3' DT I 89 " pdb=" C2' DT I 89 " both_signs ideal model delta sigma weight residual False -2.66 -2.88 0.22 2.00e-01 2.50e+01 1.24e+00 ... (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: 2.560 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.080 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16454 Z= 0.249 Angle : 0.777 8.745 23521 Z= 0.457 Chirality : 0.042 0.320 2705 Planarity : 0.006 0.098 1971 Dihedral : 24.803 147.020 6824 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 covalent geometry : bond 0.00564 (16454) covalent geometry : angle 0.77652 (23521) hydrogen bonds : bond 0.11176 ( 922) hydrogen bonds : angle 4.63218 ( 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 : 0.438 Fit side-chains REVERT: B 20 LYS cc_start: 0.8441 (tttm) cc_final: 0.7988 (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: 0.7326 (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: 0.1717 time to fit residues: 40.7323 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 : 0.348 ------------------------------------------------------------------------------- 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: 3.9990 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: 4.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 93 GLN E 68 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.113648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.081093 restraints weight = 27441.508| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.11 r_work: 0.3046 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3055 r_free = 0.3055 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3055 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16454 Z= 0.158 Angle : 0.543 5.792 23521 Z= 0.320 Chirality : 0.036 0.149 2705 Planarity : 0.004 0.053 1971 Dihedral : 28.738 139.246 4590 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.81 % Allowed : 5.55 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.24), residues: 1201 helix: 2.05 (0.19), residues: 726 sheet: 0.12 (0.58), residues: 85 loop : 0.05 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 35 TYR 0.013 0.001 TYR C 57 PHE 0.013 0.001 PHE G 25 TRP 0.005 0.001 TRP K 543 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (16454) covalent geometry : angle 0.54278 (23521) hydrogen bonds : bond 0.03954 ( 922) hydrogen bonds : angle 3.29076 ( 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 163 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 155 time to evaluate : 0.423 Fit side-chains REVERT: A 58 THR cc_start: 0.9183 (p) cc_final: 0.8979 (p) REVERT: A 59 GLU cc_start: 0.7707 (pm20) cc_final: 0.7334 (pm20) REVERT: A 123 ASP cc_start: 0.8985 (m-30) cc_final: 0.8739 (m-30) REVERT: B 20 LYS cc_start: 0.8545 (tttm) cc_final: 0.8026 (ttmt) REVERT: B 85 ASP cc_start: 0.8676 (m-30) cc_final: 0.8395 (m-30) REVERT: E 42 ARG cc_start: 0.7653 (mtm110) cc_final: 0.7255 (mtt180) REVERT: E 59 GLU cc_start: 0.8203 (pm20) cc_final: 0.7629 (pm20) REVERT: F 77 LYS cc_start: 0.8923 (mttt) cc_final: 0.8524 (mtmt) REVERT: F 92 ARG cc_start: 0.8564 (ttp80) cc_final: 0.8084 (ttp80) REVERT: H 51 ASP cc_start: 0.7876 (p0) cc_final: 0.7644 (p0) REVERT: K 202 HIS cc_start: 0.7909 (m90) cc_final: 0.7630 (m170) REVERT: K 493 LYS cc_start: 0.8634 (tttt) cc_final: 0.8381 (ttmm) REVERT: L 26 VAL cc_start: 0.9399 (t) cc_final: 0.9160 (m) outliers start: 8 outliers final: 7 residues processed: 159 average time/residue: 0.1458 time to fit residues: 32.7525 Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 136 time to evaluate : 0.430 ------------------------------------------------------------------------------- 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 H residue 32 THR 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: 6.9990 chunk 74 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 137 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.112152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.079480 restraints weight = 27390.867| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.08 r_work: 0.3028 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16454 Z= 0.163 Angle : 0.526 5.682 23521 Z= 0.310 Chirality : 0.035 0.154 2705 Planarity : 0.004 0.049 1971 Dihedral : 28.759 140.420 4590 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.01 % Allowed : 7.67 % 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: 2.07 (0.24), residues: 1201 helix: 2.21 (0.19), residues: 726 sheet: 0.14 (0.58), residues: 85 loop : 0.12 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.013 0.001 TYR D 83 PHE 0.013 0.001 PHE G 25 TRP 0.004 0.001 TRP K 543 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00366 (16454) covalent geometry : angle 0.52554 (23521) hydrogen bonds : bond 0.03619 ( 922) hydrogen bonds : angle 3.21793 ( 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 151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 141 time to evaluate : 0.430 Fit side-chains REVERT: A 58 THR cc_start: 0.9196 (p) cc_final: 0.8992 (p) REVERT: A 59 GLU cc_start: 0.7781 (pm20) cc_final: 0.7557 (pm20) REVERT: A 123 ASP cc_start: 0.9030 (m-30) cc_final: 0.8707 (m-30) REVERT: B 85 ASP cc_start: 0.8659 (m-30) cc_final: 0.8359 (m-30) REVERT: C 94 ASN cc_start: 0.8996 (t0) cc_final: 0.8703 (t0) REVERT: E 42 ARG cc_start: 0.7717 (mtm110) cc_final: 0.7286 (mtt180) REVERT: E 59 GLU cc_start: 0.8149 (pm20) cc_final: 0.7576 (pm20) REVERT: H 51 ASP cc_start: 0.7839 (p0) cc_final: 0.7599 (p0) REVERT: K 202 HIS cc_start: 0.7947 (m90) cc_final: 0.7653 (m170) REVERT: K 424 MET cc_start: 0.8488 (mmm) cc_final: 0.8284 (mmm) REVERT: K 493 LYS cc_start: 0.8637 (tttt) cc_final: 0.8381 (ttmm) REVERT: K 540 SER cc_start: 0.8985 (t) cc_final: 0.8582 (m) REVERT: L 72 ARG cc_start: 0.7000 (mtp-110) cc_final: 0.6496 (tmm-80) outliers start: 10 outliers final: 7 residues processed: 147 average time/residue: 0.1460 time to fit residues: 30.2520 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 H residue 56 SER 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: 0.8980 chunk 112 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 141 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.112276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.079730 restraints weight = 27154.085| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.06 r_work: 0.3033 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.77 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 16454 Z= 0.158 Angle : 0.520 6.506 23521 Z= 0.307 Chirality : 0.035 0.143 2705 Planarity : 0.004 0.045 1971 Dihedral : 28.748 140.175 4590 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.31 % Allowed : 8.78 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.24), residues: 1201 helix: 2.26 (0.19), residues: 726 sheet: 0.21 (0.59), residues: 85 loop : 0.20 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.011 0.001 PHE G 25 TRP 0.003 0.001 TRP K 543 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (16454) covalent geometry : angle 0.51967 (23521) hydrogen bonds : bond 0.03488 ( 922) hydrogen bonds : angle 3.14914 ( 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 156 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.402 Fit side-chains REVERT: A 58 THR cc_start: 0.9236 (p) cc_final: 0.9012 (p) REVERT: A 59 GLU cc_start: 0.7733 (pm20) cc_final: 0.7422 (pm20) REVERT: A 123 ASP cc_start: 0.9019 (m-30) cc_final: 0.8743 (m-30) REVERT: B 20 LYS cc_start: 0.8640 (tttm) cc_final: 0.8099 (ttmt) REVERT: B 85 ASP cc_start: 0.8663 (m-30) cc_final: 0.8391 (m-30) REVERT: C 94 ASN cc_start: 0.9014 (t0) cc_final: 0.8722 (t0) REVERT: E 59 GLU cc_start: 0.8150 (pm20) cc_final: 0.7587 (pm20) REVERT: F 92 ARG cc_start: 0.8672 (ttp80) cc_final: 0.8159 (ttp80) REVERT: K 202 HIS cc_start: 0.7924 (m90) cc_final: 0.7640 (m170) REVERT: K 380 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7504 (mp) REVERT: K 397 ASP cc_start: 0.8583 (t0) cc_final: 0.8348 (t0) REVERT: K 493 LYS cc_start: 0.8671 (tttt) cc_final: 0.8417 (ttmm) REVERT: K 540 SER cc_start: 0.8973 (t) cc_final: 0.8551 (m) REVERT: L 72 ARG cc_start: 0.6950 (mtp-110) cc_final: 0.6717 (mtp-110) outliers start: 13 outliers final: 8 residues processed: 149 average time/residue: 0.1495 time to fit residues: 31.4684 Evaluate side-chains 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS 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 G residue 100 VAL Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 319 ILE Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 10 optimal weight: 0.8980 chunk 133 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 134 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 112 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN F 25 ASN F 75 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.078761 restraints weight = 27809.542| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.99 r_work: 0.3039 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16454 Z= 0.199 Angle : 0.544 7.335 23521 Z= 0.317 Chirality : 0.036 0.146 2705 Planarity : 0.004 0.047 1971 Dihedral : 29.039 139.035 4590 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.41 % Allowed : 9.49 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.24), residues: 1201 helix: 2.20 (0.19), residues: 726 sheet: 0.20 (0.59), residues: 85 loop : 0.15 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 42 TYR 0.012 0.001 TYR C 57 PHE 0.017 0.002 PHE G 25 TRP 0.002 0.001 TRP K 543 HIS 0.007 0.001 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00453 (16454) covalent geometry : angle 0.54384 (23521) hydrogen bonds : bond 0.03601 ( 922) hydrogen bonds : angle 3.22626 ( 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 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.488 Fit side-chains REVERT: A 58 THR cc_start: 0.9284 (p) cc_final: 0.9050 (p) REVERT: A 59 GLU cc_start: 0.7819 (pm20) cc_final: 0.7533 (pm20) REVERT: A 123 ASP cc_start: 0.8997 (m-30) cc_final: 0.8704 (m-30) REVERT: B 20 LYS cc_start: 0.8671 (tttm) cc_final: 0.8159 (ttmt) REVERT: C 94 ASN cc_start: 0.9094 (t0) cc_final: 0.8778 (t0) REVERT: E 59 GLU cc_start: 0.8206 (pm20) cc_final: 0.7610 (pm20) REVERT: G 90 ASP cc_start: 0.8370 (t0) cc_final: 0.8046 (t0) REVERT: H 42 TYR cc_start: 0.8103 (t80) cc_final: 0.7867 (t80) REVERT: K 202 HIS cc_start: 0.7893 (m90) cc_final: 0.7628 (m170) REVERT: K 380 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7569 (mp) REVERT: K 397 ASP cc_start: 0.8605 (t0) cc_final: 0.8367 (t0) REVERT: K 493 LYS cc_start: 0.8734 (tttt) cc_final: 0.8464 (ttmm) REVERT: L 72 ARG cc_start: 0.6903 (mtp-110) cc_final: 0.6674 (mtp-110) outliers start: 14 outliers final: 10 residues processed: 148 average time/residue: 0.1431 time to fit residues: 30.0682 Evaluate side-chains 149 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 138 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 87 SER 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 Chi-restraints excluded: chain K residue 380 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 81 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 0.0010 chunk 120 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 128 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 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 = 0.3801 r_free = 0.3801 target = 0.113393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.081459 restraints weight = 27480.348| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.96 r_work: 0.3102 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2064 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= 0.137 Angle : 0.507 7.849 23521 Z= 0.301 Chirality : 0.034 0.147 2705 Planarity : 0.004 0.043 1971 Dihedral : 28.707 138.503 4590 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.51 % Allowed : 10.29 % Favored : 88.19 % 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: 2.31 (0.24), residues: 1201 helix: 2.39 (0.19), residues: 726 sheet: 0.39 (0.60), residues: 85 loop : 0.20 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 86 TYR 0.012 0.001 TYR C 57 PHE 0.009 0.001 PHE K 460 TRP 0.005 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00300 (16454) covalent geometry : angle 0.50734 (23521) hydrogen bonds : bond 0.03334 ( 922) hydrogen bonds : angle 3.06321 ( 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 159 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.430 Fit side-chains REVERT: A 58 THR cc_start: 0.9241 (p) cc_final: 0.9005 (p) REVERT: A 59 GLU cc_start: 0.7703 (pm20) cc_final: 0.7389 (pm20) REVERT: B 20 LYS cc_start: 0.8683 (tttm) cc_final: 0.8175 (ttmt) REVERT: C 94 ASN cc_start: 0.9090 (t0) cc_final: 0.8769 (t0) REVERT: E 59 GLU cc_start: 0.8058 (pm20) cc_final: 0.7487 (pm20) REVERT: E 77 ASP cc_start: 0.8469 (m-30) cc_final: 0.8005 (p0) REVERT: G 90 ASP cc_start: 0.8412 (t0) cc_final: 0.8048 (t0) REVERT: K 202 HIS cc_start: 0.7841 (m90) cc_final: 0.7606 (m170) REVERT: K 318 MET cc_start: 0.8750 (ppp) cc_final: 0.8476 (ppp) REVERT: K 397 ASP cc_start: 0.8493 (t0) cc_final: 0.8269 (t0) REVERT: K 493 LYS cc_start: 0.8706 (tttt) cc_final: 0.8451 (ttmm) outliers start: 15 outliers final: 8 residues processed: 152 average time/residue: 0.1445 time to fit residues: 31.2042 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 : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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: 0.5980 chunk 16 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 145 optimal weight: 30.0000 chunk 60 optimal weight: 0.1980 chunk 133 optimal weight: 0.0470 chunk 49 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 69 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 GLN G 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.114599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.082835 restraints weight = 27383.917| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.96 r_work: 0.3130 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2224 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= 0.133 Angle : 0.509 8.412 23521 Z= 0.299 Chirality : 0.034 0.141 2705 Planarity : 0.004 0.044 1971 Dihedral : 28.633 138.754 4590 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.91 % Allowed : 11.81 % 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: 2.43 (0.24), residues: 1201 helix: 2.50 (0.19), residues: 727 sheet: 0.56 (0.60), residues: 85 loop : 0.20 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.023 0.001 TYR D 83 PHE 0.008 0.001 PHE G 25 TRP 0.003 0.001 TRP K 543 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00289 (16454) covalent geometry : angle 0.50875 (23521) hydrogen bonds : bond 0.03277 ( 922) hydrogen bonds : angle 3.01216 ( 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 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 145 time to evaluate : 0.329 Fit side-chains REVERT: A 58 THR cc_start: 0.9140 (p) cc_final: 0.8887 (p) REVERT: A 59 GLU cc_start: 0.7664 (pm20) cc_final: 0.7356 (pm20) REVERT: B 20 LYS cc_start: 0.8692 (tttm) cc_final: 0.8186 (ttmt) REVERT: C 94 ASN cc_start: 0.9091 (t0) cc_final: 0.8774 (t0) REVERT: E 59 GLU cc_start: 0.8079 (pm20) cc_final: 0.7516 (pm20) REVERT: E 77 ASP cc_start: 0.8390 (m-30) cc_final: 0.7951 (p0) REVERT: E 120 MET cc_start: 0.8278 (mtp) cc_final: 0.7910 (mtt) REVERT: G 72 ASP cc_start: 0.8667 (m-30) cc_final: 0.8408 (m-30) REVERT: H 42 TYR cc_start: 0.8058 (t80) cc_final: 0.7805 (t80) REVERT: K 202 HIS cc_start: 0.7840 (m90) cc_final: 0.7616 (m170) REVERT: K 318 MET cc_start: 0.8718 (ppp) cc_final: 0.8465 (ppp) REVERT: K 493 LYS cc_start: 0.8705 (tttt) cc_final: 0.8460 (ttmm) outliers start: 9 outliers final: 6 residues processed: 149 average time/residue: 0.1482 time to fit residues: 30.8458 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 : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 K residue 187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 70 optimal weight: 0.9980 chunk 7 optimal weight: 0.0970 chunk 104 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 141 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 125 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.115126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.082963 restraints weight = 27896.334| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.02 r_work: 0.3123 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16454 Z= 0.138 Angle : 0.512 9.067 23521 Z= 0.300 Chirality : 0.034 0.145 2705 Planarity : 0.004 0.043 1971 Dihedral : 28.635 138.752 4590 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.11 % Allowed : 12.11 % Favored : 86.78 % 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: 2.43 (0.24), residues: 1201 helix: 2.50 (0.19), residues: 727 sheet: 0.54 (0.59), residues: 85 loop : 0.20 (0.31), residues: 389 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 0.009 0.001 PHE E 84 TRP 0.005 0.001 TRP K 543 HIS 0.003 0.000 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00304 (16454) covalent geometry : angle 0.51213 (23521) hydrogen bonds : bond 0.03303 ( 922) hydrogen bonds : angle 3.01147 ( 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 155 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 144 time to evaluate : 0.401 Fit side-chains REVERT: A 58 THR cc_start: 0.9135 (p) cc_final: 0.8877 (p) REVERT: A 59 GLU cc_start: 0.7591 (pm20) cc_final: 0.7265 (pm20) REVERT: A 123 ASP cc_start: 0.8986 (m-30) cc_final: 0.8709 (m-30) REVERT: B 20 LYS cc_start: 0.8683 (tttm) cc_final: 0.8182 (ttmt) REVERT: C 94 ASN cc_start: 0.9085 (t0) cc_final: 0.8773 (t0) REVERT: E 59 GLU cc_start: 0.8074 (pm20) cc_final: 0.7508 (pm20) REVERT: E 77 ASP cc_start: 0.8389 (m-30) cc_final: 0.7945 (p0) REVERT: G 72 ASP cc_start: 0.8673 (m-30) cc_final: 0.8426 (m-30) REVERT: H 42 TYR cc_start: 0.8093 (t80) cc_final: 0.7842 (t80) REVERT: K 202 HIS cc_start: 0.7919 (m90) cc_final: 0.7709 (m170) REVERT: K 318 MET cc_start: 0.8792 (ppp) cc_final: 0.8517 (ppp) REVERT: K 493 LYS cc_start: 0.8701 (tttt) cc_final: 0.8452 (ttmm) REVERT: L 7 THR cc_start: 0.7864 (OUTLIER) cc_final: 0.7313 (t) outliers start: 11 outliers final: 8 residues processed: 150 average time/residue: 0.1508 time to fit residues: 31.8097 Evaluate side-chains 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR 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 271 LEU 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: 4.9990 chunk 3 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 43 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.078464 restraints weight = 27900.764| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.99 r_work: 0.3033 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16454 Z= 0.223 Angle : 0.568 9.189 23521 Z= 0.325 Chirality : 0.037 0.146 2705 Planarity : 0.004 0.045 1971 Dihedral : 29.158 138.130 4590 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.11 % Allowed : 11.91 % 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: 2.11 (0.24), residues: 1201 helix: 2.27 (0.19), residues: 726 sheet: 0.32 (0.59), residues: 85 loop : 0.04 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 42 TYR 0.012 0.002 TYR G 57 PHE 0.014 0.002 PHE G 25 TRP 0.001 0.001 TRP K 543 HIS 0.006 0.001 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00515 (16454) covalent geometry : angle 0.56847 (23521) hydrogen bonds : bond 0.03678 ( 922) hydrogen bonds : angle 3.22377 ( 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 151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.400 Fit side-chains REVERT: A 58 THR cc_start: 0.9294 (p) cc_final: 0.9051 (p) REVERT: A 59 GLU cc_start: 0.7766 (pm20) cc_final: 0.7437 (pm20) REVERT: B 20 LYS cc_start: 0.8645 (tttm) cc_final: 0.8147 (ttmt) REVERT: B 84 MET cc_start: 0.8464 (mmm) cc_final: 0.8258 (mmm) REVERT: C 94 ASN cc_start: 0.9121 (t0) cc_final: 0.8801 (t0) REVERT: E 59 GLU cc_start: 0.8213 (pm20) cc_final: 0.7623 (pm20) REVERT: E 120 MET cc_start: 0.8366 (mtp) cc_final: 0.7938 (mtt) REVERT: H 42 TYR cc_start: 0.8089 (t80) cc_final: 0.7843 (t80) REVERT: K 202 HIS cc_start: 0.7973 (m90) cc_final: 0.7713 (m170) REVERT: K 318 MET cc_start: 0.8916 (ppp) cc_final: 0.8657 (ppp) REVERT: K 493 LYS cc_start: 0.8737 (tttt) cc_final: 0.8451 (ttmm) REVERT: L 7 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7469 (t) outliers start: 11 outliers final: 8 residues processed: 147 average time/residue: 0.1533 time to fit residues: 31.8603 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR 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 H residue 39 ILE Chi-restraints excluded: chain K residue 187 LEU Chi-restraints excluded: chain K residue 271 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 68 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN E 113 HIS H 84 ASN L 49 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.112882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.080660 restraints weight = 27856.448| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.00 r_work: 0.3076 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16454 Z= 0.153 Angle : 0.533 9.178 23521 Z= 0.308 Chirality : 0.035 0.146 2705 Planarity : 0.004 0.043 1971 Dihedral : 28.882 138.315 4590 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.81 % Allowed : 12.61 % Favored : 86.58 % 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: 2.24 (0.24), residues: 1201 helix: 2.37 (0.19), residues: 726 sheet: 0.36 (0.59), residues: 85 loop : 0.09 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.011 0.001 PHE G 25 TRP 0.004 0.001 TRP K 543 HIS 0.004 0.001 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00342 (16454) covalent geometry : angle 0.53326 (23521) hydrogen bonds : bond 0.03376 ( 922) hydrogen bonds : angle 3.11182 ( 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 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 58 THR cc_start: 0.9251 (p) cc_final: 0.8994 (p) REVERT: A 59 GLU cc_start: 0.7776 (pm20) cc_final: 0.7466 (pm20) REVERT: B 20 LYS cc_start: 0.8656 (tttm) cc_final: 0.8168 (ttmt) REVERT: B 84 MET cc_start: 0.8411 (mmm) cc_final: 0.8209 (mmm) REVERT: C 94 ASN cc_start: 0.9116 (t0) cc_final: 0.8801 (t0) REVERT: E 59 GLU cc_start: 0.8151 (pm20) cc_final: 0.7588 (pm20) REVERT: E 77 ASP cc_start: 0.8419 (m-30) cc_final: 0.8169 (m-30) REVERT: E 120 MET cc_start: 0.8308 (mtp) cc_final: 0.8012 (mtt) REVERT: H 42 TYR cc_start: 0.8087 (t80) cc_final: 0.7832 (t80) REVERT: H 59 MET cc_start: 0.8665 (tpp) cc_final: 0.8430 (tpp) REVERT: K 202 HIS cc_start: 0.7929 (m90) cc_final: 0.7719 (m170) REVERT: K 318 MET cc_start: 0.8922 (ppp) cc_final: 0.8427 (ppp) REVERT: K 493 LYS cc_start: 0.8731 (tttt) cc_final: 0.8447 (ttmm) REVERT: L 7 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7419 (t) outliers start: 8 outliers final: 6 residues processed: 143 average time/residue: 0.1531 time to fit residues: 30.8646 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 138 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR 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 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: 0.9990 chunk 105 optimal weight: 8.9990 chunk 145 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 117 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.113506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.081688 restraints weight = 27368.938| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.95 r_work: 0.3109 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16454 Z= 0.142 Angle : 0.524 9.093 23521 Z= 0.304 Chirality : 0.034 0.144 2705 Planarity : 0.004 0.043 1971 Dihedral : 28.784 138.711 4590 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.71 % Allowed : 12.82 % Favored : 86.48 % 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: 2.35 (0.24), residues: 1201 helix: 2.46 (0.19), residues: 726 sheet: 0.46 (0.60), residues: 85 loop : 0.10 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 86 TYR 0.013 0.001 TYR C 57 PHE 0.009 0.001 PHE E 84 TRP 0.004 0.001 TRP K 543 HIS 0.003 0.001 HIS K 347 Details of bonding type rmsd covalent geometry : bond 0.00316 (16454) covalent geometry : angle 0.52418 (23521) hydrogen bonds : bond 0.03308 ( 922) hydrogen bonds : angle 3.06777 ( 2369) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3130.43 seconds wall clock time: 54 minutes 17.60 seconds (3257.60 seconds total)