Starting phenix.real_space_refine on Thu Aug 6 07:47:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn8_40616/08_2026/8sn8_40616.cif" } resolution = 3.7 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 34.250 72.890 43.549 1.00 74.78 S ATOM 12446 SG CYS K 51 31.943 69.964 43.371 1.00 65.34 S ATOM 12470 SG CYS K 54 34.443 70.787 40.404 1.00 80.92 S ATOM 12187 SG CYS K 16 21.836 69.400 49.197 1.00 88.95 S ATOM 12205 SG CYS K 19 19.480 67.747 51.492 1.00 90.04 S ATOM 12335 SG CYS K 36 22.401 69.913 52.882 1.00 73.23 S ATOM 12357 SG CYS K 39 23.142 66.555 51.678 1.00 76.19 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 2.91, per 1000 atoms: 0.20 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 132.8, 127.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 429.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 62.6% alpha, 5.3% beta 135 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 1.99 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.546A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.556A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.912A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.848A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.710A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.542A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.578A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.545A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.685A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.796A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.960A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.598A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 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: 3.805A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.729A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 3.667A pdb=" N SER K 42 " --> pdb=" O PRO K 38 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL K 44 " --> pdb=" O PHE K 40 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LYS K 46 " --> pdb=" O SER K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.800A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.054A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.586A pdb=" N ASP L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 removed outlier: 4.267A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N SER L 91 " --> pdb=" O ASP L 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 86 through 91' Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.642A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.530A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 147 removed outlier: 3.550A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N MET L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.862A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.878A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.789A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.187A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.737A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 492 hydrogen bonds defined for protein. 1446 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3565 1.34 - 1.46: 4321 1.46 - 1.58: 6951 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC I -8 " pdb=" C2' DC I -8 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DG I 2 " pdb=" C2' DG I 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 21141 1.65 - 3.31: 982 3.31 - 4.96: 37 4.96 - 6.62: 8 6.62 - 8.27: 3 Bond angle restraints: 22171 Sorted by residual: angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.52 -2.62 6.00e-01 2.78e+00 1.91e+01 angle pdb=" O4' DA J 42 " pdb=" C4' DA J 42 " pdb=" C3' DA J 42 " ideal model delta sigma weight residual 106.00 103.39 2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 7276 35.54 - 71.07: 1315 71.07 - 106.61: 18 106.61 - 142.14: 0 142.14 - 177.68: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.68 -177.68 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.80 145.20 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" CA PHE K 53 " pdb=" C PHE K 53 " pdb=" N CYS K 54 " pdb=" CA CYS K 54 " ideal model delta harmonic sigma weight residual -180.00 -161.65 -18.35 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1576 0.035 - 0.069: 627 0.069 - 0.104: 249 0.104 - 0.138: 62 0.138 - 0.173: 2 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CB ILE D 94 " pdb=" CA ILE D 94 " pdb=" CG1 ILE D 94 " pdb=" CG2 ILE D 94 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA GLU K 25 " pdb=" N GLU K 25 " pdb=" C GLU K 25 " pdb=" CB GLU K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG K 55 " 0.146 9.50e-02 1.11e+02 6.56e-02 2.79e+00 pdb=" NE ARG K 55 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG K 55 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG K 55 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG K 55 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.62e+00 pdb=" N PRO D 103 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.026 5.00e-02 4.00e+02 3.93e-02 2.47e+00 pdb=" N PRO K 38 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.022 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 865 2.73 - 3.27: 13390 3.27 - 3.81: 26953 3.81 - 4.36: 31182 4.36 - 4.90: 47064 Nonbonded interactions: 119454 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.185 2.496 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.255 3.040 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 2.256 3.040 nonbonded pdb=" NZ LYS M 63 " pdb=" OE2 GLU M 64 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR M 22 " pdb=" OE1 GLU M 24 " model vdw 2.276 3.040 ... (remaining 119449 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.270 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 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 : 0.005 0.034 15482 Z= 0.473 Angle : 0.702 8.271 22186 Z= 0.604 Chirality : 0.043 0.173 2516 Planarity : 0.004 0.066 1794 Dihedral : 25.620 177.679 6577 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.06 (0.26), residues: 1057 helix: 2.45 (0.21), residues: 629 sheet: 1.04 (0.72), residues: 50 loop : -0.47 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 55 TYR 0.018 0.001 TYR H 40 PHE 0.014 0.001 PHE M 4 TRP 0.009 0.001 TRP K 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00525 / 0.47 (15472) covalent geometry : angle 0.69571 / 0.60 (22171) hydrogen bonds : bond 0.11204 / 7.28 ( 839) hydrogen bonds : angle 3.88805 / 2.75 ( 2136) metal coordination : bond 0.00814 / 0.37 ( 8) metal coordination : angle 4.88649 / 2.45 ( 9) link_TRANS : bond 0.00223 / 0.11 ( 2) link_TRANS : angle 0.46730 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8756 (ttmt) cc_final: 0.8553 (ttmm) REVERT: G 23 LEU cc_start: 0.9114 (mt) cc_final: 0.8770 (mt) REVERT: G 78 ILE cc_start: 0.9206 (mm) cc_final: 0.8977 (mm) REVERT: H 120 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8873 (tttp) REVERT: L 3 LEU cc_start: 0.8855 (mm) cc_final: 0.8638 (mm) REVERT: L 55 HIS cc_start: 0.7037 (m-70) cc_final: 0.6750 (m-70) REVERT: M 1 MET cc_start: 0.3502 (ttt) cc_final: 0.1500 (tpt) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1617 time to fit residues: 50.5774 Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0000 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS L 32 HIS L 34 GLN ** L 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099559 restraints weight = 42616.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.103099 restraints weight = 68593.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103832 restraints weight = 25210.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106310 restraints weight = 18905.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.106357 restraints weight = 14087.804| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.0807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15482 Z= 0.155 Angle : 0.624 11.600 22186 Z= 0.362 Chirality : 0.042 0.235 2516 Planarity : 0.004 0.041 1794 Dihedral : 28.876 175.522 4413 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.52 % Allowed : 10.39 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.01 (0.26), residues: 1057 helix: 2.35 (0.21), residues: 647 sheet: 1.04 (0.72), residues: 50 loop : -0.53 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 125 TYR 0.024 0.002 TYR L 145 PHE 0.013 0.001 PHE M 4 TRP 0.021 0.003 TRP L 33 HIS 0.007 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.15 (15472) covalent geometry : angle 0.61336 / 0.36 (22171) hydrogen bonds : bond 0.05535 / 3.65 ( 839) hydrogen bonds : angle 3.33933 / 2.37 ( 2136) metal coordination : bond 0.01163 / 0.49 ( 8) metal coordination : angle 5.63772 / 2.85 ( 9) link_TRANS : bond 0.00060 / 0.03 ( 2) link_TRANS : angle 0.43782 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8584 (ttmm) REVERT: G 23 LEU cc_start: 0.9254 (mt) cc_final: 0.8983 (mt) REVERT: H 85 LYS cc_start: 0.8985 (mttp) cc_final: 0.8657 (mtmm) REVERT: H 120 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8948 (tttp) REVERT: K 79 ILE cc_start: 0.8475 (mm) cc_final: 0.8237 (mm) REVERT: L 8 LYS cc_start: 0.8973 (tptm) cc_final: 0.8691 (tptp) REVERT: M 1 MET cc_start: 0.3448 (ttt) cc_final: 0.1424 (tpt) outliers start: 14 outliers final: 8 residues processed: 202 average time/residue: 0.1561 time to fit residues: 42.9208 Evaluate side-chains 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 187 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 100 optimal weight: 0.0470 chunk 39 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 77 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 2.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.138085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.098978 restraints weight = 37666.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.101577 restraints weight = 55978.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102523 restraints weight = 28362.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105405 restraints weight = 19561.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.105341 restraints weight = 16196.778| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15482 Z= 0.144 Angle : 0.600 11.582 22186 Z= 0.346 Chirality : 0.041 0.217 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.084 175.677 4413 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.71 % Allowed : 11.58 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 650 sheet: 0.84 (0.70), residues: 50 loop : -0.59 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 55 TYR 0.017 0.001 TYR H 40 PHE 0.010 0.001 PHE L 69 TRP 0.041 0.003 TRP L 33 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.14 (15472) covalent geometry : angle 0.59005 / 0.35 (22171) hydrogen bonds : bond 0.05106 / 3.40 ( 839) hydrogen bonds : angle 3.21200 / 2.29 ( 2136) metal coordination : bond 0.01223 / 0.55 ( 8) metal coordination : angle 5.39834 / 2.70 ( 9) link_TRANS : bond 0.00076 / 0.04 ( 2) link_TRANS : angle 0.40308 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 193 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8502 (m-10) cc_final: 0.7685 (m-10) REVERT: D 83 TYR cc_start: 0.7558 (m-10) cc_final: 0.6365 (m-80) REVERT: D 116 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8591 (ttmm) REVERT: G 23 LEU cc_start: 0.9238 (mt) cc_final: 0.8956 (mt) REVERT: H 120 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8936 (tttp) REVERT: K 55 ARG cc_start: 0.6940 (OUTLIER) cc_final: 0.6529 (mtm180) REVERT: K 56 ARG cc_start: 0.8604 (tpp80) cc_final: 0.8402 (tpp80) REVERT: K 79 ILE cc_start: 0.8201 (mm) cc_final: 0.7937 (mm) REVERT: L 8 LYS cc_start: 0.9048 (tptm) cc_final: 0.8662 (tptm) REVERT: L 30 MET cc_start: 0.7605 (mmm) cc_final: 0.7390 (mmm) REVERT: L 92 GLN cc_start: 0.8380 (mm-40) cc_final: 0.8107 (mm-40) REVERT: M 1 MET cc_start: 0.3621 (ttt) cc_final: 0.1554 (tpt) outliers start: 25 outliers final: 21 residues processed: 205 average time/residue: 0.1480 time to fit residues: 42.1088 Evaluate side-chains 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 188 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.081454 restraints weight = 48957.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.083443 restraints weight = 26389.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.085167 restraints weight = 18514.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.084968 restraints weight = 15050.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085198 restraints weight = 14689.525| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (14 function evaluations) r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15482 Z= 0.167 Angle : 0.614 11.288 22186 Z= 0.348 Chirality : 0.041 0.219 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.259 175.307 4413 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.81 % Allowed : 12.34 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1057 helix: 2.34 (0.20), residues: 650 sheet: 0.71 (0.70), residues: 50 loop : -0.65 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 90 TYR 0.016 0.002 TYR H 121 PHE 0.011 0.001 PHE H 70 TRP 0.054 0.003 TRP L 33 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.17 (15472) covalent geometry : angle 0.60358 / 0.35 (22171) hydrogen bonds : bond 0.05306 / 3.53 ( 839) hydrogen bonds : angle 3.25364 / 2.33 ( 2136) metal coordination : bond 0.01186 / 0.56 ( 8) metal coordination : angle 5.57425 / 2.81 ( 9) link_TRANS : bond 0.00045 / 0.02 ( 2) link_TRANS : angle 0.48611 / 0.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8816 (ttmt) cc_final: 0.8590 (ttmm) REVERT: F 84 MET cc_start: 0.8693 (mmm) cc_final: 0.8426 (mmm) REVERT: G 23 LEU cc_start: 0.9151 (mt) cc_final: 0.8830 (mt) REVERT: H 40 TYR cc_start: 0.8830 (m-80) cc_final: 0.8505 (m-80) REVERT: H 120 LYS cc_start: 0.9313 (ttmt) cc_final: 0.8913 (tttp) REVERT: K 55 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6836 (mtm180) REVERT: K 56 ARG cc_start: 0.8523 (tpp80) cc_final: 0.8204 (tpp80) REVERT: K 79 ILE cc_start: 0.7583 (mm) cc_final: 0.7280 (mm) REVERT: L 30 MET cc_start: 0.8316 (mmm) cc_final: 0.8085 (mmm) REVERT: L 33 TRP cc_start: 0.8543 (m100) cc_final: 0.8224 (m100) REVERT: L 92 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8546 (mm-40) outliers start: 26 outliers final: 24 residues processed: 204 average time/residue: 0.1541 time to fit residues: 43.2756 Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 188 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 99 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 126 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.082339 restraints weight = 41312.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.084264 restraints weight = 24371.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.084865 restraints weight = 17054.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.084908 restraints weight = 15248.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086738 restraints weight = 14793.063| |-----------------------------------------------------------------------------| r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 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 0.038 15482 Z= 0.144 Angle : 0.597 11.115 22186 Z= 0.340 Chirality : 0.041 0.365 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.298 175.462 4413 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.14 % Allowed : 13.42 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1057 helix: 2.39 (0.20), residues: 651 sheet: 0.76 (0.69), residues: 50 loop : -0.66 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 55 TYR 0.016 0.001 TYR D 83 PHE 0.011 0.001 PHE K 53 TRP 0.027 0.002 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (15472) covalent geometry : angle 0.58659 / 0.34 (22171) hydrogen bonds : bond 0.05007 / 3.34 ( 839) hydrogen bonds : angle 3.17879 / 2.28 ( 2136) metal coordination : bond 0.01046 / 0.47 ( 8) metal coordination : angle 5.46834 / 2.75 ( 9) link_TRANS : bond 0.00035 / 0.02 ( 2) link_TRANS : angle 0.40129 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8827 (ttmt) cc_final: 0.8613 (ttmm) REVERT: F 84 MET cc_start: 0.8757 (mmm) cc_final: 0.8529 (mmm) REVERT: G 23 LEU cc_start: 0.9140 (mt) cc_final: 0.8824 (mt) REVERT: G 95 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8737 (tttt) REVERT: H 40 TYR cc_start: 0.8834 (m-80) cc_final: 0.8536 (m-80) REVERT: H 120 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8914 (tttp) REVERT: K 55 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6781 (mtm180) REVERT: K 56 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8214 (tpp80) REVERT: L 8 LYS cc_start: 0.9474 (tptp) cc_final: 0.9158 (tptm) REVERT: L 30 MET cc_start: 0.8276 (mmm) cc_final: 0.8003 (mmm) REVERT: L 33 TRP cc_start: 0.8612 (m100) cc_final: 0.8203 (m100) REVERT: L 92 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8518 (mm-40) REVERT: L 101 LYS cc_start: 0.9553 (mmmm) cc_final: 0.9281 (mmmm) outliers start: 29 outliers final: 25 residues processed: 206 average time/residue: 0.1462 time to fit residues: 41.2639 Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain K residue 55 ARG Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.9990 chunk 63 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 110 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** 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 = 0.3720 r_free = 0.3720 target = 0.136651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.081401 restraints weight = 41403.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.083557 restraints weight = 23078.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.084955 restraints weight = 16413.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085564 restraints weight = 13664.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086163 restraints weight = 12533.892| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2942 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2942 r_free = 0.2942 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2942 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15482 Z= 0.143 Angle : 0.602 13.125 22186 Z= 0.339 Chirality : 0.042 0.505 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.340 175.386 4413 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.25 % Allowed : 13.96 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.01 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 652 sheet: 0.78 (0.69), residues: 50 loop : -0.65 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 139 TYR 0.015 0.001 TYR H 121 PHE 0.010 0.001 PHE K 53 TRP 0.020 0.002 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.14 (15472) covalent geometry : angle 0.59242 / 0.34 (22171) hydrogen bonds : bond 0.04948 / 3.30 ( 839) hydrogen bonds : angle 3.18245 / 2.29 ( 2136) metal coordination : bond 0.00982 / 0.44 ( 8) metal coordination : angle 5.32781 / 2.68 ( 9) link_TRANS : bond 0.00029 / 0.01 ( 2) link_TRANS : angle 0.40090 / 0.18 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 196 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8685 (m-10) cc_final: 0.7927 (m-10) REVERT: D 59 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8514 (tpp) REVERT: D 116 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8621 (ttmm) REVERT: F 84 MET cc_start: 0.8830 (mmm) cc_final: 0.8619 (mmm) REVERT: G 23 LEU cc_start: 0.9177 (mt) cc_final: 0.8882 (mt) REVERT: G 95 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8747 (tttt) REVERT: H 40 TYR cc_start: 0.8924 (m-80) cc_final: 0.8605 (m-80) REVERT: H 120 LYS cc_start: 0.9281 (ttmt) cc_final: 0.8921 (tttp) REVERT: K 56 ARG cc_start: 0.8525 (tpp80) cc_final: 0.8224 (tpp80) REVERT: L 8 LYS cc_start: 0.9444 (tptp) cc_final: 0.9112 (tptm) REVERT: L 30 MET cc_start: 0.8112 (mmm) cc_final: 0.7828 (mmm) REVERT: L 33 TRP cc_start: 0.8608 (m100) cc_final: 0.8142 (m100) REVERT: L 101 LYS cc_start: 0.9610 (mmmm) cc_final: 0.9369 (mmmm) outliers start: 30 outliers final: 26 residues processed: 208 average time/residue: 0.1354 time to fit residues: 38.6293 Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.0970 chunk 9 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** 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 = 0.3730 r_free = 0.3730 target = 0.137370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085247 restraints weight = 43186.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086614 restraints weight = 25441.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.086910 restraints weight = 18243.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.086975 restraints weight = 17761.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.087170 restraints weight = 17448.933| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15482 Z= 0.137 Angle : 0.601 14.855 22186 Z= 0.337 Chirality : 0.042 0.496 2516 Planarity : 0.004 0.046 1794 Dihedral : 29.380 175.337 4413 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.35 % Allowed : 14.39 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.05 (0.26), residues: 1057 helix: 2.45 (0.20), residues: 651 sheet: 0.82 (0.69), residues: 50 loop : -0.67 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 5 TYR 0.016 0.001 TYR H 121 PHE 0.010 0.001 PHE K 53 TRP 0.020 0.001 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15472) covalent geometry : angle 0.59124 / 0.34 (22171) hydrogen bonds : bond 0.04815 / 3.22 ( 839) hydrogen bonds : angle 3.15103 / 2.27 ( 2136) metal coordination : bond 0.00995 / 0.43 ( 8) metal coordination : angle 5.37431 / 2.69 ( 9) link_TRANS : bond 0.00027 / 0.01 ( 2) link_TRANS : angle 0.36594 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8701 (m-10) cc_final: 0.8149 (m-10) REVERT: D 116 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8641 (ttmm) REVERT: F 84 MET cc_start: 0.8861 (mmm) cc_final: 0.8655 (mmm) REVERT: G 23 LEU cc_start: 0.9123 (mt) cc_final: 0.8827 (mt) REVERT: G 95 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8733 (tttt) REVERT: H 40 TYR cc_start: 0.8847 (m-80) cc_final: 0.8556 (m-80) REVERT: H 120 LYS cc_start: 0.9247 (ttmt) cc_final: 0.8962 (tttp) REVERT: K 56 ARG cc_start: 0.8519 (tpp80) cc_final: 0.8305 (tpp80) REVERT: L 5 ARG cc_start: 0.8740 (tpt-90) cc_final: 0.8518 (tpt-90) REVERT: L 8 LYS cc_start: 0.9399 (tptp) cc_final: 0.9069 (tptm) REVERT: L 30 MET cc_start: 0.8124 (mmm) cc_final: 0.7814 (mmm) REVERT: L 33 TRP cc_start: 0.8665 (m100) cc_final: 0.8196 (m100) outliers start: 31 outliers final: 27 residues processed: 212 average time/residue: 0.1389 time to fit residues: 40.7149 Evaluate side-chains 220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 192 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS ** M 2 GLN ** 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 = 0.3718 r_free = 0.3718 target = 0.136447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.083364 restraints weight = 46755.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.085088 restraints weight = 27658.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.085335 restraints weight = 19292.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.085363 restraints weight = 18475.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.085521 restraints weight = 17640.363| |-----------------------------------------------------------------------------| r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15482 Z= 0.155 Angle : 0.621 14.533 22186 Z= 0.344 Chirality : 0.041 0.470 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.440 175.135 4413 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.14 % Allowed : 15.58 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1057 helix: 2.39 (0.20), residues: 653 sheet: 0.90 (0.68), residues: 50 loop : -0.72 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 90 TYR 0.016 0.001 TYR H 121 PHE 0.010 0.001 PHE H 70 TRP 0.017 0.001 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (15472) covalent geometry : angle 0.61171 / 0.34 (22171) hydrogen bonds : bond 0.05017 / 3.36 ( 839) hydrogen bonds : angle 3.20884 / 2.31 ( 2136) metal coordination : bond 0.01020 / 0.47 ( 8) metal coordination : angle 5.35047 / 2.66 ( 9) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 0.41559 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8655 (ttmm) REVERT: F 84 MET cc_start: 0.8919 (mmm) cc_final: 0.8717 (mmm) REVERT: G 23 LEU cc_start: 0.9135 (mt) cc_final: 0.8817 (mt) REVERT: G 95 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8742 (tttt) REVERT: H 40 TYR cc_start: 0.8851 (m-80) cc_final: 0.8421 (m-10) REVERT: H 120 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8968 (tttp) REVERT: K 56 ARG cc_start: 0.8492 (tpp80) cc_final: 0.8271 (tpp80) REVERT: L 8 LYS cc_start: 0.9445 (tptp) cc_final: 0.9112 (tptm) REVERT: L 30 MET cc_start: 0.8286 (mmm) cc_final: 0.7946 (mmm) REVERT: L 33 TRP cc_start: 0.8731 (m100) cc_final: 0.8147 (m100) outliers start: 29 outliers final: 25 residues processed: 203 average time/residue: 0.1419 time to fit residues: 39.6386 Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 10.9990 chunk 13 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 56 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** 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 = 0.3724 r_free = 0.3724 target = 0.136909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097057 restraints weight = 36464.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.100595 restraints weight = 55849.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.101088 restraints weight = 25684.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102329 restraints weight = 18585.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102680 restraints weight = 17627.470| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15482 Z= 0.141 Angle : 0.624 15.065 22186 Z= 0.345 Chirality : 0.041 0.459 2516 Planarity : 0.004 0.057 1794 Dihedral : 29.432 175.253 4413 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.25 % Allowed : 15.69 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1057 helix: 2.41 (0.20), residues: 653 sheet: 0.86 (0.68), residues: 50 loop : -0.69 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 90 TYR 0.016 0.001 TYR H 121 PHE 0.009 0.001 PHE K 53 TRP 0.016 0.002 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (15472) covalent geometry : angle 0.61525 / 0.34 (22171) hydrogen bonds : bond 0.04892 / 3.28 ( 839) hydrogen bonds : angle 3.17068 / 2.28 ( 2136) metal coordination : bond 0.00937 / 0.41 ( 8) metal coordination : angle 5.20883 / 2.59 ( 9) link_TRANS : bond 0.00019 / 0.01 ( 2) link_TRANS : angle 0.36530 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8900 (ttmt) cc_final: 0.8629 (ttmm) REVERT: F 84 MET cc_start: 0.8861 (mmm) cc_final: 0.8649 (mmm) REVERT: G 23 LEU cc_start: 0.9136 (mt) cc_final: 0.8884 (mt) REVERT: G 95 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8694 (tttt) REVERT: H 40 TYR cc_start: 0.8897 (m-80) cc_final: 0.8565 (m-10) REVERT: L 8 LYS cc_start: 0.8906 (tptp) cc_final: 0.8611 (tptm) REVERT: L 30 MET cc_start: 0.7597 (mmm) cc_final: 0.7377 (mmm) outliers start: 30 outliers final: 26 residues processed: 208 average time/residue: 0.1456 time to fit residues: 41.8805 Evaluate side-chains 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 189 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 0.0040 chunk 18 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 114 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** 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 = 0.3727 r_free = 0.3727 target = 0.137128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.082732 restraints weight = 49192.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085306 restraints weight = 29920.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.085724 restraints weight = 19349.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.086268 restraints weight = 16175.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.086442 restraints weight = 16767.981| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15482 Z= 0.139 Angle : 0.623 15.434 22186 Z= 0.344 Chirality : 0.041 0.473 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.438 175.241 4413 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.25 % Allowed : 15.91 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.26), residues: 1057 helix: 2.43 (0.20), residues: 651 sheet: 0.58 (0.68), residues: 50 loop : -0.71 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 136 TYR 0.023 0.001 TYR B 88 PHE 0.009 0.001 PHE K 53 TRP 0.064 0.004 TRP L 33 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (15472) covalent geometry : angle 0.61411 / 0.34 (22171) hydrogen bonds : bond 0.04862 / 3.27 ( 839) hydrogen bonds : angle 3.16289 / 2.28 ( 2136) metal coordination : bond 0.00906 / 0.39 ( 8) metal coordination : angle 5.16909 / 2.57 ( 9) link_TRANS : bond 0.00022 / 0.01 ( 2) link_TRANS : angle 0.36966 / 0.17 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 116 LYS cc_start: 0.8854 (ttmt) cc_final: 0.8642 (ttmm) REVERT: F 84 MET cc_start: 0.8905 (mmm) cc_final: 0.8694 (mmm) REVERT: G 23 LEU cc_start: 0.9135 (mt) cc_final: 0.8833 (mt) REVERT: G 95 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8730 (tttt) REVERT: H 40 TYR cc_start: 0.8893 (m-80) cc_final: 0.8639 (m-80) REVERT: L 8 LYS cc_start: 0.9443 (tptp) cc_final: 0.9090 (tptm) REVERT: L 133 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8302 (pttt) REVERT: L 147 MET cc_start: 0.6303 (mpp) cc_final: 0.5736 (mpp) outliers start: 30 outliers final: 26 residues processed: 209 average time/residue: 0.1538 time to fit residues: 44.4092 Evaluate side-chains 219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 49 LEU Chi-restraints excluded: chain K residue 54 CYS Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 133 LYS Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 chunk 24 optimal weight: 0.0870 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 2 GLN ** 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 = 0.3716 r_free = 0.3716 target = 0.136299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.082173 restraints weight = 43044.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.084409 restraints weight = 29397.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.085129 restraints weight = 17880.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.085158 restraints weight = 16761.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085292 restraints weight = 17001.669| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15482 Z= 0.158 Angle : 0.641 15.245 22186 Z= 0.350 Chirality : 0.042 0.474 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.491 175.101 4413 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.14 % Allowed : 16.56 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 651 sheet: 0.45 (0.68), residues: 50 loop : -0.78 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 136 TYR 0.018 0.001 TYR B 88 PHE 0.011 0.001 PHE L 56 TRP 0.034 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (15472) covalent geometry : angle 0.63217 / 0.35 (22171) hydrogen bonds : bond 0.05072 / 3.40 ( 839) hydrogen bonds : angle 3.21099 / 2.31 ( 2136) metal coordination : bond 0.00960 / 0.44 ( 8) metal coordination : angle 5.31601 / 2.64 ( 9) link_TRANS : bond 0.00037 / 0.02 ( 2) link_TRANS : angle 0.41782 / 0.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2504.84 seconds wall clock time: 43 minutes 47.39 seconds (2627.39 seconds total)