Starting phenix.real_space_refine on Fri Jul 3 12:56:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn8_40616/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_2026/8sn8_40616.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn8_40616/07_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-dev-6108/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: 2.66, per 1000 atoms: 0.18 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: 1.22 Conformation dependent library (CDL) restraints added in 534.5 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: 1.33 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: 2.27 Time building geometry restraints manager: 1.60 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: 21153 1.65 - 3.31: 970 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: 1.280 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.550 Find NCS groups from input model: 0.120 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.500 ------------------------------------------------------------------------------- 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 : 0.697 8.271 22186 Z= 0.600 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 0.69016 / 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 : 0.298 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: 0.8768 (mt) REVERT: G 76 THR cc_start: 0.9088 (p) cc_final: 0.8823 (t) REVERT: G 78 ILE cc_start: 0.9206 (mm) cc_final: 0.8968 (mm) REVERT: H 120 LYS cc_start: 0.9117 (ttmt) cc_final: 0.8872 (tttp) REVERT: L 3 LEU cc_start: 0.8855 (mm) cc_final: 0.8637 (mm) REVERT: L 55 HIS cc_start: 0.7037 (m-70) cc_final: 0.6747 (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: 0.1514 time to fit residues: 47.1841 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 : 0.408 ------------------------------------------------------------------------------- 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 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.084884 restraints weight = 42545.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086782 restraints weight = 26164.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086932 restraints weight = 17164.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.087033 restraints weight = 16075.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.087232 restraints weight = 16012.615| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.0811 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 : 0.617 11.595 22186 Z= 0.360 Chirality : 0.042 0.234 2516 Planarity : 0.004 0.041 1794 Dihedral : 28.919 175.105 4413 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.73 % Allowed : 10.17 % 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: 2.34 (0.21), residues: 647 sheet: 1.02 (0.72), residues: 50 loop : -0.52 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 125 TYR 0.026 0.002 TYR L 145 PHE 0.013 0.001 PHE M 4 TRP 0.019 0.002 TRP L 33 HIS 0.006 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.16 (15472) covalent geometry : angle 0.60647 / 0.36 (22171) hydrogen bonds : bond 0.05534 / 3.65 ( 839) hydrogen bonds : angle 3.34265 / 2.38 ( 2136) metal coordination : bond 0.01133 / 0.47 ( 8) metal coordination : angle 5.61799 / 2.84 ( 9) link_TRANS : bond 0.00068 / 0.04 ( 2) link_TRANS : angle 0.41843 / 0.20 ( 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 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.389 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: 0.8822 (ttmt) cc_final: 0.8591 (ttmm) REVERT: G 23 LEU cc_start: 0.9250 (mt) cc_final: 0.8891 (mt) REVERT: G 76 THR cc_start: 0.9133 (p) cc_final: 0.8883 (t) REVERT: G 78 ILE cc_start: 0.9295 (mm) cc_final: 0.9093 (mm) REVERT: H 85 LYS cc_start: 0.8965 (mttp) cc_final: 0.8651 (mtmm) REVERT: H 120 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8922 (tttp) REVERT: K 21 GLU cc_start: 0.6753 (mt-10) cc_final: 0.6383 (mt-10) REVERT: K 79 ILE cc_start: 0.8042 (mm) cc_final: 0.7779 (mm) REVERT: L 8 LYS cc_start: 0.9435 (tptm) cc_final: 0.9172 (tptp) REVERT: L 33 TRP cc_start: 0.8607 (m100) cc_final: 0.8269 (m100) REVERT: M 1 MET cc_start: 0.5058 (ttt) cc_final: 0.2718 (tpt) outliers start: 16 outliers final: 11 residues processed: 202 average time/residue: 0.1561 time to fit residues: 43.1359 Evaluate side-chains 198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 187 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 80 THR 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 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: 0.8980 chunk 100 optimal weight: 0.0370 chunk 39 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.137366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.082629 restraints weight = 37792.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.084729 restraints weight = 21776.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.086090 restraints weight = 15779.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086781 restraints weight = 13328.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.087260 restraints weight = 12254.228| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15482 Z= 0.145 Angle : 0.587 11.430 22186 Z= 0.341 Chirality : 0.040 0.213 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.126 175.427 4413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.38 % Allowed : 11.47 % Favored : 86.15 % 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: 2.04 (0.26), residues: 1057 helix: 2.39 (0.20), residues: 650 sheet: 0.91 (0.71), 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 0.023 0.001 TYR H 40 PHE 0.010 0.001 PHE L 69 TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.14 (15472) covalent geometry : angle 0.57607 / 0.34 (22171) hydrogen bonds : bond 0.05096 / 3.39 ( 839) hydrogen bonds : angle 3.21602 / 2.30 ( 2136) metal coordination : bond 0.01198 / 0.53 ( 8) metal coordination : angle 5.63405 / 2.80 ( 9) link_TRANS : bond 0.00080 / 0.04 ( 2) link_TRANS : angle 0.40634 / 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 214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 192 time to evaluate : 0.311 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: B 88 TYR cc_start: 0.8749 (m-10) cc_final: 0.7592 (m-10) REVERT: D 83 TYR cc_start: 0.7570 (m-10) cc_final: 0.6229 (m-80) REVERT: D 116 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8577 (ttmm) REVERT: G 23 LEU cc_start: 0.9294 (mt) cc_final: 0.8970 (mt) REVERT: G 76 THR cc_start: 0.9145 (p) cc_final: 0.8880 (t) REVERT: G 78 ILE cc_start: 0.9284 (mm) cc_final: 0.9012 (mm) REVERT: H 120 LYS cc_start: 0.9292 (ttmt) cc_final: 0.8889 (tttp) REVERT: K 56 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8218 (tpp80) REVERT: K 79 ILE cc_start: 0.7810 (mm) cc_final: 0.7517 (mm) REVERT: L 33 TRP cc_start: 0.8730 (m100) cc_final: 0.8287 (m100) REVERT: M 1 MET cc_start: 0.5828 (ttt) cc_final: 0.3670 (tpt) outliers start: 22 outliers final: 19 residues processed: 203 average time/residue: 0.1424 time to fit residues: 39.5604 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 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 = 0.136463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083521 restraints weight = 49080.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085469 restraints weight = 29073.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.085562 restraints weight = 19587.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.085822 restraints weight = 21097.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.085965 restraints weight = 17393.755| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1170 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= 0.159 Angle : 0.597 11.258 22186 Z= 0.342 Chirality : 0.040 0.213 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.293 175.180 4413 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.71 % Allowed : 12.88 % Favored : 84.42 % 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: 1.97 (0.26), residues: 1057 helix: 2.36 (0.20), residues: 650 sheet: 0.78 (0.69), residues: 50 loop : -0.65 (0.30), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 53 TYR 0.017 0.002 TYR D 83 PHE 0.011 0.001 PHE L 69 TRP 0.010 0.001 TRP L 33 HIS 0.003 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.16 (15472) covalent geometry : angle 0.58688 / 0.34 (22171) hydrogen bonds : bond 0.05170 / 3.44 ( 839) hydrogen bonds : angle 3.24112 / 2.32 ( 2136) metal coordination : bond 0.01145 / 0.53 ( 8) metal coordination : angle 5.59116 / 2.80 ( 9) link_TRANS : bond 0.00038 / 0.02 ( 2) link_TRANS : angle 0.47048 / 0.22 ( 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 217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 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: D 116 LYS cc_start: 0.8853 (ttmt) cc_final: 0.8619 (ttmm) REVERT: F 84 MET cc_start: 0.8658 (mmm) cc_final: 0.8438 (mmm) REVERT: G 23 LEU cc_start: 0.9139 (mt) cc_final: 0.8788 (mt) REVERT: G 76 THR cc_start: 0.9155 (p) cc_final: 0.8875 (t) REVERT: G 78 ILE cc_start: 0.9330 (mm) cc_final: 0.9070 (mm) REVERT: H 40 TYR cc_start: 0.8769 (m-80) cc_final: 0.8455 (m-10) REVERT: H 120 LYS cc_start: 0.9278 (ttmt) cc_final: 0.8926 (tttp) REVERT: K 21 GLU cc_start: 0.6161 (mt-10) cc_final: 0.5933 (mt-10) REVERT: K 56 ARG cc_start: 0.8537 (tpp80) cc_final: 0.8241 (tpp80) REVERT: K 79 ILE cc_start: 0.7775 (mm) cc_final: 0.7453 (mm) REVERT: L 33 TRP cc_start: 0.8715 (m100) cc_final: 0.8270 (m100) outliers start: 25 outliers final: 23 residues processed: 206 average time/residue: 0.1434 time to fit residues: 40.5232 Evaluate side-chains 209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 186 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 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 34 GLN 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: 0.9980 chunk 4 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 0.0980 chunk 126 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3718 r_free = 0.3718 target = 0.136555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.082970 restraints weight = 41234.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.084517 restraints weight = 23567.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.085115 restraints weight = 17111.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.085274 restraints weight = 14677.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.085584 restraints weight = 14726.748| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 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 0.043 15482 Z= 0.148 Angle : 0.597 11.087 22186 Z= 0.341 Chirality : 0.041 0.363 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.359 175.235 4413 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.71 % Allowed : 14.18 % Favored : 83.12 % 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: 1.97 (0.26), residues: 1057 helix: 2.34 (0.20), residues: 652 sheet: 0.79 (0.69), residues: 50 loop : -0.63 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 139 TYR 0.026 0.001 TYR D 83 PHE 0.011 0.001 PHE K 53 TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (15472) covalent geometry : angle 0.58632 / 0.34 (22171) hydrogen bonds : bond 0.05052 / 3.36 ( 839) hydrogen bonds : angle 3.19517 / 2.29 ( 2136) metal coordination : bond 0.01047 / 0.47 ( 8) metal coordination : angle 5.51097 / 2.75 ( 9) link_TRANS : bond 0.00040 / 0.02 ( 2) link_TRANS : angle 0.40618 / 0.19 ( 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 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 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 59 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8561 (tpp) REVERT: F 84 MET cc_start: 0.8794 (mmm) cc_final: 0.8570 (mmm) REVERT: G 23 LEU cc_start: 0.9173 (mt) cc_final: 0.8839 (mt) REVERT: G 76 THR cc_start: 0.9166 (p) cc_final: 0.8893 (t) REVERT: G 78 ILE cc_start: 0.9302 (mm) cc_final: 0.9040 (mm) REVERT: H 40 TYR cc_start: 0.8901 (m-80) cc_final: 0.8537 (m-10) REVERT: H 120 LYS cc_start: 0.9293 (ttmt) cc_final: 0.8889 (tttp) REVERT: K 21 GLU cc_start: 0.6233 (mt-10) cc_final: 0.5933 (mt-10) REVERT: K 56 ARG cc_start: 0.8496 (tpp80) cc_final: 0.8140 (tpp80) REVERT: L 8 LYS cc_start: 0.9438 (tptp) cc_final: 0.9161 (tptm) REVERT: L 33 TRP cc_start: 0.8793 (m100) cc_final: 0.8282 (m100) REVERT: L 101 LYS cc_start: 0.9554 (mmmm) cc_final: 0.9282 (mmmm) outliers start: 25 outliers final: 23 residues processed: 203 average time/residue: 0.1583 time to fit residues: 44.0181 Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 59 MET 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 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 34 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.9980 chunk 63 optimal weight: 0.0770 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 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 = 0.3731 r_free = 0.3731 target = 0.137589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.085655 restraints weight = 41457.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.086659 restraints weight = 24925.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086924 restraints weight = 18731.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.086969 restraints weight = 17395.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.087120 restraints weight = 16765.551| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 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 = 0.2934 r_free = 0.2934 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: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15482 Z= 0.133 Angle : 0.592 14.235 22186 Z= 0.335 Chirality : 0.041 0.533 2516 Planarity : 0.004 0.063 1794 Dihedral : 29.378 175.267 4413 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.49 % Allowed : 15.15 % Favored : 82.36 % 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: 2.42 (0.20), residues: 652 sheet: 0.79 (0.69), residues: 50 loop : -0.59 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 139 TYR 0.022 0.001 TYR D 83 PHE 0.012 0.001 PHE K 53 TRP 0.007 0.001 TRP L 33 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.13 (15472) covalent geometry : angle 0.58180 / 0.33 (22171) hydrogen bonds : bond 0.04762 / 3.19 ( 839) hydrogen bonds : angle 3.12186 / 2.24 ( 2136) metal coordination : bond 0.01046 / 0.45 ( 8) metal coordination : angle 5.42177 / 2.72 ( 9) link_TRANS : bond 0.00048 / 0.03 ( 2) link_TRANS : angle 0.33775 / 0.15 ( 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 224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8617 (m-10) cc_final: 0.7938 (m-10) REVERT: F 84 MET cc_start: 0.8774 (mmm) cc_final: 0.8548 (mmm) REVERT: G 23 LEU cc_start: 0.9124 (mt) cc_final: 0.8794 (mt) REVERT: G 76 THR cc_start: 0.9132 (p) cc_final: 0.8873 (t) REVERT: G 78 ILE cc_start: 0.9314 (mm) cc_final: 0.9034 (mm) REVERT: G 95 LYS cc_start: 0.9026 (OUTLIER) cc_final: 0.8735 (tttt) REVERT: H 40 TYR cc_start: 0.8840 (m-80) cc_final: 0.8484 (m-10) REVERT: H 120 LYS cc_start: 0.9228 (ttmt) cc_final: 0.8924 (tttp) REVERT: K 21 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5973 (mt-10) REVERT: K 56 ARG cc_start: 0.8413 (tpp80) cc_final: 0.8208 (tpp80) REVERT: L 8 LYS cc_start: 0.9375 (tptp) cc_final: 0.9037 (tptm) REVERT: L 33 TRP cc_start: 0.8760 (m100) cc_final: 0.8251 (m100) outliers start: 23 outliers final: 19 residues processed: 211 average time/residue: 0.1585 time to fit residues: 46.0051 Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 62 ILE 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 54 CYS Chi-restraints excluded: chain L residue 34 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.136589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.082316 restraints weight = 43243.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.084833 restraints weight = 27667.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.086315 restraints weight = 17380.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.086143 restraints weight = 16024.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.086205 restraints weight = 15295.778| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15482 Z= 0.153 Angle : 0.614 14.186 22186 Z= 0.343 Chirality : 0.041 0.456 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.476 174.995 4413 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.03 % Allowed : 15.80 % Favored : 81.17 % 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: 2.00 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 652 sheet: 0.80 (0.68), residues: 50 loop : -0.65 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.026 0.001 TYR D 83 PHE 0.010 0.001 PHE K 53 TRP 0.008 0.001 TRP K 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (15472) covalent geometry : angle 0.60479 / 0.34 (22171) hydrogen bonds : bond 0.04992 / 3.33 ( 839) hydrogen bonds : angle 3.19926 / 2.30 ( 2136) metal coordination : bond 0.00998 / 0.47 ( 8) metal coordination : angle 5.35711 / 2.65 ( 9) link_TRANS : bond 0.00033 / 0.02 ( 2) link_TRANS : angle 0.40363 / 0.18 ( 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 219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 191 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 84 MET cc_start: 0.8876 (mmm) cc_final: 0.8667 (mmm) REVERT: G 23 LEU cc_start: 0.9143 (mt) cc_final: 0.8816 (mt) REVERT: G 76 THR cc_start: 0.9162 (p) cc_final: 0.8887 (t) REVERT: G 78 ILE cc_start: 0.9333 (mm) cc_final: 0.9057 (mm) REVERT: H 40 TYR cc_start: 0.8922 (m-80) cc_final: 0.8614 (m-10) REVERT: H 120 LYS cc_start: 0.9257 (ttmt) cc_final: 0.8965 (tttp) REVERT: K 21 GLU cc_start: 0.6426 (mt-10) cc_final: 0.6186 (mt-10) REVERT: L 8 LYS cc_start: 0.9408 (tptp) cc_final: 0.9062 (tptm) REVERT: L 33 TRP cc_start: 0.8798 (m100) cc_final: 0.8246 (m100) outliers start: 28 outliers final: 24 residues processed: 205 average time/residue: 0.1490 time to fit residues: 42.0004 Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 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 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 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 34 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.0770 chunk 64 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3728 r_free = 0.3728 target = 0.137285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.084372 restraints weight = 47012.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.085537 restraints weight = 27442.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086027 restraints weight = 20898.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.086121 restraints weight = 17742.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.086320 restraints weight = 18329.222| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1559 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= 0.138 Angle : 0.602 14.769 22186 Z= 0.337 Chirality : 0.041 0.483 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.472 175.098 4413 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.81 % Allowed : 16.13 % 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: 652 sheet: 0.83 (0.68), residues: 50 loop : -0.66 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 139 TYR 0.020 0.001 TYR D 83 PHE 0.010 0.001 PHE K 53 TRP 0.014 0.001 TRP L 141 HIS 0.002 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15472) covalent geometry : angle 0.59285 / 0.34 (22171) hydrogen bonds : bond 0.04799 / 3.21 ( 839) hydrogen bonds : angle 3.14933 / 2.27 ( 2136) metal coordination : bond 0.00912 / 0.39 ( 8) metal coordination : angle 5.17718 / 2.54 ( 9) link_TRANS : bond 0.00019 / 0.01 ( 2) link_TRANS : angle 0.36016 / 0.16 ( 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 217 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 84 MET cc_start: 0.8880 (mmm) cc_final: 0.8673 (mmm) REVERT: G 23 LEU cc_start: 0.9131 (mt) cc_final: 0.8792 (mt) REVERT: G 76 THR cc_start: 0.9138 (p) cc_final: 0.8875 (t) REVERT: G 78 ILE cc_start: 0.9326 (mm) cc_final: 0.9049 (mm) REVERT: G 95 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8738 (tttt) REVERT: H 40 TYR cc_start: 0.8903 (m-80) cc_final: 0.8524 (m-10) REVERT: H 120 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8949 (tttp) REVERT: K 21 GLU cc_start: 0.6409 (mt-10) cc_final: 0.6173 (mt-10) REVERT: L 8 LYS cc_start: 0.9413 (tptp) cc_final: 0.9065 (tptm) REVERT: L 30 MET cc_start: 0.8387 (mmm) cc_final: 0.8172 (mmm) REVERT: L 33 TRP cc_start: 0.8818 (m100) cc_final: 0.8246 (m100) REVERT: L 101 LYS cc_start: 0.9515 (mmmm) cc_final: 0.9290 (mmmm) REVERT: L 147 MET cc_start: 0.6202 (mpp) cc_final: 0.5632 (mpp) outliers start: 26 outliers final: 22 residues processed: 204 average time/residue: 0.1569 time to fit residues: 44.2004 Evaluate side-chains 210 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 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 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 54 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 34 GLN 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: 6.9990 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.096948 restraints weight = 36380.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.099723 restraints weight = 55330.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100577 restraints weight = 27825.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.102598 restraints weight = 19404.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.102661 restraints weight = 18011.770| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3107 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3107 r_free = 0.3107 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3107 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15482 Z= 0.151 Angle : 0.621 15.067 22186 Z= 0.342 Chirality : 0.041 0.483 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.548 174.938 4413 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.81 % Allowed : 16.23 % Favored : 80.95 % 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: 1.93 (0.26), residues: 1057 helix: 2.36 (0.20), residues: 652 sheet: 0.84 (0.68), residues: 50 loop : -0.75 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 136 TYR 0.027 0.001 TYR D 83 PHE 0.010 0.001 PHE H 70 TRP 0.009 0.001 TRP L 141 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.15 (15472) covalent geometry : angle 0.61243 / 0.34 (22171) hydrogen bonds : bond 0.04996 / 3.34 ( 839) hydrogen bonds : angle 3.20469 / 2.31 ( 2136) metal coordination : bond 0.00958 / 0.44 ( 8) metal coordination : angle 5.28151 / 2.58 ( 9) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 0.40688 / 0.19 ( 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 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8486 (m-80) cc_final: 0.8102 (m-10) REVERT: F 84 MET cc_start: 0.8889 (mmm) cc_final: 0.8665 (mmm) REVERT: G 23 LEU cc_start: 0.9154 (mt) cc_final: 0.8895 (mt) REVERT: G 76 THR cc_start: 0.9151 (p) cc_final: 0.8884 (t) REVERT: G 78 ILE cc_start: 0.9347 (mm) cc_final: 0.9084 (mm) REVERT: G 95 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8700 (tttt) REVERT: H 40 TYR cc_start: 0.8953 (m-80) cc_final: 0.8600 (m-10) REVERT: L 8 LYS cc_start: 0.8932 (tptp) cc_final: 0.8614 (tptm) REVERT: L 33 TRP cc_start: 0.8332 (m100) cc_final: 0.8055 (m100) REVERT: L 147 MET cc_start: 0.4974 (mpp) cc_final: 0.4372 (mpp) outliers start: 26 outliers final: 21 residues processed: 201 average time/residue: 0.1467 time to fit residues: 40.7116 Evaluate side-chains 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 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 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 54 CYS Chi-restraints excluded: chain L residue 34 GLN 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: 0.5980 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 114 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3693 r_free = 0.3693 target = 0.134542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081219 restraints weight = 49104.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.083010 restraints weight = 27783.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.083023 restraints weight = 19849.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.083137 restraints weight = 18677.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.083298 restraints weight = 18667.915| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15482 Z= 0.203 Angle : 0.662 14.789 22186 Z= 0.359 Chirality : 0.043 0.462 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.664 174.883 4413 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.60 % Allowed : 16.56 % 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: 1.74 (0.26), residues: 1057 helix: 2.22 (0.20), residues: 652 sheet: 0.83 (0.68), residues: 50 loop : -0.88 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 15 TYR 0.038 0.002 TYR D 83 PHE 0.015 0.002 PHE H 70 TRP 0.009 0.001 TRP L 141 HIS 0.003 0.001 HIS G 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (15472) covalent geometry : angle 0.65327 / 0.36 (22171) hydrogen bonds : bond 0.05533 / 3.69 ( 839) hydrogen bonds : angle 3.35107 / 2.42 ( 2136) metal coordination : bond 0.01488 / 0.80 ( 8) metal coordination : angle 5.36926 / 2.65 ( 9) link_TRANS : bond 0.00096 / 0.05 ( 2) link_TRANS : angle 0.56222 / 0.27 ( 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 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 23 LEU cc_start: 0.9177 (mt) cc_final: 0.8865 (mt) REVERT: G 76 THR cc_start: 0.9213 (p) cc_final: 0.8909 (t) REVERT: G 78 ILE cc_start: 0.9410 (mm) cc_final: 0.9135 (mm) REVERT: H 40 TYR cc_start: 0.8956 (m-80) cc_final: 0.8649 (m-10) REVERT: K 56 ARG cc_start: 0.8242 (tpp80) cc_final: 0.8034 (tpp80) REVERT: K 91 ARG cc_start: 0.7041 (mmm-85) cc_final: 0.6024 (mmm-85) REVERT: L 8 LYS cc_start: 0.9400 (tptp) cc_final: 0.9028 (tptm) REVERT: L 33 TRP cc_start: 0.8857 (m100) cc_final: 0.8194 (m100) REVERT: L 147 MET cc_start: 0.6250 (mpp) cc_final: 0.5667 (mpp) outliers start: 24 outliers final: 22 residues processed: 203 average time/residue: 0.1517 time to fit residues: 42.3578 Evaluate side-chains 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 F residue 30 THR Chi-restraints excluded: chain F residue 73 THR 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 54 CYS Chi-restraints excluded: chain L residue 34 GLN 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 23 optimal weight: 2.9990 chunk 103 optimal weight: 0.0000 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 24 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN 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 = 0.3712 r_free = 0.3712 target = 0.136057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.082349 restraints weight = 42810.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.084691 restraints weight = 27572.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.084845 restraints weight = 18686.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.085128 restraints weight = 18741.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.085194 restraints weight = 17491.625| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2814 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2814 r_free = 0.2814 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2814 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15482 Z= 0.146 Angle : 0.623 15.304 22186 Z= 0.343 Chirality : 0.041 0.438 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.601 175.363 4413 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.49 % Allowed : 16.88 % Favored : 80.63 % 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: 1.83 (0.26), residues: 1057 helix: 2.29 (0.21), residues: 652 sheet: 0.77 (0.68), residues: 50 loop : -0.82 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 139 TYR 0.032 0.001 TYR D 83 PHE 0.009 0.001 PHE L 62 TRP 0.010 0.001 TRP L 141 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (15472) covalent geometry : angle 0.61416 / 0.34 (22171) hydrogen bonds : bond 0.05045 / 3.38 ( 839) hydrogen bonds : angle 3.22170 / 2.33 ( 2136) metal coordination : bond 0.00921 / 0.40 ( 8) metal coordination : angle 5.28184 / 2.63 ( 9) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 0.42765 / 0.20 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2608.26 seconds wall clock time: 45 minutes 39.22 seconds (2739.22 seconds total)