Starting phenix.real_space_refine on Fri Jul 3 12:59:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn4_40612/07_2026/8sn4_40612.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 8 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 33.347 72.273 47.031 1.00 86.22 S ATOM 12446 SG CYS K 51 34.177 68.839 45.573 1.00 81.44 S ATOM 12470 SG CYS K 54 33.180 71.557 43.284 1.00 91.27 S ATOM 12187 SG CYS K 16 23.217 66.833 52.909 1.00107.40 S ATOM 12205 SG CYS K 19 21.018 64.361 54.707 1.00109.20 S ATOM 12335 SG CYS K 36 24.056 65.730 56.569 1.00 99.38 S ATOM 12357 SG CYS K 39 24.585 63.331 53.903 1.00 91.82 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: 3.21, per 1000 atoms: 0.22 Number of scatterers: 14600 At special positions: 0 Unit cell: (111.552, 131.472, 126.16, 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: 1.18 Conformation dependent library (CDL) restraints added in 456.4 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 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " 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: 47 helices and 12 sheets defined 63.5% alpha, 5.2% beta 135 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.624A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.634A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.864A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.996A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.624A 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 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.664A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.642A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 83 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.624A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.766A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.835A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) 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 50 through 76 removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (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 removed outlier: 3.536A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.581A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.730A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.933A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.130A 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: 3.567A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.509A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.581A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 147 removed outlier: 4.138A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN L 143 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.926A 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 removed outlier: 3.521A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 7.910A 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: 6.378A 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: 7.165A 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 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.578A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 12 through 16 removed outlier: 9.416A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 2.03 Time building geometry restraints manager: 1.63 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: 3478 1.34 - 1.46: 4329 1.46 - 1.58: 7030 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 1.545 -0.029 8.00e-03 1.56e+04 1.35e+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 1.06e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 bond pdb=" C3' DC I 22 " pdb=" C2' DC I 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21325 1.85 - 3.69: 814 3.69 - 5.54: 25 5.54 - 7.39: 5 7.39 - 9.23: 2 Bond angle restraints: 22171 Sorted by residual: angle pdb=" O4' DA I -35 " pdb=" C4' DA I -35 " pdb=" C3' DA I -35 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 7271 35.62 - 71.24: 1314 71.24 - 106.86: 24 106.86 - 142.48: 0 142.48 - 178.10: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" CA ASP L 29 " pdb=" C ASP L 29 " pdb=" N MET L 30 " pdb=" CA MET L 30 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 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 38.10 -178.10 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 74.08 145.92 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2011 0.052 - 0.105: 447 0.105 - 0.157: 56 0.157 - 0.209: 1 0.209 - 0.262: 1 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CB ILE L 137 " pdb=" CA ILE L 137 " pdb=" CG1 ILE L 137 " pdb=" CG2 ILE L 137 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ARG L 136 " pdb=" N ARG L 136 " pdb=" C ARG L 136 " pdb=" CB ARG L 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.96e+00 pdb=" CG TRP L 33 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO K 38 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 43 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.025 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 421 2.69 - 3.24: 13054 3.24 - 3.79: 26064 3.79 - 4.35: 32194 4.35 - 4.90: 47740 Nonbonded interactions: 119473 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.136 2.496 nonbonded pdb=" O ASP L 87 " pdb=" OG SER L 91 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.222 3.120 nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.230 3.040 nonbonded pdb=" OG SER L 91 " pdb=" OE1 GLN L 92 " model vdw 2.237 3.040 ... (remaining 119468 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.100 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 0.051 15482 Z= 0.469 Angle : 0.702 9.232 22186 Z= 0.604 Chirality : 0.043 0.262 2516 Planarity : 0.004 0.049 1794 Dihedral : 25.751 178.102 6577 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % 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: 1.84 (0.26), residues: 1057 helix: 2.28 (0.21), residues: 643 sheet: 1.82 (0.76), residues: 48 loop : -0.85 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 136 TYR 0.022 0.001 TYR H 40 PHE 0.009 0.001 PHE D 65 TRP 0.038 0.003 TRP L 33 HIS 0.007 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.47 (15472) covalent geometry : angle 0.69767 / 0.60 (22171) hydrogen bonds : bond 0.10682 / 7.33 ( 842) hydrogen bonds : angle 4.11058 / 2.82 ( 2133) metal coordination : bond 0.01850 / 0.92 ( 8) metal coordination : angle 3.84400 / 1.99 ( 9) link_TRANS : bond 0.00188 / 0.09 ( 2) link_TRANS : angle 0.45399 / 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 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m110) REVERT: C 11 SER cc_start: 0.8505 (t) cc_final: 0.8201 (p) REVERT: D 40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8378 (m-80) REVERT: D 51 ASP cc_start: 0.7967 (p0) cc_final: 0.7741 (p0) REVERT: F 74 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7890 (tm-30) REVERT: L 7 ASN cc_start: 0.9107 (m-40) cc_final: 0.8813 (m110) REVERT: M 1 MET cc_start: 0.8023 (tmm) cc_final: 0.7345 (tmm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1165 time to fit residues: 34.6678 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN K 83 HIS M 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.136668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.078519 restraints weight = 41178.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.080765 restraints weight = 24639.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.081859 restraints weight = 16892.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.081821 restraints weight = 14138.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.082032 restraints weight = 14503.701| |-----------------------------------------------------------------------------| r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2797 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2797 r_free = 0.2797 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (9 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 15482 Z= 0.324 Angle : 0.779 12.962 22186 Z= 0.426 Chirality : 0.050 0.288 2516 Planarity : 0.006 0.067 1794 Dihedral : 29.268 173.182 4413 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.60 % Allowed : 11.26 % 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: 1.31 (0.26), residues: 1057 helix: 1.80 (0.20), residues: 649 sheet: 1.74 (0.76), residues: 53 loop : -1.04 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 79 TYR 0.030 0.003 TYR H 83 PHE 0.015 0.003 PHE D 70 TRP 0.033 0.004 TRP L 33 HIS 0.008 0.002 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00751 / 0.32 (15472) covalent geometry : angle 0.76916 / 0.43 (22171) hydrogen bonds : bond 0.07060 / 4.73 ( 842) hydrogen bonds : angle 3.88585 / 2.70 ( 2133) metal coordination : bond 0.01258 / 0.64 ( 8) metal coordination : angle 6.12518 / 2.86 ( 9) link_TRANS : bond 0.00229 / 0.11 ( 2) link_TRANS : angle 0.40457 / 0.18 ( 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8448 (m110) cc_final: 0.8203 (m110) REVERT: C 61 GLU cc_start: 0.9183 (tp30) cc_final: 0.8690 (tp30) REVERT: C 75 LYS cc_start: 0.8185 (mmtp) cc_final: 0.7956 (mmtt) REVERT: D 51 ASP cc_start: 0.7970 (p0) cc_final: 0.7724 (p0) REVERT: F 73 THR cc_start: 0.9486 (t) cc_final: 0.9210 (m) REVERT: F 74 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7813 (tm-30) REVERT: H 68 ASP cc_start: 0.9196 (t70) cc_final: 0.8934 (t0) REVERT: L 7 ASN cc_start: 0.9629 (m-40) cc_final: 0.9365 (m110) REVERT: L 60 TYR cc_start: 0.8910 (t80) cc_final: 0.8558 (t80) REVERT: M 1 MET cc_start: 0.8400 (tmm) cc_final: 0.7630 (tmm) REVERT: M 4 PHE cc_start: 0.9025 (m-10) cc_final: 0.8753 (m-10) outliers start: 24 outliers final: 19 residues processed: 194 average time/residue: 0.1135 time to fit residues: 31.4008 Evaluate side-chains 191 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 110 LEU 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: 7.9990 chunk 39 optimal weight: 0.5980 chunk 101 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS 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 = 0.140090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.091990 restraints weight = 36915.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.091593 restraints weight = 21857.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092445 restraints weight = 18443.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093329 restraints weight = 14788.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.093401 restraints weight = 14215.848| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2995 r_free = 0.2995 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15482 Z= 0.151 Angle : 0.618 10.342 22186 Z= 0.356 Chirality : 0.042 0.221 2516 Planarity : 0.005 0.049 1794 Dihedral : 29.182 176.303 4413 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.95 % Allowed : 15.48 % Favored : 82.58 % 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: 1.77 (0.26), residues: 1057 helix: 2.25 (0.20), residues: 648 sheet: 1.91 (0.77), residues: 53 loop : -1.06 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.027 0.002 TYR H 40 PHE 0.013 0.001 PHE L 50 TRP 0.031 0.003 TRP L 141 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (15472) covalent geometry : angle 0.60957 / 0.36 (22171) hydrogen bonds : bond 0.05311 / 3.57 ( 842) hydrogen bonds : angle 3.41358 / 2.36 ( 2133) metal coordination : bond 0.00628 / 0.26 ( 8) metal coordination : angle 4.98977 / 2.42 ( 9) link_TRANS : bond 0.00143 / 0.07 ( 2) link_TRANS : angle 0.30869 / 0.14 ( 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 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8816 (pm20) cc_final: 0.8584 (pm20) REVERT: B 25 ASN cc_start: 0.8373 (m110) cc_final: 0.8095 (m110) REVERT: C 61 GLU cc_start: 0.9138 (tp30) cc_final: 0.8638 (tp30) REVERT: D 40 TYR cc_start: 0.9259 (m-80) cc_final: 0.8505 (m-80) REVERT: D 51 ASP cc_start: 0.8104 (p0) cc_final: 0.7881 (p0) REVERT: E 90 MET cc_start: 0.8438 (mmm) cc_final: 0.8179 (mmp) REVERT: F 73 THR cc_start: 0.9485 (t) cc_final: 0.9220 (m) REVERT: F 74 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7726 (tm-30) REVERT: G 13 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8528 (mmtt) REVERT: H 68 ASP cc_start: 0.9199 (t70) cc_final: 0.8890 (t0) REVERT: H 83 TYR cc_start: 0.8617 (m-10) cc_final: 0.7973 (m-10) REVERT: K 83 HIS cc_start: 0.7903 (t-90) cc_final: 0.7677 (t70) REVERT: L 7 ASN cc_start: 0.9425 (m-40) cc_final: 0.9163 (m110) REVERT: L 32 HIS cc_start: 0.7089 (m90) cc_final: 0.6478 (m90) REVERT: L 60 TYR cc_start: 0.8626 (t80) cc_final: 0.8305 (t80) REVERT: M 1 MET cc_start: 0.8083 (tmm) cc_final: 0.7184 (tmm) outliers start: 18 outliers final: 13 residues processed: 185 average time/residue: 0.1137 time to fit residues: 30.1060 Evaluate side-chains 180 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 167 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.6980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 60 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 128 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.083241 restraints weight = 47963.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.085442 restraints weight = 24615.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086038 restraints weight = 14995.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.086738 restraints weight = 14611.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.086598 restraints weight = 13269.796| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1399 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= 0.148 Angle : 0.610 9.883 22186 Z= 0.350 Chirality : 0.042 0.240 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.243 176.282 4413 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.38 % Allowed : 15.80 % Favored : 81.82 % 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: 1.85 (0.26), residues: 1057 helix: 2.36 (0.20), residues: 650 sheet: 1.75 (0.78), residues: 53 loop : -1.11 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.027 0.001 TYR H 40 PHE 0.016 0.001 PHE L 50 TRP 0.043 0.004 TRP L 33 HIS 0.005 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (15472) covalent geometry : angle 0.60253 / 0.35 (22171) hydrogen bonds : bond 0.05032 / 3.41 ( 842) hydrogen bonds : angle 3.37948 / 2.33 ( 2133) metal coordination : bond 0.00631 / 0.28 ( 8) metal coordination : angle 4.64404 / 2.27 ( 9) link_TRANS : bond 0.00110 / 0.05 ( 2) link_TRANS : angle 0.22677 / 0.10 ( 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 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8820 (pm20) cc_final: 0.8487 (pm20) REVERT: B 25 ASN cc_start: 0.8490 (m110) cc_final: 0.8199 (m110) REVERT: C 61 GLU cc_start: 0.9153 (tp30) cc_final: 0.8667 (tp30) REVERT: C 74 LYS cc_start: 0.8890 (mmmt) cc_final: 0.8550 (mttm) REVERT: D 40 TYR cc_start: 0.9246 (m-80) cc_final: 0.8564 (m-80) REVERT: D 51 ASP cc_start: 0.8165 (p0) cc_final: 0.7934 (p0) REVERT: F 73 THR cc_start: 0.9496 (t) cc_final: 0.9188 (m) REVERT: F 74 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7694 (tm-30) REVERT: H 68 ASP cc_start: 0.9145 (t70) cc_final: 0.8812 (t0) REVERT: L 4 LYS cc_start: 0.9004 (ptpt) cc_final: 0.8516 (pttm) REVERT: L 7 ASN cc_start: 0.9632 (m-40) cc_final: 0.9375 (m110) REVERT: L 30 MET cc_start: 0.8315 (tpp) cc_final: 0.8106 (tpt) REVERT: L 32 HIS cc_start: 0.8539 (m90) cc_final: 0.8080 (m90) REVERT: L 37 ILE cc_start: 0.8811 (tp) cc_final: 0.8231 (tp) REVERT: L 38 MET cc_start: 0.8557 (pmm) cc_final: 0.7584 (mpp) REVERT: M 1 MET cc_start: 0.8492 (tmm) cc_final: 0.7592 (tmm) outliers start: 22 outliers final: 19 residues processed: 186 average time/residue: 0.1268 time to fit residues: 33.6106 Evaluate side-chains 185 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 126 optimal weight: 5.9990 chunk 60 optimal weight: 0.3980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS L 55 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.139310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092621 restraints weight = 40501.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.092689 restraints weight = 26987.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.093543 restraints weight = 20219.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.094396 restraints weight = 14618.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.094763 restraints weight = 13533.011| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15482 Z= 0.152 Angle : 0.606 9.433 22186 Z= 0.346 Chirality : 0.041 0.241 2516 Planarity : 0.004 0.046 1794 Dihedral : 29.308 176.179 4413 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.71 % Allowed : 17.42 % Favored : 79.87 % 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: 1.85 (0.26), residues: 1057 helix: 2.38 (0.20), residues: 650 sheet: 1.56 (0.76), residues: 53 loop : -1.11 (0.30), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.026 0.001 TYR H 40 PHE 0.018 0.001 PHE L 50 TRP 0.023 0.002 TRP L 33 HIS 0.006 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.15 (15472) covalent geometry : angle 0.59903 / 0.35 (22171) hydrogen bonds : bond 0.05010 / 3.39 ( 842) hydrogen bonds : angle 3.33805 / 2.31 ( 2133) metal coordination : bond 0.00746 / 0.35 ( 8) metal coordination : angle 4.56804 / 2.24 ( 9) link_TRANS : bond 0.00103 / 0.05 ( 2) link_TRANS : angle 0.20572 / 0.08 ( 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 194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8396 (tpp80) cc_final: 0.7847 (ttm110) REVERT: A 59 GLU cc_start: 0.8800 (pm20) cc_final: 0.8548 (pm20) REVERT: B 25 ASN cc_start: 0.8479 (m110) cc_final: 0.8199 (m110) REVERT: C 61 GLU cc_start: 0.9132 (tp30) cc_final: 0.8623 (tp30) REVERT: C 74 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8557 (mttm) REVERT: D 40 TYR cc_start: 0.9273 (m-80) cc_final: 0.8565 (m-80) REVERT: D 51 ASP cc_start: 0.8069 (p0) cc_final: 0.7833 (p0) REVERT: E 59 GLU cc_start: 0.7897 (pt0) cc_final: 0.7684 (pm20) REVERT: F 73 THR cc_start: 0.9514 (t) cc_final: 0.9258 (m) REVERT: F 74 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7680 (tm-30) REVERT: H 68 ASP cc_start: 0.9163 (t70) cc_final: 0.8817 (t0) REVERT: L 4 LYS cc_start: 0.8683 (ptpt) cc_final: 0.8058 (pttm) REVERT: L 7 ASN cc_start: 0.9354 (m-40) cc_final: 0.9129 (m110) REVERT: L 30 MET cc_start: 0.7845 (tpp) cc_final: 0.7638 (tpt) REVERT: L 37 ILE cc_start: 0.8437 (tp) cc_final: 0.8075 (tp) REVERT: L 38 MET cc_start: 0.8202 (pmm) cc_final: 0.7177 (mpp) REVERT: M 1 MET cc_start: 0.7849 (tmm) cc_final: 0.6979 (tmm) outliers start: 25 outliers final: 20 residues processed: 180 average time/residue: 0.1276 time to fit residues: 32.5480 Evaluate side-chains 185 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.139274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.081441 restraints weight = 40549.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084064 restraints weight = 23732.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.084652 restraints weight = 17401.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.085518 restraints weight = 13629.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.085723 restraints weight = 13711.577| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2886 r_free = 0.2886 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2886 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1593 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= 0.157 Angle : 0.614 9.440 22186 Z= 0.349 Chirality : 0.042 0.244 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.358 176.098 4413 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 18.29 % Favored : 79.00 % 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: 1.85 (0.26), residues: 1057 helix: 2.37 (0.20), residues: 650 sheet: 1.51 (0.77), residues: 53 loop : -1.08 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.036 0.002 TYR H 83 PHE 0.019 0.001 PHE L 50 TRP 0.020 0.002 TRP L 33 HIS 0.026 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (15472) covalent geometry : angle 0.60710 / 0.35 (22171) hydrogen bonds : bond 0.05005 / 3.38 ( 842) hydrogen bonds : angle 3.32419 / 2.31 ( 2133) metal coordination : bond 0.00808 / 0.38 ( 8) metal coordination : angle 4.73013 / 2.36 ( 9) link_TRANS : bond 0.00093 / 0.04 ( 2) link_TRANS : angle 0.20456 / 0.08 ( 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 198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 173 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8379 (tpp80) cc_final: 0.7835 (ttm110) REVERT: B 25 ASN cc_start: 0.8439 (m110) cc_final: 0.8182 (m110) REVERT: C 61 GLU cc_start: 0.9147 (tp30) cc_final: 0.8665 (tp30) REVERT: C 74 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8502 (mttm) REVERT: D 40 TYR cc_start: 0.9255 (m-80) cc_final: 0.8614 (m-80) REVERT: D 51 ASP cc_start: 0.8071 (p0) cc_final: 0.7828 (p0) REVERT: F 73 THR cc_start: 0.9547 (t) cc_final: 0.9297 (m) REVERT: F 74 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7633 (tm-30) REVERT: H 68 ASP cc_start: 0.9170 (t70) cc_final: 0.8869 (t0) REVERT: L 4 LYS cc_start: 0.8962 (ptpt) cc_final: 0.8373 (pttm) REVERT: L 7 ASN cc_start: 0.9617 (m-40) cc_final: 0.9328 (m110) REVERT: L 32 HIS cc_start: 0.8318 (m90) cc_final: 0.7966 (m90) REVERT: M 1 MET cc_start: 0.8422 (tmm) cc_final: 0.7524 (tmm) outliers start: 25 outliers final: 22 residues processed: 186 average time/residue: 0.1379 time to fit residues: 36.2843 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094871 restraints weight = 42382.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.095029 restraints weight = 30337.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.095305 restraints weight = 29484.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.096130 restraints weight = 17305.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.097167 restraints weight = 14982.961| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3039 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15482 Z= 0.146 Angle : 0.605 9.345 22186 Z= 0.344 Chirality : 0.041 0.241 2516 Planarity : 0.004 0.045 1794 Dihedral : 29.382 176.302 4413 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.81 % Allowed : 18.51 % Favored : 78.68 % 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: 1.92 (0.26), residues: 1057 helix: 2.44 (0.21), residues: 650 sheet: 1.44 (0.77), residues: 53 loop : -1.07 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.027 0.001 TYR H 40 PHE 0.019 0.001 PHE L 50 TRP 0.030 0.002 TRP L 33 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (15472) covalent geometry : angle 0.59736 / 0.34 (22171) hydrogen bonds : bond 0.04867 / 3.30 ( 842) hydrogen bonds : angle 3.27386 / 2.27 ( 2133) metal coordination : bond 0.00866 / 0.41 ( 8) metal coordination : angle 4.71456 / 2.36 ( 9) link_TRANS : bond 0.00074 / 0.04 ( 2) link_TRANS : angle 0.17828 / 0.07 ( 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 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7857 (ttm110) REVERT: B 25 ASN cc_start: 0.8433 (m110) cc_final: 0.8159 (m110) REVERT: C 61 GLU cc_start: 0.9137 (tp30) cc_final: 0.8632 (tp30) REVERT: C 74 LYS cc_start: 0.8883 (mmmt) cc_final: 0.8501 (mttm) REVERT: D 40 TYR cc_start: 0.9275 (m-80) cc_final: 0.8639 (m-80) REVERT: D 51 ASP cc_start: 0.8074 (p0) cc_final: 0.7844 (p0) REVERT: D 71 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7522 (mm-30) REVERT: D 113 GLU cc_start: 0.7999 (tt0) cc_final: 0.7798 (mt-10) REVERT: F 73 THR cc_start: 0.9536 (t) cc_final: 0.9298 (m) REVERT: F 74 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7641 (tm-30) REVERT: H 68 ASP cc_start: 0.9128 (t70) cc_final: 0.8757 (t0) REVERT: L 4 LYS cc_start: 0.8669 (ptpt) cc_final: 0.8102 (pttm) REVERT: L 7 ASN cc_start: 0.9369 (m-40) cc_final: 0.9111 (m110) REVERT: L 55 HIS cc_start: 0.8146 (t-170) cc_final: 0.7943 (t-170) REVERT: M 1 MET cc_start: 0.7889 (tmm) cc_final: 0.7029 (tmm) outliers start: 26 outliers final: 26 residues processed: 182 average time/residue: 0.1272 time to fit residues: 32.6833 Evaluate side-chains 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 169 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 120 VAL Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE 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: 8.9990 chunk 64 optimal weight: 0.3980 chunk 68 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 120 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS L 46 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.083712 restraints weight = 45940.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.084919 restraints weight = 23525.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.085053 restraints weight = 15507.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.085436 restraints weight = 15267.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.085486 restraints weight = 15083.489| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15482 Z= 0.155 Angle : 0.609 9.408 22186 Z= 0.345 Chirality : 0.041 0.245 2516 Planarity : 0.005 0.045 1794 Dihedral : 29.416 176.176 4413 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.03 % Allowed : 18.51 % Favored : 78.46 % 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: 1.88 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 650 sheet: 1.37 (0.77), residues: 53 loop : -1.08 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.027 0.002 TYR H 40 PHE 0.020 0.001 PHE L 50 TRP 0.025 0.003 TRP L 33 HIS 0.006 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (15472) covalent geometry : angle 0.60189 / 0.34 (22171) hydrogen bonds : bond 0.04933 / 3.34 ( 842) hydrogen bonds : angle 3.27369 / 2.28 ( 2133) metal coordination : bond 0.00873 / 0.42 ( 8) metal coordination : angle 4.70426 / 2.35 ( 9) link_TRANS : bond 0.00079 / 0.04 ( 2) link_TRANS : angle 0.17454 / 0.07 ( 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 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8381 (tpp80) cc_final: 0.7835 (ttm110) REVERT: B 25 ASN cc_start: 0.8511 (m110) cc_final: 0.8222 (m110) REVERT: C 61 GLU cc_start: 0.9135 (tp30) cc_final: 0.8666 (tp30) REVERT: C 74 LYS cc_start: 0.8887 (mmmt) cc_final: 0.8490 (mttm) REVERT: D 40 TYR cc_start: 0.9266 (m-80) cc_final: 0.8649 (m-80) REVERT: D 51 ASP cc_start: 0.8110 (p0) cc_final: 0.7870 (p0) REVERT: D 71 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7556 (mm-30) REVERT: F 73 THR cc_start: 0.9531 (t) cc_final: 0.9274 (m) REVERT: F 74 GLU cc_start: 0.8178 (tm-30) cc_final: 0.7615 (tm-30) REVERT: H 68 ASP cc_start: 0.9176 (t70) cc_final: 0.8908 (t0) REVERT: L 4 LYS cc_start: 0.8936 (ptpt) cc_final: 0.8442 (pttm) REVERT: L 7 ASN cc_start: 0.9603 (m-40) cc_final: 0.9303 (m110) REVERT: M 1 MET cc_start: 0.8410 (tmm) cc_final: 0.7493 (tmm) outliers start: 28 outliers final: 24 residues processed: 187 average time/residue: 0.1245 time to fit residues: 33.2311 Evaluate side-chains 192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0770 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098361 restraints weight = 35683.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.096977 restraints weight = 44933.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.098424 restraints weight = 39784.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.098811 restraints weight = 23775.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.100425 restraints weight = 19809.043| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 0.032 15482 Z= 0.142 Angle : 0.606 9.688 22186 Z= 0.343 Chirality : 0.041 0.241 2516 Planarity : 0.005 0.044 1794 Dihedral : 29.423 176.361 4413 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.81 % Allowed : 19.59 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.26), residues: 1057 helix: 2.45 (0.20), residues: 650 sheet: 1.37 (0.77), residues: 53 loop : -1.05 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.027 0.002 TYR H 40 PHE 0.020 0.001 PHE L 50 TRP 0.025 0.003 TRP L 33 HIS 0.012 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (15472) covalent geometry : angle 0.59882 / 0.34 (22171) hydrogen bonds : bond 0.04804 / 3.26 ( 842) hydrogen bonds : angle 3.21161 / 2.23 ( 2133) metal coordination : bond 0.00906 / 0.44 ( 8) metal coordination : angle 4.60901 / 2.31 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.14402 / 0.06 ( 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 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8358 (tpp80) cc_final: 0.7882 (ttm110) REVERT: B 25 ASN cc_start: 0.8447 (m110) cc_final: 0.8176 (m110) REVERT: C 61 GLU cc_start: 0.9138 (tp30) cc_final: 0.8643 (tp30) REVERT: C 74 LYS cc_start: 0.8886 (mmmt) cc_final: 0.8504 (mttm) REVERT: D 40 TYR cc_start: 0.9273 (m-80) cc_final: 0.8601 (m-80) REVERT: D 51 ASP cc_start: 0.8046 (p0) cc_final: 0.7833 (p0) REVERT: D 71 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7493 (mm-30) REVERT: F 73 THR cc_start: 0.9533 (t) cc_final: 0.9312 (m) REVERT: F 74 GLU cc_start: 0.8157 (tm-30) cc_final: 0.7606 (tm-30) REVERT: H 68 ASP cc_start: 0.9121 (t70) cc_final: 0.8732 (t0) REVERT: L 4 LYS cc_start: 0.8519 (ptpt) cc_final: 0.7887 (pttm) REVERT: L 7 ASN cc_start: 0.9265 (m-40) cc_final: 0.9033 (m110) REVERT: M 1 MET cc_start: 0.7750 (tmm) cc_final: 0.6971 (tmm) outliers start: 26 outliers final: 24 residues processed: 190 average time/residue: 0.1367 time to fit residues: 36.6883 Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 0.9980 chunk 18 optimal weight: 0.0470 chunk 81 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 86 optimal weight: 20.0000 chunk 66 optimal weight: 0.1980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.141567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.085054 restraints weight = 48456.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086275 restraints weight = 24993.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.086441 restraints weight = 16126.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.087023 restraints weight = 15542.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.087008 restraints weight = 15413.204| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15482 Z= 0.136 Angle : 0.602 9.730 22186 Z= 0.342 Chirality : 0.041 0.239 2516 Planarity : 0.005 0.054 1794 Dihedral : 29.425 176.518 4413 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 20.02 % Favored : 77.60 % 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: 1.98 (0.26), residues: 1057 helix: 2.49 (0.21), residues: 650 sheet: 1.29 (0.75), residues: 53 loop : -1.02 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 136 TYR 0.024 0.001 TYR H 40 PHE 0.021 0.001 PHE L 50 TRP 0.057 0.004 TRP L 33 HIS 0.004 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.14 (15472) covalent geometry : angle 0.59540 / 0.34 (22171) hydrogen bonds : bond 0.04656 / 3.18 ( 842) hydrogen bonds : angle 3.19241 / 2.21 ( 2133) metal coordination : bond 0.00939 / 0.45 ( 8) metal coordination : angle 4.44744 / 2.24 ( 9) link_TRANS : bond 0.00061 / 0.03 ( 2) link_TRANS : angle 0.11847 / 0.05 ( 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 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8355 (tpp80) cc_final: 0.7814 (ttm110) REVERT: B 25 ASN cc_start: 0.8441 (m110) cc_final: 0.8173 (m110) REVERT: C 61 GLU cc_start: 0.9129 (tp30) cc_final: 0.8666 (tp30) REVERT: C 74 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8503 (mttm) REVERT: D 40 TYR cc_start: 0.9254 (m-80) cc_final: 0.8631 (m-80) REVERT: D 51 ASP cc_start: 0.8079 (p0) cc_final: 0.7852 (p0) REVERT: D 71 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7573 (mm-30) REVERT: F 74 GLU cc_start: 0.8176 (tm-30) cc_final: 0.7682 (tm-30) REVERT: G 74 LYS cc_start: 0.9052 (mtmt) cc_final: 0.8787 (mttm) REVERT: H 47 GLN cc_start: 0.8556 (tt0) cc_final: 0.8226 (mt0) REVERT: H 68 ASP cc_start: 0.9168 (t70) cc_final: 0.8901 (t0) REVERT: L 4 LYS cc_start: 0.8757 (ptpt) cc_final: 0.8230 (pttm) REVERT: L 7 ASN cc_start: 0.9581 (m-40) cc_final: 0.9260 (m110) REVERT: M 1 MET cc_start: 0.8414 (tmm) cc_final: 0.7500 (tmm) outliers start: 22 outliers final: 19 residues processed: 193 average time/residue: 0.1379 time to fit residues: 37.9301 Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 178 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 127 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.140365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.084785 restraints weight = 42123.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.086011 restraints weight = 24192.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.085929 restraints weight = 18273.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086342 restraints weight = 17035.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.086432 restraints weight = 16285.683| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15482 Z= 0.156 Angle : 0.623 9.648 22186 Z= 0.348 Chirality : 0.041 0.250 2516 Planarity : 0.005 0.056 1794 Dihedral : 29.496 176.044 4413 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.27 % Allowed : 20.67 % Favored : 77.06 % 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: 1.88 (0.26), residues: 1057 helix: 2.40 (0.21), residues: 650 sheet: 1.24 (0.77), residues: 53 loop : -1.04 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 136 TYR 0.048 0.002 TYR F 88 PHE 0.021 0.001 PHE L 50 TRP 0.048 0.003 TRP L 33 HIS 0.003 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (15472) covalent geometry : angle 0.61622 / 0.35 (22171) hydrogen bonds : bond 0.04910 / 3.35 ( 842) hydrogen bonds : angle 3.25527 / 2.24 ( 2133) metal coordination : bond 0.00961 / 0.46 ( 8) metal coordination : angle 4.56358 / 2.30 ( 9) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.57659 / 0.33 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2379.32 seconds wall clock time: 41 minutes 44.15 seconds (2504.15 seconds total)