Starting phenix.real_space_refine on Fri Jul 3 12:58:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn6_40614/07_2026/8sn6_40614.map" } 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 17 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 32.578 74.262 46.883 1.00 88.39 S ATOM 12446 SG CYS K 51 31.271 71.186 45.070 1.00 91.68 S ATOM 12470 SG CYS K 54 32.612 74.141 43.059 1.00 96.59 S ATOM 12187 SG CYS K 16 22.251 68.673 52.194 1.00104.88 S ATOM 12205 SG CYS K 19 20.908 65.621 54.027 1.00100.49 S ATOM 12335 SG CYS K 36 23.441 67.769 55.828 1.00 94.61 S ATOM 12357 SG CYS K 39 24.460 65.513 53.151 1.00 91.60 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: 3.19, per 1000 atoms: 0.22 Number of scatterers: 14600 At special positions: 0 Unit cell: (110.224, 134.128, 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: 0.93 Conformation dependent library (CDL) restraints added in 494.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " 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: 46 helices and 13 sheets defined 62.9% alpha, 5.9% beta 135 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 removed outlier: 3.587A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.560A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (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: 3.873A 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: 3.846A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.504A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.564A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.672A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.539A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.824A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.600A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.029A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.529A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.696A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) 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: 3.697A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.775A 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 10 through 15 removed outlier: 3.806A pdb=" N CYS K 14 " --> pdb=" O SER K 10 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 10 through 15' Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 67 removed outlier: 3.749A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.502A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE K 80 " --> pdb=" O LEU K 76 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN K 81 " --> pdb=" O TRP K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.859A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.686A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.926A pdb=" N VAL L 102 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU L 103 " --> pdb=" O ILE L 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.921A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.918A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.612A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.768A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 8.117A 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: 6.996A 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: 7.254A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.813A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 26 through 28 removed outlier: 3.805A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 25 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 496 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 1.35 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: 3591 1.34 - 1.46: 4442 1.46 - 1.58: 6804 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 1.543 -0.027 8.00e-03 1.56e+04 1.10e+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 1.09e+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' DA I -22 " pdb=" C2' DA I -22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 20851 1.47 - 2.94: 1234 2.94 - 4.41: 56 4.41 - 5.88: 23 5.88 - 7.35: 7 Bond angle restraints: 22171 Sorted by residual: angle pdb=" O4' DA J 42 " pdb=" C4' DA J 42 " pdb=" C3' DA J 42 " ideal model delta sigma weight residual 106.00 103.02 2.98 6.00e-01 2.78e+00 2.46e+01 angle pdb=" O4' DA I 17 " pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 106.00 103.25 2.75 6.00e-01 2.78e+00 2.10e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I 3 " pdb=" C4 DT I 3 " pdb=" O4 DT I 3 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT I -43 " pdb=" C4 DT I -43 " pdb=" O4 DT I -43 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.23: 7238 35.23 - 70.47: 1347 70.47 - 105.70: 24 105.70 - 140.94: 0 140.94 - 176.17: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.17 -176.17 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 71.38 148.62 1 3.50e+01 8.16e-04 1.45e+01 dihedral pdb=" CB GLU G 56 " pdb=" CG GLU G 56 " pdb=" CD GLU G 56 " pdb=" OE1 GLU G 56 " ideal model delta sinusoidal sigma weight residual 0.00 -88.89 88.89 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1467 0.032 - 0.064: 676 0.064 - 0.096: 257 0.096 - 0.128: 109 0.128 - 0.160: 7 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA ARG L 125 " pdb=" N ARG L 125 " pdb=" C ARG L 125 " pdb=" CB ARG L 125 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA LYS L 101 " pdb=" N LYS L 101 " pdb=" C LYS L 101 " pdb=" CB LYS L 101 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 25 " -0.011 2.00e-02 2.50e+03 2.17e-02 4.70e+00 pdb=" C GLU K 25 " 0.038 2.00e-02 2.50e+03 pdb=" O GLU K 25 " -0.014 2.00e-02 2.50e+03 pdb=" N PRO K 26 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.02e-02 2.84e+00 pdb=" N9 DA I -35 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.000 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.009 2.00e-02 2.50e+03 1.02e-02 2.60e+00 pdb=" CG TRP L 33 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.001 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 233 2.65 - 3.21: 12387 3.21 - 3.77: 25809 3.77 - 4.34: 32710 4.34 - 4.90: 48516 Nonbonded interactions: 119655 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.084 2.496 nonbonded pdb=" O ARG L 125 " pdb=" OG1 THR L 129 " model vdw 2.135 3.040 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.161 3.040 nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.172 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.228 3.040 ... (remaining 119650 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: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 17.000 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 15482 Z= 0.480 Angle : 0.712 7.352 22186 Z= 0.600 Chirality : 0.044 0.160 2516 Planarity : 0.004 0.038 1794 Dihedral : 25.930 176.171 6577 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.68 % 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: 1.99 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 626 sheet: 1.10 (0.75), residues: 50 loop : -0.53 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 68 TYR 0.018 0.001 TYR H 83 PHE 0.015 0.001 PHE L 56 TRP 0.026 0.003 TRP L 33 HIS 0.002 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.48 (15472) covalent geometry : angle 0.70758 / 0.60 (22171) hydrogen bonds : bond 0.10679 / 6.79 ( 843) hydrogen bonds : angle 4.14569 / 3.15 ( 2151) metal coordination : bond 0.01060 / 0.53 ( 8) metal coordination : angle 4.15496 / 2.12 ( 9) link_TRANS : bond 0.00129 / 0.07 ( 2) link_TRANS : angle 0.51959 / 0.20 ( 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 243 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ASP cc_start: 0.8084 (m-30) cc_final: 0.7869 (m-30) REVERT: A 94 GLU cc_start: 0.8400 (tp30) cc_final: 0.7955 (mm-30) REVERT: C 75 LYS cc_start: 0.8757 (mmtp) cc_final: 0.8550 (mttm) REVERT: C 95 LYS cc_start: 0.8850 (tptt) cc_final: 0.8643 (tptm) REVERT: D 33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7873 (mtp-110) REVERT: D 86 ARG cc_start: 0.8743 (mmt-90) cc_final: 0.8382 (mmt90) REVERT: H 100 LEU cc_start: 0.9442 (mt) cc_final: 0.9172 (mp) REVERT: K 42 SER cc_start: 0.7939 (p) cc_final: 0.7269 (p) REVERT: K 66 THR cc_start: 0.7827 (m) cc_final: 0.7607 (m) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1412 time to fit residues: 47.1119 Evaluate side-chains 199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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: 10.0000 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0050 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 95 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS M 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.131228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.094612 restraints weight = 46630.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.098668 restraints weight = 61302.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.098910 restraints weight = 24286.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.100861 restraints weight = 19003.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.100713 restraints weight = 17156.693| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (10 function evaluations) r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 15482 Z= 0.158 Angle : 0.637 17.522 22186 Z= 0.366 Chirality : 0.042 0.242 2516 Planarity : 0.004 0.038 1794 Dihedral : 29.086 174.131 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.30 % Allowed : 10.28 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.26), residues: 1057 helix: 2.37 (0.20), residues: 648 sheet: 1.07 (0.70), residues: 55 loop : -0.58 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 5 TYR 0.045 0.002 TYR L 134 PHE 0.038 0.002 PHE L 62 TRP 0.016 0.002 TRP L 33 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (15472) covalent geometry : angle 0.62217 / 0.36 (22171) hydrogen bonds : bond 0.05387 / 3.56 ( 843) hydrogen bonds : angle 3.55488 / 2.64 ( 2151) metal coordination : bond 0.03467 / 1.73 ( 8) metal coordination : angle 6.93648 / 3.64 ( 9) link_TRANS : bond 0.00113 / 0.06 ( 2) link_TRANS : angle 0.41944 / 0.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.7619 (pm20) REVERT: A 94 GLU cc_start: 0.8362 (tp30) cc_final: 0.8104 (mm-30) REVERT: C 95 LYS cc_start: 0.8937 (tptt) cc_final: 0.8651 (tptm) REVERT: D 33 ARG cc_start: 0.8197 (mtp-110) cc_final: 0.7768 (mtp-110) REVERT: D 86 ARG cc_start: 0.8807 (mmt-90) cc_final: 0.8325 (mmt90) REVERT: E 125 GLN cc_start: 0.8393 (mt0) cc_final: 0.8027 (mp10) REVERT: H 100 LEU cc_start: 0.9427 (mt) cc_final: 0.9158 (mp) REVERT: K 66 THR cc_start: 0.8268 (m) cc_final: 0.7937 (m) REVERT: K 68 ARG cc_start: 0.7249 (ptp90) cc_final: 0.6687 (mtm180) REVERT: L 141 TRP cc_start: 0.7109 (t-100) cc_final: 0.6908 (t-100) outliers start: 12 outliers final: 9 residues processed: 211 average time/residue: 0.1348 time to fit residues: 39.3031 Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 192 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 101 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.130686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.088602 restraints weight = 41012.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.088302 restraints weight = 26004.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088959 restraints weight = 22643.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.090612 restraints weight = 18098.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.090516 restraints weight = 17169.200| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15482 Z= 0.152 Angle : 0.611 11.910 22186 Z= 0.351 Chirality : 0.041 0.246 2516 Planarity : 0.004 0.054 1794 Dihedral : 29.131 174.447 4413 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.73 % Allowed : 11.69 % Favored : 86.58 % 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: 2.08 (0.26), residues: 1057 helix: 2.43 (0.20), residues: 649 sheet: 0.97 (0.71), residues: 55 loop : -0.59 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 5 TYR 0.026 0.002 TYR L 134 PHE 0.016 0.001 PHE K 40 TRP 0.012 0.002 TRP L 33 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (15472) covalent geometry : angle 0.60023 / 0.35 (22171) hydrogen bonds : bond 0.04986 / 3.31 ( 843) hydrogen bonds : angle 3.38704 / 2.50 ( 2151) metal coordination : bond 0.02199 / 1.10 ( 8) metal coordination : angle 5.73511 / 3.01 ( 9) link_TRANS : bond 0.00147 / 0.08 ( 2) link_TRANS : angle 0.34699 / 0.17 ( 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 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8269 (tp30) cc_final: 0.8015 (mm-30) REVERT: C 95 LYS cc_start: 0.8933 (tptt) cc_final: 0.8624 (tptm) REVERT: D 33 ARG cc_start: 0.8224 (mtp-110) cc_final: 0.7746 (mtp-110) REVERT: D 86 ARG cc_start: 0.8826 (mmt-90) cc_final: 0.8319 (mmt90) REVERT: E 125 GLN cc_start: 0.8397 (mt0) cc_final: 0.7984 (mp10) REVERT: H 100 LEU cc_start: 0.9355 (mt) cc_final: 0.9095 (mp) REVERT: K 66 THR cc_start: 0.8311 (m) cc_final: 0.7972 (m) REVERT: K 68 ARG cc_start: 0.7238 (ptp90) cc_final: 0.6779 (mtm180) REVERT: L 75 HIS cc_start: 0.8516 (t-90) cc_final: 0.8289 (t-90) outliers start: 16 outliers final: 10 residues processed: 205 average time/residue: 0.1302 time to fit residues: 37.0620 Evaluate side-chains 199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 45 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS M 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.130862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080891 restraints weight = 53094.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.082468 restraints weight = 26228.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.083847 restraints weight = 16100.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.084230 restraints weight = 16013.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.083969 restraints weight = 13586.458| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15482 Z= 0.148 Angle : 0.602 11.851 22186 Z= 0.346 Chirality : 0.041 0.360 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.137 174.411 4413 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.84 % Allowed : 13.31 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.26), residues: 1057 helix: 2.44 (0.20), residues: 650 sheet: 0.95 (0.71), residues: 55 loop : -0.61 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.021 0.001 TYR L 134 PHE 0.012 0.001 PHE K 40 TRP 0.008 0.001 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (15472) covalent geometry : angle 0.59356 / 0.35 (22171) hydrogen bonds : bond 0.04822 / 3.20 ( 843) hydrogen bonds : angle 3.30277 / 2.44 ( 2151) metal coordination : bond 0.01830 / 0.92 ( 8) metal coordination : angle 5.13822 / 2.70 ( 9) link_TRANS : bond 0.00115 / 0.06 ( 2) link_TRANS : angle 0.33445 / 0.16 ( 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 216 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8189 (t0) cc_final: 0.7943 (t0) REVERT: C 95 LYS cc_start: 0.8928 (tptt) cc_final: 0.8639 (tptm) REVERT: D 33 ARG cc_start: 0.8228 (mtp-110) cc_final: 0.7704 (mtp-110) REVERT: E 125 GLN cc_start: 0.8420 (mt0) cc_final: 0.8071 (mp10) REVERT: K 66 THR cc_start: 0.8269 (m) cc_final: 0.7945 (m) REVERT: K 68 ARG cc_start: 0.7561 (ptp90) cc_final: 0.6980 (mtm180) REVERT: L 8 LYS cc_start: 0.8865 (mppt) cc_final: 0.8398 (tptp) REVERT: L 75 HIS cc_start: 0.8704 (t-90) cc_final: 0.8362 (t-90) outliers start: 17 outliers final: 12 residues processed: 205 average time/residue: 0.1310 time to fit residues: 37.0897 Evaluate side-chains 202 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 190 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 126 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.128329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.079305 restraints weight = 45300.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.079251 restraints weight = 26569.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.079706 restraints weight = 18536.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080006 restraints weight = 18344.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.080188 restraints weight = 16378.037| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15482 Z= 0.178 Angle : 0.634 12.072 22186 Z= 0.355 Chirality : 0.042 0.323 2516 Planarity : 0.004 0.057 1794 Dihedral : 29.238 173.960 4413 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.38 % Allowed : 13.96 % Favored : 83.66 % 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: 1.95 (0.26), residues: 1057 helix: 2.36 (0.20), residues: 649 sheet: 1.21 (0.75), residues: 50 loop : -0.76 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 55 TYR 0.022 0.002 TYR H 83 PHE 0.015 0.002 PHE L 62 TRP 0.012 0.002 TRP L 93 HIS 0.005 0.001 HIS H 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.18 (15472) covalent geometry : angle 0.62292 / 0.35 (22171) hydrogen bonds : bond 0.05180 / 3.46 ( 843) hydrogen bonds : angle 3.36982 / 2.49 ( 2151) metal coordination : bond 0.01963 / 0.99 ( 8) metal coordination : angle 5.94176 / 3.22 ( 9) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.37968 / 0.16 ( 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 219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 197 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8257 (t0) cc_final: 0.7972 (t0) REVERT: C 95 LYS cc_start: 0.9046 (tptt) cc_final: 0.8698 (tptm) REVERT: D 33 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7788 (mtp-110) REVERT: E 125 GLN cc_start: 0.8493 (mt0) cc_final: 0.8164 (mt0) REVERT: K 66 THR cc_start: 0.8261 (m) cc_final: 0.7963 (m) REVERT: K 68 ARG cc_start: 0.7525 (ptp90) cc_final: 0.7167 (mtm180) REVERT: L 9 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8291 (mm-30) REVERT: L 75 HIS cc_start: 0.8737 (t-90) cc_final: 0.8230 (t-90) REVERT: L 134 TYR cc_start: 0.7734 (t80) cc_final: 0.7088 (m-80) REVERT: L 145 TYR cc_start: 0.6633 (OUTLIER) cc_final: 0.6242 (m-10) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.1307 time to fit residues: 36.7799 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 190 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 122 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.129036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.089268 restraints weight = 44830.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.089841 restraints weight = 41017.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090422 restraints weight = 35561.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.090413 restraints weight = 23053.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.091703 restraints weight = 19696.892| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15482 Z= 0.153 Angle : 0.622 12.992 22186 Z= 0.350 Chirality : 0.041 0.335 2516 Planarity : 0.004 0.055 1794 Dihedral : 29.210 174.098 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.95 % Allowed : 15.58 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.26), residues: 1057 helix: 2.39 (0.20), residues: 650 sheet: 1.24 (0.75), residues: 50 loop : -0.73 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG L 90 TYR 0.018 0.001 TYR L 145 PHE 0.019 0.001 PHE L 62 TRP 0.010 0.002 TRP L 93 HIS 0.004 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (15472) covalent geometry : angle 0.61042 / 0.35 (22171) hydrogen bonds : bond 0.04918 / 3.28 ( 843) hydrogen bonds : angle 3.27161 / 2.41 ( 2151) metal coordination : bond 0.01747 / 0.89 ( 8) metal coordination : angle 5.86284 / 3.19 ( 9) link_TRANS : bond 0.00089 / 0.05 ( 2) link_TRANS : angle 0.31492 / 0.13 ( 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 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8482 (tp30) cc_final: 0.8012 (mm-30) REVERT: C 73 ASN cc_start: 0.8326 (t0) cc_final: 0.8053 (t0) REVERT: C 95 LYS cc_start: 0.9021 (tptt) cc_final: 0.8672 (tptm) REVERT: D 33 ARG cc_start: 0.8258 (mtp-110) cc_final: 0.7779 (mtp-110) REVERT: E 125 GLN cc_start: 0.8452 (mt0) cc_final: 0.8095 (mt0) REVERT: K 66 THR cc_start: 0.8401 (m) cc_final: 0.8080 (m) REVERT: L 8 LYS cc_start: 0.8579 (mppt) cc_final: 0.8322 (tptp) REVERT: L 9 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7526 (mm-30) REVERT: L 69 PHE cc_start: 0.7653 (m-80) cc_final: 0.7357 (m-80) REVERT: L 75 HIS cc_start: 0.8343 (t-90) cc_final: 0.8112 (t-90) outliers start: 18 outliers final: 13 residues processed: 208 average time/residue: 0.1297 time to fit residues: 37.2905 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 143 GLN Chi-restraints excluded: chain L residue 145 TYR 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: 0.4980 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.128796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.079371 restraints weight = 46929.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.079741 restraints weight = 26469.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.080037 restraints weight = 19532.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.080667 restraints weight = 18048.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.080632 restraints weight = 15780.987| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2888 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.12 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2888 r_free = 0.2888 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2888 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15482 Z= 0.156 Angle : 0.622 13.418 22186 Z= 0.349 Chirality : 0.041 0.321 2516 Planarity : 0.004 0.042 1794 Dihedral : 29.233 174.076 4413 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.06 % Allowed : 15.48 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 650 sheet: 1.19 (0.74), residues: 50 loop : -0.72 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 55 TYR 0.017 0.001 TYR H 83 PHE 0.013 0.001 PHE L 62 TRP 0.012 0.002 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (15472) covalent geometry : angle 0.61244 / 0.35 (22171) hydrogen bonds : bond 0.04901 / 3.27 ( 843) hydrogen bonds : angle 3.24969 / 2.39 ( 2151) metal coordination : bond 0.01729 / 0.87 ( 8) metal coordination : angle 5.55259 / 2.94 ( 9) link_TRANS : bond 0.00067 / 0.04 ( 2) link_TRANS : angle 0.30561 / 0.12 ( 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 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8507 (tp30) cc_final: 0.8198 (mm-30) REVERT: C 73 ASN cc_start: 0.8308 (t0) cc_final: 0.8107 (t0) REVERT: C 95 LYS cc_start: 0.9055 (tptt) cc_final: 0.8693 (tptm) REVERT: D 33 ARG cc_start: 0.8257 (mtp-110) cc_final: 0.7740 (mtp-110) REVERT: E 59 GLU cc_start: 0.8755 (pm20) cc_final: 0.8417 (pm20) REVERT: E 125 GLN cc_start: 0.8523 (mt0) cc_final: 0.8197 (mt0) REVERT: H 119 THR cc_start: 0.9529 (t) cc_final: 0.9307 (t) REVERT: K 66 THR cc_start: 0.8272 (m) cc_final: 0.7973 (m) REVERT: L 8 LYS cc_start: 0.8954 (mppt) cc_final: 0.8449 (tptp) REVERT: L 9 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8210 (mm-30) REVERT: L 69 PHE cc_start: 0.8161 (m-80) cc_final: 0.7898 (m-80) REVERT: L 75 HIS cc_start: 0.8725 (t-90) cc_final: 0.8434 (t-90) REVERT: L 144 LYS cc_start: 0.9126 (pptt) cc_final: 0.8923 (pptt) REVERT: L 145 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6553 (m-10) outliers start: 19 outliers final: 12 residues processed: 208 average time/residue: 0.1322 time to fit residues: 37.9316 Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 127 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 100 optimal weight: 0.0060 chunk 94 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.129517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.076826 restraints weight = 51189.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.078988 restraints weight = 26618.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080470 restraints weight = 18209.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.081393 restraints weight = 14842.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.081747 restraints weight = 13290.142| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2928 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2928 r_free = 0.2928 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2928 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15482 Z= 0.141 Angle : 0.622 13.763 22186 Z= 0.348 Chirality : 0.041 0.336 2516 Planarity : 0.004 0.069 1794 Dihedral : 29.208 174.272 4413 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.62 % Allowed : 16.67 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.26), residues: 1057 helix: 2.50 (0.21), residues: 649 sheet: 1.21 (0.74), residues: 50 loop : -0.66 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 90 TYR 0.014 0.001 TYR H 83 PHE 0.013 0.001 PHE L 62 TRP 0.011 0.002 TRP L 93 HIS 0.006 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.14 (15472) covalent geometry : angle 0.60662 / 0.35 (22171) hydrogen bonds : bond 0.04644 / 3.09 ( 843) hydrogen bonds : angle 3.18740 / 2.34 ( 2151) metal coordination : bond 0.01772 / 0.90 ( 8) metal coordination : angle 6.89025 / 3.66 ( 9) link_TRANS : bond 0.00085 / 0.04 ( 2) link_TRANS : angle 0.24681 / 0.10 ( 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 224 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8416 (tp30) cc_final: 0.8118 (mm-30) REVERT: C 73 ASN cc_start: 0.8320 (t0) cc_final: 0.8057 (t0) REVERT: C 95 LYS cc_start: 0.9013 (tptt) cc_final: 0.8666 (tptm) REVERT: D 33 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7723 (mtp-110) REVERT: E 59 GLU cc_start: 0.8707 (pm20) cc_final: 0.8348 (pm20) REVERT: E 125 GLN cc_start: 0.8528 (mt0) cc_final: 0.8175 (mt0) REVERT: H 119 THR cc_start: 0.9515 (t) cc_final: 0.9305 (t) REVERT: K 66 THR cc_start: 0.8371 (m) cc_final: 0.8029 (m) REVERT: L 9 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8005 (mm-30) REVERT: L 69 PHE cc_start: 0.8075 (m-80) cc_final: 0.7819 (m-80) REVERT: L 75 HIS cc_start: 0.8677 (t-90) cc_final: 0.8392 (t-90) REVERT: L 143 GLN cc_start: 0.9555 (mm110) cc_final: 0.9322 (mp10) REVERT: L 145 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.6427 (m-10) outliers start: 15 outliers final: 11 residues processed: 217 average time/residue: 0.1317 time to fit residues: 39.3283 Evaluate side-chains 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 206 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 0.0170 chunk 56 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 43 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.129754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089658 restraints weight = 39740.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.088898 restraints weight = 36570.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.090501 restraints weight = 27585.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.090844 restraints weight = 20161.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091090 restraints weight = 20760.903| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15482 Z= 0.143 Angle : 0.632 14.168 22186 Z= 0.353 Chirality : 0.041 0.343 2516 Planarity : 0.004 0.041 1794 Dihedral : 29.220 174.306 4413 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.16 % Allowed : 16.56 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 650 sheet: 1.27 (0.75), residues: 49 loop : -0.67 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.039 0.002 TYR L 60 PHE 0.015 0.001 PHE L 62 TRP 0.010 0.002 TRP L 93 HIS 0.004 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.14 (15472) covalent geometry : angle 0.62192 / 0.35 (22171) hydrogen bonds : bond 0.04605 / 3.07 ( 843) hydrogen bonds : angle 3.19602 / 2.33 ( 2151) metal coordination : bond 0.01602 / 0.81 ( 8) metal coordination : angle 5.62563 / 2.98 ( 9) link_TRANS : bond 0.00078 / 0.04 ( 2) link_TRANS : angle 0.23797 / 0.09 ( 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 223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 203 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8257 (tp30) cc_final: 0.7908 (mm-30) REVERT: C 16 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7945 (t) REVERT: C 73 ASN cc_start: 0.8380 (t0) cc_final: 0.8111 (t0) REVERT: C 95 LYS cc_start: 0.9019 (tptt) cc_final: 0.8668 (tptm) REVERT: D 33 ARG cc_start: 0.8250 (mtp-110) cc_final: 0.7749 (mtp-110) REVERT: E 59 GLU cc_start: 0.8740 (pm20) cc_final: 0.8376 (pm20) REVERT: E 125 GLN cc_start: 0.8490 (mt0) cc_final: 0.8118 (mt0) REVERT: H 119 THR cc_start: 0.9501 (t) cc_final: 0.9248 (t) REVERT: K 66 THR cc_start: 0.8388 (m) cc_final: 0.8042 (m) REVERT: L 8 LYS cc_start: 0.8603 (mppt) cc_final: 0.8388 (tptp) REVERT: L 69 PHE cc_start: 0.7634 (m-80) cc_final: 0.7398 (m-80) REVERT: L 75 HIS cc_start: 0.8178 (t-90) cc_final: 0.7900 (t-90) REVERT: L 145 TYR cc_start: 0.6226 (OUTLIER) cc_final: 0.5846 (m-10) outliers start: 20 outliers final: 15 residues processed: 213 average time/residue: 0.1290 time to fit residues: 37.7935 Evaluate side-chains 219 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 104 optimal weight: 0.3980 chunk 114 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.129119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.078128 restraints weight = 53906.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.079930 restraints weight = 29449.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.080784 restraints weight = 20480.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.081012 restraints weight = 17101.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.081134 restraints weight = 16602.760| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15482 Z= 0.158 Angle : 0.647 14.489 22186 Z= 0.360 Chirality : 0.041 0.351 2516 Planarity : 0.004 0.061 1794 Dihedral : 29.261 174.226 4413 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.06 % Allowed : 16.99 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.26), residues: 1057 helix: 2.37 (0.21), residues: 651 sheet: 1.31 (0.76), residues: 49 loop : -0.64 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 90 TYR 0.069 0.002 TYR L 134 PHE 0.013 0.001 PHE L 62 TRP 0.014 0.002 TRP L 93 HIS 0.003 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (15472) covalent geometry : angle 0.63790 / 0.36 (22171) hydrogen bonds : bond 0.04755 / 3.17 ( 843) hydrogen bonds : angle 3.26460 / 2.39 ( 2151) metal coordination : bond 0.01610 / 0.81 ( 8) metal coordination : angle 5.41956 / 2.86 ( 9) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.28245 / 0.11 ( 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 218 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8361 (tp30) cc_final: 0.8110 (mm-30) REVERT: C 16 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (t) REVERT: C 95 LYS cc_start: 0.9039 (tptt) cc_final: 0.8685 (tptm) REVERT: D 33 ARG cc_start: 0.8263 (mtp-110) cc_final: 0.7748 (mtp-110) REVERT: E 59 GLU cc_start: 0.8770 (pm20) cc_final: 0.8415 (pm20) REVERT: E 125 GLN cc_start: 0.8529 (mt0) cc_final: 0.8221 (mt0) REVERT: H 119 THR cc_start: 0.9539 (t) cc_final: 0.9291 (t) REVERT: K 66 THR cc_start: 0.8379 (m) cc_final: 0.8033 (m) REVERT: L 69 PHE cc_start: 0.8215 (m-80) cc_final: 0.7889 (m-80) REVERT: L 145 TYR cc_start: 0.6946 (OUTLIER) cc_final: 0.6522 (m-10) REVERT: M 42 ARG cc_start: 0.6741 (mmt180) cc_final: 0.6459 (mmt180) outliers start: 19 outliers final: 15 residues processed: 209 average time/residue: 0.1461 time to fit residues: 41.4845 Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Chi-restraints excluded: chain L residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.075631 restraints weight = 46697.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.076885 restraints weight = 26897.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.077943 restraints weight = 19610.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.077844 restraints weight = 17280.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.078010 restraints weight = 16492.215| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15482 Z= 0.205 Angle : 0.691 14.582 22186 Z= 0.378 Chirality : 0.043 0.384 2516 Planarity : 0.004 0.044 1794 Dihedral : 29.400 173.526 4413 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.38 % Allowed : 16.99 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.26), residues: 1057 helix: 2.20 (0.21), residues: 649 sheet: 1.15 (0.74), residues: 50 loop : -0.75 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 90 TYR 0.033 0.002 TYR L 134 PHE 0.015 0.002 PHE K 40 TRP 0.022 0.002 TRP L 93 HIS 0.004 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.20 (15472) covalent geometry : angle 0.68117 / 0.38 (22171) hydrogen bonds : bond 0.05431 / 3.63 ( 843) hydrogen bonds : angle 3.46457 / 2.54 ( 2151) metal coordination : bond 0.01987 / 1.00 ( 8) metal coordination : angle 5.68898 / 2.91 ( 9) link_TRANS : bond 0.00123 / 0.06 ( 2) link_TRANS : angle 0.42155 / 0.17 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2264.68 seconds wall clock time: 39 minutes 44.75 seconds (2384.75 seconds total)