Starting phenix.real_space_refine on Thu Aug 6 07:48:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn6_40614/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn6_40614/08_2026/8sn6_40614.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 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: 3.14, 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: 1.02 Conformation dependent library (CDL) restraints added in 416.7 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: 2.07 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: 1.33 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: 20830 1.47 - 2.94: 1255 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: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 16.870 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.260 ------------------------------------------------------------------------------- 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 : 0.718 7.352 22186 Z= 0.604 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 0.71308 / 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 : 0.383 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: 0.1518 time to fit residues: 50.6634 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 : 0.361 ------------------------------------------------------------------------------- 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: 9.9990 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 = 0.3721 r_free = 0.3721 target = 0.131295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094963 restraints weight = 46645.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097760 restraints weight = 64555.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.098654 restraints weight = 28326.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100551 restraints weight = 20825.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100566 restraints weight = 18550.092| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (10 function evaluations) r_final: 0.3134 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 15482 Z= 0.158 Angle : 0.642 14.284 22186 Z= 0.369 Chirality : 0.042 0.269 2516 Planarity : 0.004 0.039 1794 Dihedral : 29.054 174.525 4413 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.30 % Allowed : 10.17 % Favored : 88.53 % 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: 1.14 (0.71), residues: 55 loop : -0.60 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 5 TYR 0.043 0.002 TYR L 134 PHE 0.039 0.002 PHE L 62 TRP 0.018 0.002 TRP L 33 HIS 0.004 0.001 HIS K 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.16 (15472) covalent geometry : angle 0.63083 / 0.37 (22171) hydrogen bonds : bond 0.05272 / 3.50 ( 843) hydrogen bonds : angle 3.52161 / 2.61 ( 2151) metal coordination : bond 0.03682 / 1.81 ( 8) metal coordination : angle 6.03092 / 3.16 ( 9) link_TRANS : bond 0.00127 / 0.07 ( 2) link_TRANS : angle 0.44149 / 0.22 ( 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 220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 208 time to evaluate : 0.359 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: 0.8390 (OUTLIER) cc_final: 0.7890 (pm20) REVERT: A 94 GLU cc_start: 0.8352 (tp30) cc_final: 0.8103 (mm-30) REVERT: C 95 LYS cc_start: 0.8927 (tptt) cc_final: 0.8645 (tptm) REVERT: D 33 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7803 (mtp-110) REVERT: D 86 ARG cc_start: 0.8797 (mmt-90) cc_final: 0.8319 (mmt90) REVERT: E 125 GLN cc_start: 0.8423 (mt0) cc_final: 0.8029 (mp10) REVERT: H 100 LEU cc_start: 0.9426 (mt) cc_final: 0.9161 (mp) REVERT: K 66 THR cc_start: 0.8276 (m) cc_final: 0.7943 (m) REVERT: K 68 ARG cc_start: 0.7255 (ptp90) cc_final: 0.6694 (mtm180) outliers start: 12 outliers final: 9 residues processed: 213 average time/residue: 0.1447 time to fit residues: 42.7483 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 : 0.395 ------------------------------------------------------------------------------- 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: 1.9990 chunk 105 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 73 ASN L 0 HIS L 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.093095 restraints weight = 41003.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.094912 restraints weight = 58079.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.095039 restraints weight = 39692.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.096015 restraints weight = 25077.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.096773 restraints weight = 21533.590| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 15482 Z= 0.154 Angle : 0.624 12.293 22186 Z= 0.355 Chirality : 0.042 0.252 2516 Planarity : 0.004 0.061 1794 Dihedral : 29.085 174.754 4413 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.73 % Allowed : 12.66 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.26), residues: 1057 helix: 2.41 (0.20), residues: 649 sheet: 0.87 (0.70), residues: 55 loop : -0.58 (0.32), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 33 TYR 0.032 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 0.00285 / 0.15 (15472) covalent geometry : angle 0.61367 / 0.35 (22171) hydrogen bonds : bond 0.04987 / 3.31 ( 843) hydrogen bonds : angle 3.39942 / 2.52 ( 2151) metal coordination : bond 0.02039 / 1.02 ( 8) metal coordination : angle 5.72014 / 3.01 ( 9) link_TRANS : bond 0.00146 / 0.08 ( 2) link_TRANS : angle 0.33585 / 0.16 ( 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 215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.384 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: A 94 GLU cc_start: 0.8273 (tp30) cc_final: 0.8031 (mm-30) REVERT: C 95 LYS cc_start: 0.8893 (tptt) cc_final: 0.8619 (tptm) REVERT: D 33 ARG cc_start: 0.8231 (mtp-110) cc_final: 0.7771 (mtp-110) REVERT: D 86 ARG cc_start: 0.8748 (mmt-90) cc_final: 0.8295 (mmt90) REVERT: E 125 GLN cc_start: 0.8402 (mt0) cc_final: 0.7918 (mp10) REVERT: H 100 LEU cc_start: 0.9406 (mt) cc_final: 0.9126 (mp) REVERT: K 66 THR cc_start: 0.8308 (m) cc_final: 0.7963 (m) REVERT: K 68 ARG cc_start: 0.7108 (ptp90) cc_final: 0.6721 (mtm180) REVERT: L 74 TYR cc_start: 0.8220 (t80) cc_final: 0.7774 (t80) outliers start: 16 outliers final: 10 residues processed: 204 average time/residue: 0.1504 time to fit residues: 42.6000 Evaluate side-chains 198 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.400 ------------------------------------------------------------------------------- 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: 0.6980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 32 optimal weight: 0.0670 chunk 45 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 128 optimal weight: 30.0000 chunk 35 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7322 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.130635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.080378 restraints weight = 52978.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.081917 restraints weight = 26448.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.083638 restraints weight = 16721.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.083624 restraints weight = 15407.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.083256 restraints weight = 13826.127| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1356 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= 0.149 Angle : 0.615 12.204 22186 Z= 0.350 Chirality : 0.041 0.368 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.086 174.672 4413 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.84 % Allowed : 13.85 % Favored : 84.31 % 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: 2.10 (0.26), residues: 1057 helix: 2.43 (0.20), residues: 650 sheet: 0.99 (0.71), residues: 55 loop : -0.57 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 33 TYR 0.026 0.002 TYR L 134 PHE 0.014 0.001 PHE L 62 TRP 0.009 0.001 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (15472) covalent geometry : angle 0.60623 / 0.35 (22171) hydrogen bonds : bond 0.04840 / 3.22 ( 843) hydrogen bonds : angle 3.30846 / 2.44 ( 2151) metal coordination : bond 0.01799 / 0.90 ( 8) metal coordination : angle 5.23791 / 2.74 ( 9) link_TRANS : bond 0.00116 / 0.06 ( 2) link_TRANS : angle 0.33884 / 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 214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 197 time to evaluate : 0.369 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 94 GLU cc_start: 0.8286 (tp30) cc_final: 0.8079 (mm-30) REVERT: C 73 ASN cc_start: 0.8182 (t0) cc_final: 0.7926 (t0) REVERT: C 95 LYS cc_start: 0.8945 (tptt) cc_final: 0.8658 (tptm) REVERT: D 33 ARG cc_start: 0.8232 (mtp-110) cc_final: 0.7707 (mtp-110) REVERT: E 125 GLN cc_start: 0.8416 (mt0) cc_final: 0.8098 (mt0) REVERT: K 66 THR cc_start: 0.8273 (m) cc_final: 0.7953 (m) REVERT: K 68 ARG cc_start: 0.7549 (ptp90) cc_final: 0.6957 (mtm180) REVERT: L 74 TYR cc_start: 0.8549 (t80) cc_final: 0.8090 (t80) REVERT: L 134 TYR cc_start: 0.7739 (t80) cc_final: 0.7111 (t80) outliers start: 17 outliers final: 12 residues processed: 204 average time/residue: 0.1420 time to fit residues: 40.2575 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 4 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 87 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 54 optimal weight: 0.1980 chunk 126 optimal weight: 20.0000 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3714 r_free = 0.3714 target = 0.130328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091128 restraints weight = 45649.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.090946 restraints weight = 41710.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091804 restraints weight = 37223.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.091900 restraints weight = 23256.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092986 restraints weight = 20252.544| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15482 Z= 0.139 Angle : 0.609 13.019 22186 Z= 0.344 Chirality : 0.041 0.326 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.080 174.766 4413 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.52 % Allowed : 14.83 % 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: 2.13 (0.26), residues: 1057 helix: 2.48 (0.21), residues: 650 sheet: 1.27 (0.75), residues: 50 loop : -0.65 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 55 TYR 0.017 0.001 TYR H 83 PHE 0.009 0.001 PHE L 62 TRP 0.013 0.002 TRP L 93 HIS 0.005 0.001 HIS L 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (15472) covalent geometry : angle 0.59494 / 0.34 (22171) hydrogen bonds : bond 0.04639 / 3.09 ( 843) hydrogen bonds : angle 3.21219 / 2.37 ( 2151) metal coordination : bond 0.01674 / 0.84 ( 8) metal coordination : angle 6.61447 / 3.59 ( 9) link_TRANS : bond 0.00129 / 0.07 ( 2) link_TRANS : angle 0.26910 / 0.13 ( 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 215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.364 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: 0.8206 (tp30) cc_final: 0.7984 (mm-30) REVERT: C 73 ASN cc_start: 0.8338 (t0) cc_final: 0.8028 (t0) REVERT: C 95 LYS cc_start: 0.8929 (tptt) cc_final: 0.8622 (tptm) REVERT: D 33 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7935 (mtp-110) REVERT: E 125 GLN cc_start: 0.8393 (mt0) cc_final: 0.8022 (mt0) REVERT: K 66 THR cc_start: 0.8377 (m) cc_final: 0.8026 (m) REVERT: K 68 ARG cc_start: 0.7382 (ptp90) cc_final: 0.7165 (mtm180) REVERT: L 8 LYS cc_start: 0.8612 (mppt) cc_final: 0.8294 (tptp) REVERT: L 74 TYR cc_start: 0.8326 (t80) cc_final: 0.8051 (t80) REVERT: L 134 TYR cc_start: 0.6854 (t80) cc_final: 0.6569 (t80) outliers start: 14 outliers final: 10 residues processed: 208 average time/residue: 0.1402 time to fit residues: 40.1193 Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 193 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 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 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: 6.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 122 optimal weight: 20.0000 chunk 32 optimal weight: 0.1980 chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 10 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.130094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.091007 restraints weight = 45257.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092768 restraints weight = 40713.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.092926 restraints weight = 33245.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092701 restraints weight = 22867.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093910 restraints weight = 19577.567| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15482 Z= 0.145 Angle : 0.615 12.824 22186 Z= 0.347 Chirality : 0.041 0.338 2516 Planarity : 0.004 0.059 1794 Dihedral : 29.109 174.623 4413 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.52 % Allowed : 16.13 % Favored : 82.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.26), residues: 1057 helix: 2.52 (0.20), residues: 650 sheet: 1.26 (0.75), residues: 50 loop : -0.61 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 90 TYR 0.015 0.001 TYR H 83 PHE 0.013 0.001 PHE L 62 TRP 0.011 0.002 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (15472) covalent geometry : angle 0.60535 / 0.35 (22171) hydrogen bonds : bond 0.04664 / 3.10 ( 843) hydrogen bonds : angle 3.19447 / 2.35 ( 2151) metal coordination : bond 0.01634 / 0.82 ( 8) metal coordination : angle 5.54162 / 2.97 ( 9) link_TRANS : bond 0.00081 / 0.04 ( 2) link_TRANS : angle 0.28557 / 0.12 ( 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 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.257 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: 0.8227 (tp30) cc_final: 0.8000 (mm-30) REVERT: C 73 ASN cc_start: 0.8354 (t0) cc_final: 0.8061 (t0) REVERT: C 95 LYS cc_start: 0.8941 (tptt) cc_final: 0.8634 (tptm) REVERT: D 33 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7984 (mtp-110) REVERT: E 125 GLN cc_start: 0.8447 (mt0) cc_final: 0.8041 (mt0) REVERT: K 66 THR cc_start: 0.8394 (m) cc_final: 0.8054 (m) REVERT: L 9 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7703 (mm-30) REVERT: L 69 PHE cc_start: 0.7541 (m-80) cc_final: 0.7237 (m-80) REVERT: L 74 TYR cc_start: 0.8294 (t80) cc_final: 0.8015 (t80) REVERT: L 134 TYR cc_start: 0.6856 (t80) cc_final: 0.6403 (t80) REVERT: L 145 TYR cc_start: 0.6273 (OUTLIER) cc_final: 0.5853 (m-10) outliers start: 14 outliers final: 11 residues processed: 205 average time/residue: 0.1193 time to fit residues: 33.8910 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 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 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 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: 2.9990 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 62 optimal weight: 0.0070 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.129508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.080239 restraints weight = 47017.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.080415 restraints weight = 26944.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.081351 restraints weight = 18309.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081689 restraints weight = 17469.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.081644 restraints weight = 15735.343| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.09 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15482 Z= 0.154 Angle : 0.627 13.182 22186 Z= 0.351 Chirality : 0.042 0.331 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.145 174.496 4413 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.95 % Allowed : 16.13 % Favored : 81.93 % 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: 2.11 (0.26), residues: 1057 helix: 2.46 (0.20), residues: 650 sheet: 1.38 (0.74), residues: 50 loop : -0.64 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 33 TYR 0.021 0.001 TYR L 60 PHE 0.015 0.001 PHE L 62 TRP 0.011 0.002 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.15 (15472) covalent geometry : angle 0.61743 / 0.35 (22171) hydrogen bonds : bond 0.04752 / 3.16 ( 843) hydrogen bonds : angle 3.22829 / 2.37 ( 2151) metal coordination : bond 0.01638 / 0.83 ( 8) metal coordination : angle 5.37902 / 2.86 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.24656 / 0.10 ( 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 215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8298 (tp30) cc_final: 0.8077 (mm-30) REVERT: C 73 ASN cc_start: 0.8296 (t0) cc_final: 0.7998 (t0) REVERT: C 95 LYS cc_start: 0.9021 (tptt) cc_final: 0.8678 (tptm) REVERT: D 33 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7911 (mtp-110) REVERT: E 56 LYS cc_start: 0.9309 (ttpp) cc_final: 0.9079 (ttpt) REVERT: E 94 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7644 (mm-30) REVERT: E 125 GLN cc_start: 0.8452 (mt0) cc_final: 0.8143 (mt0) REVERT: K 66 THR cc_start: 0.8315 (m) cc_final: 0.7992 (m) REVERT: L 8 LYS cc_start: 0.8927 (mppt) cc_final: 0.8530 (tptp) REVERT: L 9 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8127 (mm-30) REVERT: L 69 PHE cc_start: 0.7935 (m-80) cc_final: 0.7633 (m-80) REVERT: L 74 TYR cc_start: 0.8414 (t80) cc_final: 0.8116 (t80) REVERT: L 133 LYS cc_start: 0.8977 (tppt) cc_final: 0.8613 (tppt) REVERT: L 134 TYR cc_start: 0.7823 (t80) cc_final: 0.7304 (t80) REVERT: L 145 TYR cc_start: 0.6681 (OUTLIER) cc_final: 0.6092 (m-10) outliers start: 18 outliers final: 11 residues processed: 206 average time/residue: 0.1400 time to fit residues: 40.3306 Evaluate side-chains 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 195 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 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 102 VAL Chi-restraints excluded: chain L residue 143 GLN 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: 3.9990 chunk 64 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 30.0000 chunk 4 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.129574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.076935 restraints weight = 51042.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.079099 restraints weight = 26659.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.080564 restraints weight = 18327.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.081431 restraints weight = 14969.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.081836 restraints weight = 13489.002| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 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 = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15482 Z= 0.148 Angle : 0.628 13.617 22186 Z= 0.351 Chirality : 0.041 0.348 2516 Planarity : 0.004 0.055 1794 Dihedral : 29.148 174.469 4413 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.06 % Allowed : 16.02 % Favored : 81.93 % 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: 2.48 (0.21), residues: 650 sheet: 1.26 (0.73), residues: 50 loop : -0.64 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 90 TYR 0.018 0.001 TYR L 45 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 0.00274 / 0.15 (15472) covalent geometry : angle 0.61726 / 0.35 (22171) hydrogen bonds : bond 0.04702 / 3.13 ( 843) hydrogen bonds : angle 3.19296 / 2.34 ( 2151) metal coordination : bond 0.01638 / 0.84 ( 8) metal coordination : angle 5.81752 / 3.13 ( 9) link_TRANS : bond 0.00072 / 0.04 ( 2) link_TRANS : angle 0.24839 / 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 220 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.400 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: 0.8263 (tp30) cc_final: 0.8017 (mm-30) REVERT: C 16 THR cc_start: 0.8181 (OUTLIER) cc_final: 0.7913 (t) REVERT: C 73 ASN cc_start: 0.8308 (t0) cc_final: 0.8037 (t0) REVERT: C 95 LYS cc_start: 0.9018 (tptt) cc_final: 0.8670 (tptm) REVERT: D 33 ARG cc_start: 0.8235 (mtp-110) cc_final: 0.7892 (mtp-110) REVERT: E 56 LYS cc_start: 0.9329 (ttpp) cc_final: 0.9094 (ttpt) REVERT: E 94 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7464 (mm-30) REVERT: E 125 GLN cc_start: 0.8526 (mt0) cc_final: 0.8220 (mt0) REVERT: K 66 THR cc_start: 0.8373 (m) cc_final: 0.8031 (m) REVERT: L 8 LYS cc_start: 0.8936 (mppt) cc_final: 0.8529 (tptp) REVERT: L 9 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8141 (mm-30) REVERT: L 69 PHE cc_start: 0.8113 (m-80) cc_final: 0.7776 (m-80) REVERT: L 74 TYR cc_start: 0.8428 (t80) cc_final: 0.8043 (t80) REVERT: L 134 TYR cc_start: 0.7889 (t80) cc_final: 0.7132 (t80) REVERT: L 145 TYR cc_start: 0.6787 (OUTLIER) cc_final: 0.6408 (m-10) outliers start: 19 outliers final: 12 residues processed: 212 average time/residue: 0.1488 time to fit residues: 43.8373 Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 199 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 50 PHE Chi-restraints excluded: chain L residue 98 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3703 r_free = 0.3703 target = 0.129511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088834 restraints weight = 39624.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087830 restraints weight = 35416.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.089266 restraints weight = 28242.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.089711 restraints weight = 20842.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.089907 restraints weight = 21309.180| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- 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 = 0.07 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15482 Z= 0.151 Angle : 0.640 14.200 22186 Z= 0.355 Chirality : 0.041 0.330 2516 Planarity : 0.004 0.040 1794 Dihedral : 29.171 174.398 4413 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.73 % Allowed : 16.67 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.26), residues: 1057 helix: 2.41 (0.21), residues: 650 sheet: 1.32 (0.75), residues: 49 loop : -0.65 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.013 0.001 TYR K 64 PHE 0.012 0.001 PHE L 62 TRP 0.011 0.002 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.15 (15472) covalent geometry : angle 0.63087 / 0.35 (22171) hydrogen bonds : bond 0.04718 / 3.14 ( 843) hydrogen bonds : angle 3.20993 / 2.34 ( 2151) metal coordination : bond 0.01603 / 0.81 ( 8) metal coordination : angle 5.32363 / 2.78 ( 9) link_TRANS : bond 0.00069 / 0.04 ( 2) link_TRANS : angle 0.25790 / 0.10 ( 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 215 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 199 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8144 (tp30) cc_final: 0.7851 (mm-30) REVERT: C 16 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7940 (t) REVERT: C 73 ASN cc_start: 0.8383 (t0) cc_final: 0.8105 (t0) REVERT: C 95 LYS cc_start: 0.9035 (tptt) cc_final: 0.8685 (tptm) REVERT: D 33 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7933 (mtp-110) REVERT: E 56 LYS cc_start: 0.9278 (ttpp) cc_final: 0.9017 (ttpt) REVERT: E 59 GLU cc_start: 0.8732 (pm20) cc_final: 0.8408 (pm20) REVERT: E 94 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7621 (mm-30) REVERT: E 125 GLN cc_start: 0.8515 (mt0) cc_final: 0.8150 (mt0) REVERT: H 119 THR cc_start: 0.9500 (t) cc_final: 0.9205 (t) REVERT: L 8 LYS cc_start: 0.8641 (mppt) cc_final: 0.8414 (tptp) REVERT: L 69 PHE cc_start: 0.7729 (m-80) cc_final: 0.7446 (m-80) REVERT: L 145 TYR cc_start: 0.6218 (OUTLIER) cc_final: 0.5873 (m-10) outliers start: 16 outliers final: 12 residues processed: 208 average time/residue: 0.1511 time to fit residues: 43.5475 Evaluate side-chains 209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 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 98 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.127276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.075074 restraints weight = 53774.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.076998 restraints weight = 29009.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.078837 restraints weight = 20238.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.078901 restraints weight = 15714.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.078982 restraints weight = 14362.550| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2861 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2861 r_free = 0.2861 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15482 Z= 0.207 Angle : 0.696 15.442 22186 Z= 0.378 Chirality : 0.044 0.391 2516 Planarity : 0.005 0.071 1794 Dihedral : 29.308 173.812 4413 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.84 % Allowed : 17.10 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.26), residues: 1057 helix: 2.27 (0.21), residues: 649 sheet: 1.13 (0.74), residues: 50 loop : -0.72 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 90 TYR 0.041 0.002 TYR L 134 PHE 0.015 0.002 PHE K 40 TRP 0.010 0.002 TRP L 93 HIS 0.008 0.001 HIS L 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15472) covalent geometry : angle 0.68733 / 0.38 (22171) hydrogen bonds : bond 0.05400 / 3.60 ( 843) hydrogen bonds : angle 3.42062 / 2.50 ( 2151) metal coordination : bond 0.01921 / 0.97 ( 8) metal coordination : angle 5.64806 / 2.90 ( 9) link_TRANS : bond 0.00152 / 0.07 ( 2) link_TRANS : angle 0.40767 / 0.16 ( 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 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 196 time to evaluate : 0.237 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 95 LYS cc_start: 0.9079 (tptt) cc_final: 0.8729 (tptm) REVERT: D 33 ARG cc_start: 0.8273 (mtp-110) cc_final: 0.7779 (mtp-110) REVERT: E 94 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7811 (mm-30) REVERT: E 125 GLN cc_start: 0.8529 (mt0) cc_final: 0.8267 (mt0) REVERT: H 119 THR cc_start: 0.9572 (t) cc_final: 0.9289 (t) REVERT: L 9 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8694 (mm-30) REVERT: L 69 PHE cc_start: 0.8159 (m-80) cc_final: 0.7899 (m-80) REVERT: L 93 TRP cc_start: 0.8712 (t-100) cc_final: 0.8410 (t-100) REVERT: L 145 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.6056 (m-10) outliers start: 17 outliers final: 14 residues processed: 204 average time/residue: 0.1365 time to fit residues: 38.4542 Evaluate side-chains 207 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.413 ------------------------------------------------------------------------------- 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 L residue 50 PHE Chi-restraints excluded: chain L residue 98 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 128 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 127 optimal weight: 7.9990 chunk 17 optimal weight: 6.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- 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 = 0.3683 r_free = 0.3683 target = 0.128059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.089003 restraints weight = 46696.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.088523 restraints weight = 46525.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.089137 restraints weight = 38265.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091723 restraints weight = 22696.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.091520 restraints weight = 18775.308| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15482 Z= 0.171 Angle : 0.669 14.170 22186 Z= 0.369 Chirality : 0.042 0.359 2516 Planarity : 0.004 0.042 1794 Dihedral : 29.267 174.027 4413 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.84 % Allowed : 17.53 % 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: 1.91 (0.26), residues: 1057 helix: 2.31 (0.21), residues: 649 sheet: 1.16 (0.73), residues: 50 loop : -0.73 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 33 TYR 0.046 0.002 TYR L 134 PHE 0.014 0.001 PHE L 62 TRP 0.009 0.002 TRP L 93 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.17 (15472) covalent geometry : angle 0.66031 / 0.37 (22171) hydrogen bonds : bond 0.05073 / 3.38 ( 843) hydrogen bonds : angle 3.33566 / 2.44 ( 2151) metal coordination : bond 0.01849 / 0.93 ( 8) metal coordination : angle 5.30540 / 2.74 ( 9) link_TRANS : bond 0.00089 / 0.04 ( 2) link_TRANS : angle 0.36091 / 0.14 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2439.35 seconds wall clock time: 42 minutes 42.25 seconds (2562.25 seconds total)