Starting phenix.real_space_refine on Fri Jul 3 12:34:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.cif" model { file = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f86_28915/07_2026/8f86_28915.cif" } resolution = 3.1 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= 0.011 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 1 6.06 5 P 297 5.49 5 S 22 5.16 5 C 8111 2.51 5 N 2698 2.21 5 O 3271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14400 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 868 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 861 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3050 Classifications: {'DNA': 148} Link IDs: {'rna3p': 147} Chain: "J" Number of atoms: 3015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3015 Classifications: {'DNA': 148} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 147} Chain: "K" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2242 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 270} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'ZSL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13207 SG CYS K 141 67.069 70.011 64.643 1.00144.83 S ATOM 13227 SG CYS K 144 69.022 69.847 67.742 1.00126.49 S ATOM 13392 SG CYS K 166 69.504 67.199 65.177 1.00126.37 S ATOM 13470 SG CYS K 177 66.155 67.223 67.101 1.00122.41 S Time building chain proxies: 3.26, per 1000 atoms: 0.23 Number of scatterers: 14400 At special positions: 0 Unit cell: (116.2, 134.46, 119.52, 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 1 29.99 S 22 16.00 P 297 15.00 O 3271 8.00 N 2698 7.00 C 8111 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 Atom "HETATM14390 O37 ZSL A 201 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 394.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 141 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 166 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 144 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 177 " Number of angles added : 6 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 11 sheets defined 61.0% alpha, 4.5% beta 147 base pairs and 234 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.912A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.711A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.676A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.571A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.510A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.814A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.509A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.663A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.866A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.530A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.597A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.030A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.520A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 120 Processing helix chain 'K' and resid 26 through 44 removed outlier: 4.015A pdb=" N GLN K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 60 removed outlier: 4.043A pdb=" N ALA K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N SER K 59 " --> pdb=" O ILE K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 76 Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.812A pdb=" N MET K 96 " --> pdb=" O THR K 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 122 Processing helix chain 'K' and resid 193 through 207 Processing helix chain 'K' and resid 220 through 223 removed outlier: 3.631A pdb=" N GLY K 223 " --> pdb=" O ARG K 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 220 through 223' Processing helix chain 'K' and resid 224 through 231 removed outlier: 3.841A pdb=" N LYS K 230 " --> pdb=" O PRO K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.107A pdb=" N ARG A 83 " --> pdb=" O VAL F 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 45 through 46 removed outlier: 7.611A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA6, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.544A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.914A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.773A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 107 through 110 removed outlier: 6.639A pdb=" N VAL K 47 " --> pdb=" O ARG K 108 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU K 110 " --> pdb=" O VAL K 47 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N PHE K 49 " --> pdb=" O LEU K 110 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL K 48 " --> pdb=" O ILE K 211 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N LEU K 213 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS K 50 " --> pdb=" O LEU K 213 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE K 254 " --> pdb=" O LEU K 236 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ILE K 238 " --> pdb=" O ILE K 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 147 through 149 removed outlier: 6.652A pdb=" N VAL K 138 " --> pdb=" O THR K 184 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR K 184 " --> pdb=" O VAL K 138 " (cutoff:3.500A) 462 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 379 hydrogen bonds 758 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 234 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.53 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: 3963 1.34 - 1.47: 4876 1.47 - 1.60: 5835 1.60 - 1.72: 551 1.72 - 1.85: 39 Bond restraints: 15264 Sorted by residual: bond pdb=" O38 ZSL A 201 " pdb=" P44 ZSL A 201 " ideal model delta sigma weight residual 1.493 1.397 0.096 2.00e-02 2.50e+03 2.30e+01 bond pdb=" C20 ZSL A 201 " pdb=" S46 ZSL A 201 " ideal model delta sigma weight residual 1.830 1.746 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C25 ZSL A 201 " pdb=" C27 ZSL A 201 " ideal model delta sigma weight residual 1.386 1.465 -0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C20 ZSL A 201 " pdb=" O36 ZSL A 201 " ideal model delta sigma weight residual 1.391 1.463 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" O39 ZSL A 201 " pdb=" P44 ZSL A 201 " ideal model delta sigma weight residual 1.497 1.567 -0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 15259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.47: 21886 5.47 - 10.94: 15 10.94 - 16.41: 0 16.41 - 21.87: 1 21.87 - 27.34: 1 Bond angle restraints: 21903 Sorted by residual: angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP1 DG I 21 " ideal model delta sigma weight residual 108.00 80.66 27.34 3.00e+00 1.11e-01 8.31e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" OP2 DG I 21 " ideal model delta sigma weight residual 108.00 87.49 20.51 3.00e+00 1.11e-01 4.67e+01 angle pdb=" N3 DT J -43 " pdb=" C4 DT J -43 " pdb=" O4 DT J -43 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.09e+01 angle pdb=" N3 DT I -24 " pdb=" C4 DT I -24 " pdb=" O4 DT I -24 " ideal model delta sigma weight residual 119.90 122.63 -2.73 6.00e-01 2.78e+00 2.07e+01 angle pdb=" O4' DT I 14 " pdb=" C4' DT I 14 " pdb=" C3' DT I 14 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 ... (remaining 21898 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.47: 7075 34.47 - 68.95: 1361 68.95 - 103.42: 27 103.42 - 137.89: 0 137.89 - 172.37: 2 Dihedral angle restraints: 8465 sinusoidal: 5427 harmonic: 3038 Sorted by residual: dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 47.63 172.37 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 59.57 160.43 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA THR K 184 " pdb=" C THR K 184 " pdb=" N ILE K 185 " pdb=" CA ILE K 185 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 8462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.404: 2494 0.404 - 0.809: 0 0.809 - 1.213: 0 1.213 - 1.618: 0 1.618 - 2.022: 1 Chirality restraints: 2495 Sorted by residual: chirality pdb=" P DG I 21 " pdb=" OP1 DG I 21 " pdb=" OP2 DG I 21 " pdb=" O5' DG I 21 " both_signs ideal model delta sigma weight residual True 2.34 0.31 2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" C PRO K 221 " pdb=" CB PRO K 221 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C17 ZSL A 201 " pdb=" C16 ZSL A 201 " pdb=" C18 ZSL A 201 " pdb=" O32 ZSL A 201 " both_signs ideal model delta sigma weight residual False 2.48 2.69 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 2492 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG K 220 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO K 221 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO K 221 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO K 221 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC J -50 " -0.004 2.00e-02 2.50e+03 1.91e-02 8.20e+00 pdb=" N1 DC J -50 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DC J -50 " 0.047 2.00e-02 2.50e+03 pdb=" O2 DC J -50 " -0.030 2.00e-02 2.50e+03 pdb=" N3 DC J -50 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC J -50 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC J -50 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC J -50 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC J -50 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 51 " -0.011 2.00e-02 2.50e+03 1.14e-02 3.91e+00 pdb=" N9 DG I 51 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DG I 51 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG I 51 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 51 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 51 " -0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 51 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 51 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DG I 51 " -0.024 2.00e-02 2.50e+03 pdb=" N2 DG I 51 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DG I 51 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 51 " 0.004 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 88 2.52 - 3.12: 10598 3.12 - 3.71: 26010 3.71 - 4.31: 34845 4.31 - 4.90: 51988 Nonbonded interactions: 123529 Sorted by model distance: nonbonded pdb=" OG SER K 112 " pdb=" OD1 ASN K 114 " model vdw 1.927 3.040 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 1.966 3.040 nonbonded pdb=" OG1 THR K 244 " pdb=" OD1 ASP K 247 " model vdw 1.980 3.040 nonbonded pdb=" OD2 ASP K 63 " pdb=" O32 ZSL A 201 " model vdw 2.022 3.040 nonbonded pdb=" O LYS C 119 " pdb=" OG1 THR C 120 " model vdw 2.070 3.040 ... (remaining 123524 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' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.560 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 0.119 15269 Z= 0.498 Angle : 0.798 27.343 21909 Z= 0.633 Chirality : 0.070 2.022 2495 Planarity : 0.005 0.110 1751 Dihedral : 26.366 172.368 6505 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.22 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 21.33 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.27), residues: 1035 helix: 2.14 (0.21), residues: 610 sheet: -2.76 (0.79), residues: 44 loop : -2.14 (0.29), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 83 TYR 0.014 0.001 TYR B 51 PHE 0.010 0.001 PHE A 67 TRP 0.010 0.001 TRP K 276 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00585 / 0.49 (15264) covalent geometry : angle 0.79563 / 0.63 (21903) hydrogen bonds : bond 0.09595 / 6.66 ( 841) hydrogen bonds : angle 4.10449 / 2.91 ( 2126) metal coordination : bond 0.00763 / 0.37 ( 4) metal coordination : angle 3.66743 / 1.79 ( 6) Misc. bond : bond 0.07753 / 4.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8096 (mmm) cc_final: 0.7881 (mmm) REVERT: C 92 GLU cc_start: 0.8514 (mp0) cc_final: 0.8227 (mp0) REVERT: D 118 TYR cc_start: 0.8688 (t80) cc_final: 0.8391 (t80) REVERT: F 31 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8472 (mtpp) REVERT: F 77 LYS cc_start: 0.8789 (mttp) cc_final: 0.8521 (mmtt) REVERT: G 36 LYS cc_start: 0.8428 (tptp) cc_final: 0.8054 (tppt) REVERT: G 41 GLU cc_start: 0.8370 (tt0) cc_final: 0.8156 (mp0) REVERT: G 91 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7917 (tm-30) REVERT: H 32 GLU cc_start: 0.8066 (pt0) cc_final: 0.7854 (mt-10) REVERT: H 110 GLU cc_start: 0.7787 (tt0) cc_final: 0.7577 (mm-30) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1357 time to fit residues: 21.5687 Evaluate side-chains 94 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 35 optimal weight: 2.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 4 ASN K 100 GLN K 133 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.079201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.059191 restraints weight = 65070.989| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.91 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 15269 Z= 0.183 Angle : 0.702 26.885 21909 Z= 0.401 Chirality : 0.061 2.074 2495 Planarity : 0.005 0.110 1751 Dihedral : 28.934 170.799 4460 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.86 % Favored : 95.94 % Rotamer: Outliers : 1.72 % Allowed : 19.84 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.27), residues: 1035 helix: 2.19 (0.21), residues: 615 sheet: -2.49 (0.82), residues: 34 loop : -1.87 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 36 TYR 0.025 0.002 TYR E 54 PHE 0.016 0.002 PHE A 67 TRP 0.007 0.001 TRP K 71 HIS 0.004 0.001 HIS K 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.18 (15264) covalent geometry : angle 0.70139 / 0.40 (21903) hydrogen bonds : bond 0.05536 / 3.73 ( 841) hydrogen bonds : angle 3.41477 / 2.42 ( 2126) metal coordination : bond 0.01298 / 0.61 ( 4) metal coordination : angle 2.27803 / 1.30 ( 6) Misc. bond : bond 0.02110 / 1.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.7579 (tp30) cc_final: 0.7368 (tp30) REVERT: C 92 GLU cc_start: 0.8368 (mp0) cc_final: 0.7631 (mp0) REVERT: C 110 ASN cc_start: 0.7207 (p0) cc_final: 0.6868 (p0) REVERT: D 118 TYR cc_start: 0.8538 (t80) cc_final: 0.8288 (t80) REVERT: G 93 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8503 (mp) REVERT: K 5 TYR cc_start: 0.5319 (m-80) cc_final: 0.4759 (m-80) REVERT: K 93 GLN cc_start: 0.7950 (tp40) cc_final: 0.7653 (tp-100) REVERT: K 136 MET cc_start: 0.7332 (mmm) cc_final: 0.7001 (mmm) outliers start: 15 outliers final: 4 residues processed: 118 average time/residue: 0.1197 time to fit residues: 20.1422 Evaluate side-chains 99 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 162 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 109 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 126 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 89 optimal weight: 30.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 44 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.078736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058787 restraints weight = 65612.458| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.82 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 15269 Z= 0.176 Angle : 0.669 26.887 21909 Z= 0.382 Chirality : 0.059 2.043 2495 Planarity : 0.005 0.115 1751 Dihedral : 29.155 171.716 4460 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 2.64 % Allowed : 18.81 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.06 (0.27), residues: 1035 helix: 2.27 (0.21), residues: 614 sheet: -2.46 (0.80), residues: 34 loop : -1.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 175 TYR 0.018 0.001 TYR G 39 PHE 0.016 0.002 PHE A 67 TRP 0.009 0.001 TRP K 71 HIS 0.009 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.18 (15264) covalent geometry : angle 0.66714 / 0.38 (21903) hydrogen bonds : bond 0.05233 / 3.53 ( 841) hydrogen bonds : angle 3.26852 / 2.34 ( 2126) metal coordination : bond 0.01234 / 0.59 ( 4) metal coordination : angle 2.77677 / 1.61 ( 6) Misc. bond : bond 0.00576 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 94 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7420 (mt-10) REVERT: C 91 GLU cc_start: 0.7628 (tp30) cc_final: 0.7375 (tp30) REVERT: C 92 GLU cc_start: 0.8374 (mp0) cc_final: 0.7667 (mp0) REVERT: D 56 MET cc_start: 0.8335 (tpp) cc_final: 0.8115 (tpp) REVERT: D 118 TYR cc_start: 0.8492 (t80) cc_final: 0.8227 (t80) REVERT: G 93 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8589 (mp) REVERT: K 5 TYR cc_start: 0.5278 (m-80) cc_final: 0.4751 (m-80) REVERT: K 35 TRP cc_start: 0.6958 (OUTLIER) cc_final: 0.6429 (m-90) REVERT: K 93 GLN cc_start: 0.7988 (tp40) cc_final: 0.7737 (tp-100) REVERT: K 136 MET cc_start: 0.7343 (mmm) cc_final: 0.6890 (mmm) REVERT: K 213 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6174 (mt) REVERT: K 262 MET cc_start: 0.8838 (mtp) cc_final: 0.8460 (mtp) outliers start: 23 outliers final: 10 residues processed: 115 average time/residue: 0.1129 time to fit residues: 18.8571 Evaluate side-chains 101 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 50.0000 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 101 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 102 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 99 optimal weight: 20.0000 chunk 43 optimal weight: 0.6980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN K 4 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.078962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.059049 restraints weight = 65496.620| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.82 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15269 Z= 0.158 Angle : 0.648 26.866 21909 Z= 0.369 Chirality : 0.058 2.035 2495 Planarity : 0.005 0.116 1751 Dihedral : 29.228 170.155 4460 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.81 % Rotamer: Outliers : 3.56 % Allowed : 18.00 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.19 (0.27), residues: 1035 helix: 2.41 (0.21), residues: 610 sheet: -2.52 (0.78), residues: 34 loop : -1.66 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.015 0.001 TYR E 54 PHE 0.015 0.002 PHE A 67 TRP 0.009 0.001 TRP K 71 HIS 0.006 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.16 (15264) covalent geometry : angle 0.64689 / 0.37 (21903) hydrogen bonds : bond 0.04942 / 3.34 ( 841) hydrogen bonds : angle 3.14655 / 2.27 ( 2126) metal coordination : bond 0.01027 / 0.50 ( 4) metal coordination : angle 2.41313 / 1.40 ( 6) Misc. bond : bond 0.00167 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8272 (pttt) cc_final: 0.7641 (ptpp) REVERT: B 63 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7407 (mt-10) REVERT: C 91 GLU cc_start: 0.7632 (tp30) cc_final: 0.7349 (tp30) REVERT: C 92 GLU cc_start: 0.8335 (mp0) cc_final: 0.7632 (mp0) REVERT: D 118 TYR cc_start: 0.8486 (t80) cc_final: 0.8152 (t80) REVERT: G 91 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 93 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8638 (mp) REVERT: H 98 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7705 (mm) REVERT: K 5 TYR cc_start: 0.5281 (m-80) cc_final: 0.4781 (m-80) REVERT: K 93 GLN cc_start: 0.7885 (tp40) cc_final: 0.7638 (tp-100) REVERT: K 136 MET cc_start: 0.7315 (mmm) cc_final: 0.6866 (mmm) REVERT: K 262 MET cc_start: 0.8835 (mtp) cc_final: 0.8632 (mtp) outliers start: 31 outliers final: 18 residues processed: 123 average time/residue: 0.1227 time to fit residues: 21.2149 Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 162 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 71 optimal weight: 7.9990 chunk 73 optimal weight: 50.0000 chunk 4 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 52 optimal weight: 7.9990 overall best weight: 1.3902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN D 44 GLN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.059428 restraints weight = 65370.737| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.82 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 15269 Z= 0.152 Angle : 0.641 26.867 21909 Z= 0.364 Chirality : 0.058 2.026 2495 Planarity : 0.005 0.118 1751 Dihedral : 29.258 169.790 4460 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.09 % Favored : 96.71 % Rotamer: Outliers : 2.98 % Allowed : 19.27 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.26), residues: 1035 helix: 2.47 (0.20), residues: 610 sheet: -2.56 (0.76), residues: 34 loop : -1.61 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.014 0.001 TYR G 39 PHE 0.027 0.002 PHE E 78 TRP 0.009 0.001 TRP K 71 HIS 0.006 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (15264) covalent geometry : angle 0.63980 / 0.36 (21903) hydrogen bonds : bond 0.04818 / 3.25 ( 841) hydrogen bonds : angle 3.07062 / 2.21 ( 2126) metal coordination : bond 0.00981 / 0.48 ( 4) metal coordination : angle 2.33627 / 1.36 ( 6) Misc. bond : bond 0.00177 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.379 Fit side-chains REVERT: A 122 LYS cc_start: 0.8287 (pttt) cc_final: 0.7643 (ptpp) REVERT: C 91 GLU cc_start: 0.7636 (tp30) cc_final: 0.7350 (tp30) REVERT: C 92 GLU cc_start: 0.8320 (mp0) cc_final: 0.7651 (mp0) REVERT: D 56 MET cc_start: 0.8298 (tpp) cc_final: 0.7973 (tpp) REVERT: D 118 TYR cc_start: 0.8473 (t80) cc_final: 0.8181 (t80) REVERT: E 125 GLN cc_start: 0.8213 (mp10) cc_final: 0.7593 (mp10) REVERT: G 91 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7734 (tm-30) REVERT: G 93 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8672 (mp) REVERT: H 98 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7689 (mm) REVERT: K 5 TYR cc_start: 0.5439 (m-80) cc_final: 0.5001 (m-80) REVERT: K 93 GLN cc_start: 0.7943 (tp40) cc_final: 0.7696 (tp-100) REVERT: K 136 MET cc_start: 0.7308 (mmm) cc_final: 0.7061 (mmm) REVERT: K 206 ASN cc_start: 0.8740 (t0) cc_final: 0.8463 (t0) outliers start: 26 outliers final: 16 residues processed: 115 average time/residue: 0.1167 time to fit residues: 19.2120 Evaluate side-chains 107 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 89 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 12 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 125 optimal weight: 0.0980 chunk 104 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 126 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.079496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.059514 restraints weight = 65186.471| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.79 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 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 0.096 15269 Z= 0.144 Angle : 0.641 26.845 21909 Z= 0.362 Chirality : 0.057 2.024 2495 Planarity : 0.005 0.119 1751 Dihedral : 29.221 169.256 4460 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.80 % Favored : 97.00 % Rotamer: Outliers : 2.98 % Allowed : 19.84 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.38 (0.26), residues: 1035 helix: 2.55 (0.21), residues: 610 sheet: -2.48 (0.78), residues: 34 loop : -1.55 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.014 0.001 TYR C 57 PHE 0.017 0.002 PHE K 49 TRP 0.006 0.001 TRP K 35 HIS 0.005 0.001 HIS K 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15264) covalent geometry : angle 0.63960 / 0.36 (21903) hydrogen bonds : bond 0.04681 / 3.16 ( 841) hydrogen bonds : angle 3.05019 / 2.21 ( 2126) metal coordination : bond 0.00839 / 0.41 ( 4) metal coordination : angle 2.32067 / 1.35 ( 6) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 94 time to evaluate : 0.298 Fit side-chains REVERT: A 122 LYS cc_start: 0.8285 (pttt) cc_final: 0.7644 (ptpp) REVERT: B 77 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8671 (mmtm) REVERT: B 96 THR cc_start: 0.8324 (p) cc_final: 0.8069 (t) REVERT: C 91 GLU cc_start: 0.7632 (tp30) cc_final: 0.7357 (tp30) REVERT: C 92 GLU cc_start: 0.8319 (mp0) cc_final: 0.7646 (mp0) REVERT: D 118 TYR cc_start: 0.8443 (t80) cc_final: 0.8146 (t80) REVERT: E 125 GLN cc_start: 0.8243 (mp10) cc_final: 0.7598 (mp10) REVERT: G 90 ASP cc_start: 0.7404 (t0) cc_final: 0.7181 (m-30) REVERT: G 91 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7752 (tm-30) REVERT: G 93 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8639 (mp) REVERT: H 98 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7702 (mm) REVERT: K 5 TYR cc_start: 0.5470 (m-80) cc_final: 0.5076 (m-80) REVERT: K 93 GLN cc_start: 0.7932 (tp40) cc_final: 0.7686 (tp-100) REVERT: K 206 ASN cc_start: 0.8711 (t0) cc_final: 0.8449 (t0) REVERT: K 262 MET cc_start: 0.8586 (mtp) cc_final: 0.8304 (mtt) outliers start: 26 outliers final: 20 residues processed: 116 average time/residue: 0.1113 time to fit residues: 18.4931 Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 0.5980 chunk 87 optimal weight: 50.0000 chunk 113 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.079215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.059504 restraints weight = 65314.766| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 2.79 r_work: 0.3287 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 15269 Z= 0.161 Angle : 0.644 26.904 21909 Z= 0.362 Chirality : 0.057 2.014 2495 Planarity : 0.005 0.121 1751 Dihedral : 29.274 168.875 4460 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.38 % Favored : 96.43 % Rotamer: Outliers : 3.56 % Allowed : 18.81 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.33 (0.26), residues: 1035 helix: 2.51 (0.21), residues: 610 sheet: -2.53 (0.79), residues: 34 loop : -1.57 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 172 TYR 0.014 0.001 TYR E 54 PHE 0.018 0.002 PHE E 78 TRP 0.010 0.002 TRP K 71 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (15264) covalent geometry : angle 0.64323 / 0.36 (21903) hydrogen bonds : bond 0.04839 / 3.27 ( 841) hydrogen bonds : angle 3.06303 / 2.21 ( 2126) metal coordination : bond 0.01059 / 0.51 ( 4) metal coordination : angle 2.22065 / 1.30 ( 6) Misc. bond : bond 0.00039 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 92 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8414 (pttt) cc_final: 0.8136 (pttp) REVERT: B 77 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8825 (mmtm) REVERT: C 91 GLU cc_start: 0.7977 (tp30) cc_final: 0.7718 (tp30) REVERT: C 92 GLU cc_start: 0.8529 (mp0) cc_final: 0.7896 (mp0) REVERT: D 56 MET cc_start: 0.8638 (tpp) cc_final: 0.8362 (tpp) REVERT: D 118 TYR cc_start: 0.8647 (t80) cc_final: 0.8347 (t80) REVERT: E 73 GLU cc_start: 0.8499 (tt0) cc_final: 0.8211 (tt0) REVERT: E 125 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7820 (mp10) REVERT: G 36 LYS cc_start: 0.8145 (tptp) cc_final: 0.7555 (tttt) REVERT: G 91 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8109 (tm-30) REVERT: G 93 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8623 (mp) REVERT: H 98 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7676 (mm) REVERT: K 93 GLN cc_start: 0.8086 (tp40) cc_final: 0.7804 (tp-100) REVERT: K 206 ASN cc_start: 0.8860 (t0) cc_final: 0.8589 (t0) outliers start: 31 outliers final: 20 residues processed: 117 average time/residue: 0.1125 time to fit residues: 19.0121 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 110 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 112 optimal weight: 9.9990 chunk 69 optimal weight: 0.0370 chunk 118 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 76 GLN E 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.079000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.058940 restraints weight = 65147.180| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.82 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15269 Z= 0.170 Angle : 0.656 26.887 21909 Z= 0.366 Chirality : 0.057 2.014 2495 Planarity : 0.005 0.122 1751 Dihedral : 29.352 168.871 4460 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.90 % Favored : 96.91 % Rotamer: Outliers : 3.33 % Allowed : 19.61 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.29 (0.26), residues: 1035 helix: 2.47 (0.21), residues: 611 sheet: -2.53 (0.77), residues: 34 loop : -1.59 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.021 0.001 TYR K 5 PHE 0.017 0.002 PHE E 78 TRP 0.009 0.001 TRP K 71 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.17 (15264) covalent geometry : angle 0.65485 / 0.37 (21903) hydrogen bonds : bond 0.04880 / 3.30 ( 841) hydrogen bonds : angle 3.10846 / 2.25 ( 2126) metal coordination : bond 0.01174 / 0.56 ( 4) metal coordination : angle 2.35792 / 1.37 ( 6) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8295 (pttt) cc_final: 0.8018 (pttp) REVERT: B 77 LYS cc_start: 0.8895 (mmmt) cc_final: 0.8694 (mmtm) REVERT: B 96 THR cc_start: 0.8391 (p) cc_final: 0.8157 (t) REVERT: C 91 GLU cc_start: 0.7681 (tp30) cc_final: 0.7411 (tp30) REVERT: C 92 GLU cc_start: 0.8363 (mp0) cc_final: 0.7654 (mp0) REVERT: D 118 TYR cc_start: 0.8483 (t80) cc_final: 0.8249 (t80) REVERT: E 73 GLU cc_start: 0.8082 (tt0) cc_final: 0.7833 (tt0) REVERT: E 125 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7597 (mp10) REVERT: G 36 LYS cc_start: 0.7983 (tptp) cc_final: 0.7384 (tttt) REVERT: G 91 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7492 (tm-30) REVERT: G 95 LYS cc_start: 0.9024 (ttmm) cc_final: 0.8499 (mtmt) REVERT: H 98 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7718 (mm) REVERT: K 5 TYR cc_start: 0.5035 (m-10) cc_final: 0.4812 (m-80) REVERT: K 93 GLN cc_start: 0.7936 (tp40) cc_final: 0.7656 (tp-100) REVERT: K 206 ASN cc_start: 0.8661 (t0) cc_final: 0.8384 (t0) outliers start: 29 outliers final: 19 residues processed: 115 average time/residue: 0.1425 time to fit residues: 23.2009 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 19 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 75 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN C 38 ASN E 76 GLN ** K 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.078820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058701 restraints weight = 65447.040| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.82 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 15269 Z= 0.178 Angle : 0.664 26.928 21909 Z= 0.371 Chirality : 0.057 2.012 2495 Planarity : 0.005 0.123 1751 Dihedral : 29.404 168.812 4460 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 3.56 % Allowed : 19.38 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.26), residues: 1035 helix: 2.45 (0.21), residues: 611 sheet: -2.58 (0.76), residues: 34 loop : -1.59 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.012 0.001 TYR E 54 PHE 0.051 0.002 PHE K 64 TRP 0.015 0.002 TRP K 71 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.18 (15264) covalent geometry : angle 0.66244 / 0.37 (21903) hydrogen bonds : bond 0.04929 / 3.33 ( 841) hydrogen bonds : angle 3.14454 / 2.29 ( 2126) metal coordination : bond 0.01232 / 0.59 ( 4) metal coordination : angle 2.37391 / 1.37 ( 6) Misc. bond : bond 0.00038 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8323 (pttt) cc_final: 0.8027 (pttp) REVERT: B 96 THR cc_start: 0.8386 (p) cc_final: 0.8159 (t) REVERT: C 91 GLU cc_start: 0.7704 (tp30) cc_final: 0.7441 (tp30) REVERT: C 92 GLU cc_start: 0.8368 (mp0) cc_final: 0.7661 (mp0) REVERT: D 56 MET cc_start: 0.8401 (tpp) cc_final: 0.8129 (tpp) REVERT: D 118 TYR cc_start: 0.8486 (t80) cc_final: 0.8249 (t80) REVERT: E 73 GLU cc_start: 0.8090 (tt0) cc_final: 0.7836 (tt0) REVERT: E 125 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: F 31 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8230 (mtpp) REVERT: G 36 LYS cc_start: 0.7964 (tptp) cc_final: 0.7360 (tttt) REVERT: G 91 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7677 (tm-30) REVERT: H 98 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7718 (mm) REVERT: K 5 TYR cc_start: 0.4905 (m-10) cc_final: 0.4480 (m-80) REVERT: K 93 GLN cc_start: 0.7913 (tp40) cc_final: 0.7591 (tp-100) REVERT: K 206 ASN cc_start: 0.8662 (t0) cc_final: 0.8378 (t0) outliers start: 31 outliers final: 24 residues processed: 117 average time/residue: 0.1455 time to fit residues: 24.1948 Evaluate side-chains 116 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 22 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 95 optimal weight: 9.9990 chunk 73 optimal weight: 50.0000 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 36 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.078380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.058144 restraints weight = 65228.531| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.84 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 15269 Z= 0.202 Angle : 0.690 26.951 21909 Z= 0.381 Chirality : 0.058 2.007 2495 Planarity : 0.005 0.124 1751 Dihedral : 29.559 169.119 4460 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.35 % Favored : 95.46 % Rotamer: Outliers : 2.75 % Allowed : 20.18 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.11 (0.26), residues: 1035 helix: 2.31 (0.21), residues: 611 sheet: -2.67 (0.76), residues: 34 loop : -1.62 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.021 0.002 TYR E 54 PHE 0.043 0.002 PHE K 64 TRP 0.013 0.002 TRP K 71 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (15264) covalent geometry : angle 0.68862 / 0.38 (21903) hydrogen bonds : bond 0.05245 / 3.54 ( 841) hydrogen bonds : angle 3.25505 / 2.37 ( 2126) metal coordination : bond 0.01435 / 0.68 ( 4) metal coordination : angle 2.70203 / 1.53 ( 6) Misc. bond : bond 0.00048 / 0.03 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2070 Ramachandran restraints generated. 1035 Oldfield, 0 Emsley, 1035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8318 (pttt) cc_final: 0.8017 (pttp) REVERT: C 91 GLU cc_start: 0.7783 (tp30) cc_final: 0.7548 (tp30) REVERT: C 92 GLU cc_start: 0.8403 (mp0) cc_final: 0.7755 (mp0) REVERT: D 56 MET cc_start: 0.8445 (tpp) cc_final: 0.8157 (tpp) REVERT: D 118 TYR cc_start: 0.8507 (t80) cc_final: 0.8257 (t80) REVERT: E 73 GLU cc_start: 0.8072 (tt0) cc_final: 0.7820 (tt0) REVERT: E 125 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: F 31 LYS cc_start: 0.8525 (mtmt) cc_final: 0.8255 (mtpp) REVERT: G 36 LYS cc_start: 0.7951 (tptp) cc_final: 0.7346 (tttt) REVERT: G 91 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7655 (tm-30) REVERT: G 95 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8645 (mtmt) REVERT: H 98 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7696 (mm) REVERT: K 5 TYR cc_start: 0.4967 (m-10) cc_final: 0.4544 (m-80) REVERT: K 206 ASN cc_start: 0.8646 (t0) cc_final: 0.8350 (t0) outliers start: 24 outliers final: 22 residues processed: 110 average time/residue: 0.1482 time to fit residues: 23.1910 Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 15 LYS Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 139 GLU Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 262 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 116 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.078922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.058994 restraints weight = 65119.204| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.84 r_work: 0.3257 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 15269 Z= 0.159 Angle : 0.667 26.898 21909 Z= 0.370 Chirality : 0.058 2.015 2495 Planarity : 0.005 0.124 1751 Dihedral : 29.519 169.499 4460 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.48 % Favored : 96.33 % Rotamer: Outliers : 2.98 % Allowed : 20.41 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.22 (0.26), residues: 1035 helix: 2.40 (0.21), residues: 611 sheet: -2.58 (0.77), residues: 34 loop : -1.59 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 92 TYR 0.019 0.002 TYR B 98 PHE 0.039 0.002 PHE K 64 TRP 0.011 0.001 TRP K 71 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.16 (15264) covalent geometry : angle 0.66600 / 0.37 (21903) hydrogen bonds : bond 0.04843 / 3.26 ( 841) hydrogen bonds : angle 3.15670 / 2.31 ( 2126) metal coordination : bond 0.01053 / 0.51 ( 4) metal coordination : angle 2.66957 / 1.54 ( 6) Misc. bond : bond 0.00030 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2900.83 seconds wall clock time: 50 minutes 33.25 seconds (3033.25 seconds total)