Starting phenix.real_space_refine on Thu Jun 12 17:47:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f86_28915/06_2025/8f86_28915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f86_28915/06_2025/8f86_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_28915/06_2025/8f86_28915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f86_28915/06_2025/8f86_28915.map" model { file = "/net/cci-nas-00/data/ceres_data/8f86_28915/06_2025/8f86_28915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f86_28915/06_2025/8f86_28915.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.94, per 1000 atoms: 0.62 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: 3.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 5.81 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: 5.58 Time building geometry restraints manager: 3.97 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=" CA PRO K 221 " pdb=" N PRO K 221 " pdb=" CD PRO K 221 " ideal model delta sigma weight residual 112.00 105.90 6.10 1.40e+00 5.10e-01 1.90e+01 angle pdb=" O3' DG I 20 " pdb=" P DG I 21 " pdb=" O5' DG I 21 " ideal model delta sigma weight residual 104.00 97.66 6.34 1.50e+00 4.44e-01 1.79e+01 angle pdb=" OP1 DG I 21 " pdb=" P DG I 21 " pdb=" OP2 DG I 21 " ideal model delta sigma weight residual 120.00 130.44 -10.44 3.00e+00 1.11e-01 1.21e+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 - 0.406: 2494 0.406 - 0.813: 0 0.813 - 1.219: 0 1.219 - 1.626: 0 1.626 - 2.032: 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 2.35 0.31 2.03 2.00e-01 2.50e+01 1.03e+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: 2.710 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: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 39.780 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.004 0.119 15269 Z= 0.211 Angle : 0.666 27.343 21909 Z= 0.374 Chirality : 0.057 2.032 2495 Planarity : 0.005 0.110 1751 Dihedral : 26.366 172.368 6505 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 8.46 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.010 0.001 TRP K 276 HIS 0.004 0.001 HIS A 113 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR B 51 ARG 0.008 0.000 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.09595 ( 841) hydrogen bonds : angle 4.10449 ( 2126) metal coordination : bond 0.00763 ( 4) metal coordination : angle 3.66743 ( 6) covalent geometry : bond 0.00421 (15264) covalent geometry : angle 0.66373 (21903) Misc. bond : bond 0.07753 ( 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 : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8097 (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: 0.3313 time to fit residues: 52.0383 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 : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.2980 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 44 GLN ** K 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 HIS K 224 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.079367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059610 restraints weight = 65312.012| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.80 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 15269 Z= 0.176 Angle : 0.641 26.977 21909 Z= 0.355 Chirality : 0.055 2.065 2495 Planarity : 0.005 0.112 1751 Dihedral : 28.759 173.332 4460 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 2.06 % Allowed : 19.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1035 helix: 2.45 (0.21), residues: 611 sheet: -1.92 (1.06), residues: 24 loop : -1.72 (0.30), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP K 71 HIS 0.004 0.001 HIS F 75 PHE 0.017 0.002 PHE A 67 TYR 0.020 0.002 TYR E 54 ARG 0.004 0.001 ARG D 83 Details of bonding type rmsd hydrogen bonds : bond 0.04441 ( 841) hydrogen bonds : angle 3.16213 ( 2126) metal coordination : bond 0.00760 ( 4) metal coordination : angle 2.05520 ( 6) covalent geometry : bond 0.00392 (15264) covalent geometry : angle 0.63981 (21903) Misc. bond : bond 0.00049 ( 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 130 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8097 (tt0) cc_final: 0.7888 (tt0) REVERT: B 63 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7367 (mt-10) REVERT: C 59 THR cc_start: 0.7626 (OUTLIER) cc_final: 0.6978 (m) REVERT: C 92 GLU cc_start: 0.8328 (mp0) cc_final: 0.7552 (mp0) REVERT: D 56 MET cc_start: 0.8367 (tpp) cc_final: 0.8141 (tpp) REVERT: D 118 TYR cc_start: 0.8472 (t80) cc_final: 0.8163 (t80) REVERT: G 36 LYS cc_start: 0.8260 (tptp) cc_final: 0.7913 (tppt) REVERT: G 39 TYR cc_start: 0.8363 (m-80) cc_final: 0.7992 (m-80) REVERT: G 90 ASP cc_start: 0.7374 (t0) cc_final: 0.7078 (m-30) REVERT: G 93 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8582 (mp) REVERT: K 5 TYR cc_start: 0.5436 (m-80) cc_final: 0.4997 (m-80) REVERT: K 35 TRP cc_start: 0.6922 (OUTLIER) cc_final: 0.6406 (m-90) REVERT: K 93 GLN cc_start: 0.7999 (tp40) cc_final: 0.7798 (tp-100) REVERT: K 136 MET cc_start: 0.7349 (mmm) cc_final: 0.7027 (mmm) REVERT: K 262 MET cc_start: 0.8861 (mtp) cc_final: 0.8616 (mtp) outliers start: 18 outliers final: 6 residues processed: 127 average time/residue: 0.2939 time to fit residues: 53.4959 Evaluate side-chains 103 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 65 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain K residue 35 TRP Chi-restraints excluded: chain K residue 139 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN H 64 ASN K 100 GLN K 224 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.077839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.058378 restraints weight = 65555.005| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.79 r_work: 0.3225 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 15269 Z= 0.300 Angle : 0.683 26.960 21909 Z= 0.378 Chirality : 0.057 2.011 2495 Planarity : 0.005 0.118 1751 Dihedral : 29.148 175.890 4460 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.64 % Favored : 95.17 % Rotamer: Outliers : 3.78 % Allowed : 19.15 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1035 helix: 2.04 (0.21), residues: 607 sheet: -2.63 (0.80), residues: 34 loop : -1.76 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 71 HIS 0.008 0.002 HIS K 133 PHE 0.026 0.002 PHE E 78 TYR 0.014 0.002 TYR E 54 ARG 0.004 0.001 ARG K 175 Details of bonding type rmsd hydrogen bonds : bond 0.05443 ( 841) hydrogen bonds : angle 3.43913 ( 2126) metal coordination : bond 0.01841 ( 4) metal coordination : angle 3.53082 ( 6) covalent geometry : bond 0.00670 (15264) covalent geometry : angle 0.68068 (21903) Misc. bond : bond 0.00032 ( 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 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8415 (pttt) cc_final: 0.7943 (ptpp) REVERT: C 59 THR cc_start: 0.7957 (OUTLIER) cc_final: 0.7756 (t) REVERT: C 92 GLU cc_start: 0.8585 (mp0) cc_final: 0.7818 (mp0) REVERT: D 118 TYR cc_start: 0.8709 (t80) cc_final: 0.8424 (t80) REVERT: E 125 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7959 (mp10) REVERT: F 31 LYS cc_start: 0.8617 (mtmt) cc_final: 0.8344 (mtpp) REVERT: G 36 LYS cc_start: 0.8445 (tptp) cc_final: 0.8120 (tppt) REVERT: G 91 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8040 (tm-30) REVERT: H 98 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7664 (mm) REVERT: K 5 TYR cc_start: 0.5168 (m-80) cc_final: 0.4331 (m-80) REVERT: K 136 MET cc_start: 0.7862 (mmm) cc_final: 0.7359 (mmm) REVERT: K 262 MET cc_start: 0.8948 (mtp) cc_final: 0.8697 (mtp) outliers start: 33 outliers final: 13 residues processed: 119 average time/residue: 0.2918 time to fit residues: 49.6556 Evaluate side-chains 102 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 D residue 49 THR Chi-restraints excluded: chain D residue 51 ILE 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 50 ILE 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 162 THR Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 242 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.079799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.060002 restraints weight = 65064.146| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.73 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1772 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= 0.150 Angle : 0.613 26.824 21909 Z= 0.339 Chirality : 0.053 2.025 2495 Planarity : 0.005 0.117 1751 Dihedral : 28.846 172.718 4460 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % Rotamer: Outliers : 2.06 % Allowed : 20.99 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1035 helix: 2.52 (0.21), residues: 610 sheet: -1.76 (1.04), residues: 24 loop : -1.58 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 71 HIS 0.006 0.001 HIS K 133 PHE 0.014 0.002 PHE A 67 TYR 0.011 0.001 TYR G 57 ARG 0.006 0.000 ARG K 172 Details of bonding type rmsd hydrogen bonds : bond 0.04028 ( 841) hydrogen bonds : angle 2.95005 ( 2126) metal coordination : bond 0.00672 ( 4) metal coordination : angle 2.26337 ( 6) covalent geometry : bond 0.00328 (15264) covalent geometry : angle 0.61226 (21903) Misc. bond : bond 0.00032 ( 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 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 1.939 Fit side-chains REVERT: A 120 MET cc_start: 0.8253 (OUTLIER) cc_final: 0.8022 (mtm) REVERT: A 122 LYS cc_start: 0.8215 (pttt) cc_final: 0.7941 (pttp) REVERT: B 96 THR cc_start: 0.8426 (p) cc_final: 0.8160 (t) REVERT: C 59 THR cc_start: 0.7561 (OUTLIER) cc_final: 0.6920 (m) REVERT: C 92 GLU cc_start: 0.8287 (mp0) cc_final: 0.7978 (mp0) REVERT: D 56 MET cc_start: 0.8359 (tpp) cc_final: 0.8081 (tpp) REVERT: D 118 TYR cc_start: 0.8442 (t80) cc_final: 0.8125 (t80) REVERT: E 90 MET cc_start: 0.7981 (mmm) cc_final: 0.7692 (mmm) REVERT: E 125 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7666 (mp10) REVERT: G 36 LYS cc_start: 0.8203 (tptp) cc_final: 0.7858 (tppt) REVERT: G 90 ASP cc_start: 0.7352 (t0) cc_final: 0.7148 (m-30) REVERT: G 91 GLU cc_start: 0.8196 (tm-30) cc_final: 0.7451 (tm-30) REVERT: G 93 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8516 (mp) REVERT: G 95 LYS cc_start: 0.9060 (ttmm) cc_final: 0.8550 (mtmt) REVERT: H 59 MET cc_start: 0.7948 (mmm) cc_final: 0.7328 (mmt) REVERT: H 90 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7832 (mm-30) REVERT: K 5 TYR cc_start: 0.5401 (m-80) cc_final: 0.4729 (m-80) REVERT: K 136 MET cc_start: 0.7389 (mmm) cc_final: 0.6972 (mmm) REVERT: K 206 ASN cc_start: 0.8658 (t0) cc_final: 0.8421 (t0) outliers start: 18 outliers final: 7 residues processed: 114 average time/residue: 0.2966 time to fit residues: 48.5155 Evaluate side-chains 103 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 E residue 118 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 93 LEU 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 6 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN E 125 GLN ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.078850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.058995 restraints weight = 64533.848| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.83 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 15269 Z= 0.203 Angle : 0.622 27.086 21909 Z= 0.344 Chirality : 0.054 2.005 2495 Planarity : 0.005 0.120 1751 Dihedral : 28.960 175.246 4460 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.09 % Favored : 96.71 % Rotamer: Outliers : 2.52 % Allowed : 20.53 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.27), residues: 1035 helix: 2.49 (0.21), residues: 610 sheet: -2.54 (0.78), residues: 34 loop : -1.66 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 35 HIS 0.005 0.001 HIS K 133 PHE 0.018 0.002 PHE K 49 TYR 0.011 0.001 TYR G 57 ARG 0.005 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04362 ( 841) hydrogen bonds : angle 3.06767 ( 2126) metal coordination : bond 0.01211 ( 4) metal coordination : angle 2.39741 ( 6) covalent geometry : bond 0.00453 (15264) covalent geometry : angle 0.62052 (21903) Misc. bond : bond 0.00033 ( 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: 22 poor density : 98 time to evaluate : 1.080 Fit side-chains REVERT: A 122 LYS cc_start: 0.8285 (pttt) cc_final: 0.7987 (pttp) REVERT: B 77 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8691 (mmtm) REVERT: B 96 THR cc_start: 0.8398 (p) cc_final: 0.8148 (t) REVERT: C 59 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7050 (m) REVERT: C 92 GLU cc_start: 0.8395 (mp0) cc_final: 0.7638 (mp0) REVERT: D 118 TYR cc_start: 0.8525 (t80) cc_final: 0.8258 (t80) REVERT: E 90 MET cc_start: 0.8085 (mmm) cc_final: 0.7752 (mmm) REVERT: E 125 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7792 (mp10) REVERT: F 31 LYS cc_start: 0.8529 (mtmt) cc_final: 0.8220 (mtpp) REVERT: G 36 LYS cc_start: 0.8267 (tptp) cc_final: 0.7900 (tppt) REVERT: G 91 GLU cc_start: 0.8217 (tm-30) cc_final: 0.7607 (tm-30) REVERT: H 90 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7735 (mm-30) REVERT: H 98 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7708 (mm) REVERT: K 5 TYR cc_start: 0.5551 (m-80) cc_final: 0.4947 (m-80) REVERT: K 136 MET cc_start: 0.7405 (mmm) cc_final: 0.6966 (mmm) REVERT: K 206 ASN cc_start: 0.8732 (t0) cc_final: 0.8436 (t0) REVERT: K 262 MET cc_start: 0.8914 (mtp) cc_final: 0.8530 (mtp) outliers start: 22 outliers final: 11 residues processed: 116 average time/residue: 0.2924 time to fit residues: 48.3708 Evaluate side-chains 106 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 93 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 47 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 53 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3933 r_free = 0.3933 target = 0.078762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058824 restraints weight = 64983.292| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.87 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 15269 Z= 0.210 Angle : 0.621 27.014 21909 Z= 0.345 Chirality : 0.054 2.007 2495 Planarity : 0.005 0.122 1751 Dihedral : 29.014 174.914 4460 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.00 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 20.41 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.26), residues: 1035 helix: 2.41 (0.21), residues: 611 sheet: -2.53 (0.78), residues: 34 loop : -1.68 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 71 HIS 0.005 0.001 HIS A 113 PHE 0.014 0.002 PHE A 67 TYR 0.015 0.001 TYR E 54 ARG 0.006 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 841) hydrogen bonds : angle 3.07650 ( 2126) metal coordination : bond 0.01263 ( 4) metal coordination : angle 2.46928 ( 6) covalent geometry : bond 0.00474 (15264) covalent geometry : angle 0.62010 (21903) Misc. bond : bond 0.00033 ( 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: 25 poor density : 95 time to evaluate : 1.097 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8286 (pttt) cc_final: 0.7658 (ptpp) REVERT: B 77 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8697 (mmtm) REVERT: B 96 THR cc_start: 0.8391 (p) cc_final: 0.8144 (t) REVERT: C 59 THR cc_start: 0.7732 (OUTLIER) cc_final: 0.7044 (m) REVERT: C 92 GLU cc_start: 0.8405 (mp0) cc_final: 0.7655 (mp0) REVERT: D 56 MET cc_start: 0.8337 (tpp) cc_final: 0.8038 (tpp) REVERT: D 118 TYR cc_start: 0.8522 (t80) cc_final: 0.8267 (t80) REVERT: E 90 MET cc_start: 0.8074 (mmm) cc_final: 0.7709 (mmm) REVERT: E 125 GLN cc_start: 0.8368 (OUTLIER) cc_final: 0.7795 (mp10) REVERT: F 31 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8236 (mtpp) REVERT: G 36 LYS cc_start: 0.8262 (tptp) cc_final: 0.7901 (tppt) REVERT: G 91 GLU cc_start: 0.8166 (tm-30) cc_final: 0.7749 (tm-30) REVERT: H 90 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7675 (mm-30) REVERT: H 98 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7687 (mm) REVERT: K 5 TYR cc_start: 0.5574 (m-80) cc_final: 0.4970 (m-80) REVERT: K 136 MET cc_start: 0.7426 (mmm) cc_final: 0.7008 (mmm) REVERT: K 206 ASN cc_start: 0.8746 (t0) cc_final: 0.8439 (t0) REVERT: K 262 MET cc_start: 0.8945 (mtp) cc_final: 0.8603 (mtp) outliers start: 25 outliers final: 16 residues processed: 114 average time/residue: 0.2965 time to fit residues: 47.9755 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.932 ------------------------------------------------------------------------------- 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 57 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 G residue 90 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 177 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 67 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 117 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.077941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.058142 restraints weight = 64973.435| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.84 r_work: 0.3226 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.113 15269 Z= 0.278 Angle : 0.662 27.114 21909 Z= 0.367 Chirality : 0.056 2.001 2495 Planarity : 0.005 0.125 1751 Dihedral : 29.207 174.631 4460 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 3.44 % Allowed : 20.41 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.26), residues: 1035 helix: 2.19 (0.21), residues: 611 sheet: -2.55 (0.80), residues: 34 loop : -1.75 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.018 0.002 PHE K 49 TYR 0.011 0.002 TYR E 54 ARG 0.007 0.001 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04994 ( 841) hydrogen bonds : angle 3.28320 ( 2126) metal coordination : bond 0.01720 ( 4) metal coordination : angle 3.22824 ( 6) covalent geometry : bond 0.00624 (15264) covalent geometry : angle 0.66010 (21903) Misc. bond : bond 0.00037 ( 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 1.290 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8399 (pttt) cc_final: 0.7781 (ptpp) REVERT: B 77 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8829 (mmtm) REVERT: C 59 THR cc_start: 0.7917 (OUTLIER) cc_final: 0.7691 (t) REVERT: C 92 GLU cc_start: 0.8596 (mp0) cc_final: 0.7902 (mp0) REVERT: D 118 TYR cc_start: 0.8713 (t80) cc_final: 0.8479 (t80) REVERT: E 90 MET cc_start: 0.8415 (mmm) cc_final: 0.8205 (mmm) REVERT: E 125 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: F 31 LYS cc_start: 0.8526 (mtmt) cc_final: 0.8232 (mtpp) REVERT: G 36 LYS cc_start: 0.8485 (tptp) cc_final: 0.8135 (tppt) REVERT: G 91 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8029 (tm-30) REVERT: H 90 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8096 (mm-30) REVERT: H 98 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7647 (mm) REVERT: K 5 TYR cc_start: 0.5209 (m-80) cc_final: 0.4542 (m-80) REVERT: K 136 MET cc_start: 0.7889 (mmm) cc_final: 0.7406 (mmm) REVERT: K 206 ASN cc_start: 0.8817 (t0) cc_final: 0.8497 (t0) REVERT: K 262 MET cc_start: 0.8977 (mtp) cc_final: 0.8702 (mtp) outliers start: 30 outliers final: 21 residues processed: 115 average time/residue: 0.4626 time to fit residues: 78.3310 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 89 time to evaluate : 2.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 50 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 57 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 50 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU 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 47 VAL Chi-restraints excluded: chain K residue 177 CYS 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 92 optimal weight: 3.9990 chunk 102 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3921 r_free = 0.3921 target = 0.078248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.058030 restraints weight = 64634.237| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 2.81 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 15269 Z= 0.236 Angle : 0.639 27.022 21909 Z= 0.355 Chirality : 0.055 2.004 2495 Planarity : 0.005 0.126 1751 Dihedral : 29.186 174.340 4460 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.77 % Favored : 96.04 % Rotamer: Outliers : 3.10 % Allowed : 20.41 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1035 helix: 2.23 (0.21), residues: 612 sheet: -2.62 (0.78), residues: 34 loop : -1.71 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.019 0.002 PHE K 64 TYR 0.017 0.002 TYR E 54 ARG 0.007 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 841) hydrogen bonds : angle 3.22265 ( 2126) metal coordination : bond 0.01434 ( 4) metal coordination : angle 3.00904 ( 6) covalent geometry : bond 0.00529 (15264) covalent geometry : angle 0.63667 (21903) Misc. bond : bond 0.00036 ( 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 117 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 90 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8267 (pttt) cc_final: 0.7635 (ptpp) REVERT: B 77 LYS cc_start: 0.8925 (mmmt) cc_final: 0.8716 (mmtm) REVERT: C 59 THR cc_start: 0.7724 (OUTLIER) cc_final: 0.7494 (t) REVERT: C 92 GLU cc_start: 0.8367 (mp0) cc_final: 0.7636 (mp0) REVERT: D 56 MET cc_start: 0.8447 (tpp) cc_final: 0.8178 (tpp) REVERT: D 118 TYR cc_start: 0.8527 (t80) cc_final: 0.8254 (t80) REVERT: E 90 MET cc_start: 0.8069 (mmm) cc_final: 0.7827 (mmm) REVERT: E 125 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.7628 (mp10) REVERT: F 31 LYS cc_start: 0.8562 (mtmt) cc_final: 0.8252 (mtpp) REVERT: G 36 LYS cc_start: 0.8351 (tptp) cc_final: 0.7992 (tppt) REVERT: G 91 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7722 (tm-30) REVERT: G 95 LYS cc_start: 0.9056 (ttmm) cc_final: 0.8826 (mttp) REVERT: H 90 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7687 (mm-30) REVERT: H 98 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7691 (mm) REVERT: K 5 TYR cc_start: 0.5508 (m-80) cc_final: 0.4744 (m-80) REVERT: K 136 MET cc_start: 0.7419 (mmm) cc_final: 0.6991 (mmm) REVERT: K 206 ASN cc_start: 0.8661 (t0) cc_final: 0.8381 (t0) outliers start: 27 outliers final: 20 residues processed: 113 average time/residue: 0.3187 time to fit residues: 52.0542 Evaluate side-chains 110 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 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 57 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 50 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 23 ILE Chi-restraints excluded: chain K residue 177 CYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3929 r_free = 0.3929 target = 0.078541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.058549 restraints weight = 64222.978| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.82 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15269 Z= 0.204 Angle : 0.634 27.011 21909 Z= 0.352 Chirality : 0.054 2.003 2495 Planarity : 0.005 0.126 1751 Dihedral : 29.149 174.143 4460 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 3.33 % Allowed : 21.79 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.26), residues: 1035 helix: 2.32 (0.21), residues: 612 sheet: -2.49 (0.81), residues: 34 loop : -1.65 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.040 0.002 PHE K 64 TYR 0.014 0.001 TYR B 98 ARG 0.007 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 841) hydrogen bonds : angle 3.15736 ( 2126) metal coordination : bond 0.01239 ( 4) metal coordination : angle 2.75548 ( 6) covalent geometry : bond 0.00457 (15264) covalent geometry : angle 0.63210 (21903) Misc. bond : bond 0.00030 ( 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 119 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8290 (pttt) cc_final: 0.7659 (ptpp) REVERT: B 96 THR cc_start: 0.8388 (p) cc_final: 0.8141 (t) REVERT: C 59 THR cc_start: 0.7708 (OUTLIER) cc_final: 0.7012 (m) REVERT: C 92 GLU cc_start: 0.8353 (mp0) cc_final: 0.7654 (mp0) REVERT: D 56 MET cc_start: 0.8382 (tpp) cc_final: 0.8111 (tpp) REVERT: D 118 TYR cc_start: 0.8517 (t80) cc_final: 0.8253 (t80) REVERT: E 90 MET cc_start: 0.8053 (mmm) cc_final: 0.7812 (mmm) REVERT: E 125 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: F 31 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8251 (mtpp) REVERT: G 36 LYS cc_start: 0.8307 (tptp) cc_final: 0.7930 (tptp) REVERT: G 91 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7729 (tm-30) REVERT: G 95 LYS cc_start: 0.9040 (ttmm) cc_final: 0.8783 (mttp) REVERT: H 90 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7673 (mm-30) REVERT: H 98 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7699 (mm) REVERT: K 5 TYR cc_start: 0.5428 (m-80) cc_final: 0.4769 (m-80) REVERT: K 136 MET cc_start: 0.7375 (mmm) cc_final: 0.6984 (mmm) REVERT: K 206 ASN cc_start: 0.8735 (t0) cc_final: 0.8456 (t0) REVERT: K 213 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6374 (mt) REVERT: K 262 MET cc_start: 0.8770 (mtp) cc_final: 0.8446 (mtp) outliers start: 29 outliers final: 20 residues processed: 114 average time/residue: 0.3118 time to fit residues: 51.2079 Evaluate side-chains 112 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 57 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 G residue 93 LEU 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 23 ILE Chi-restraints excluded: chain K residue 47 VAL Chi-restraints excluded: chain K residue 64 PHE Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 213 LEU Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 242 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.0270 chunk 119 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 106 optimal weight: 0.0470 chunk 65 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.0000 chunk 43 optimal weight: 4.9990 overall best weight: 0.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 38 ASN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.080044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.060663 restraints weight = 64603.479| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.79 r_work: 0.3322 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2407 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= 0.141 Angle : 0.610 26.848 21909 Z= 0.337 Chirality : 0.053 2.006 2495 Planarity : 0.005 0.125 1751 Dihedral : 28.842 173.358 4460 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.22 % Favored : 97.58 % Rotamer: Outliers : 2.41 % Allowed : 22.71 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.27), residues: 1035 helix: 2.60 (0.21), residues: 614 sheet: -2.11 (0.85), residues: 34 loop : -1.53 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 71 HIS 0.005 0.001 HIS A 113 PHE 0.025 0.002 PHE K 64 TYR 0.015 0.001 TYR E 54 ARG 0.009 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 841) hydrogen bonds : angle 2.92175 ( 2126) metal coordination : bond 0.00554 ( 4) metal coordination : angle 2.24279 ( 6) covalent geometry : bond 0.00309 (15264) covalent geometry : angle 0.60897 (21903) Misc. bond : bond 0.00035 ( 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 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 93 time to evaluate : 1.511 Fit side-chains REVERT: A 122 LYS cc_start: 0.8289 (pttt) cc_final: 0.8020 (pttp) REVERT: A 123 ASP cc_start: 0.8041 (m-30) cc_final: 0.7572 (m-30) REVERT: B 96 THR cc_start: 0.8487 (p) cc_final: 0.8232 (t) REVERT: C 59 THR cc_start: 0.7790 (OUTLIER) cc_final: 0.7207 (m) REVERT: C 92 GLU cc_start: 0.8477 (mp0) cc_final: 0.7867 (mp0) REVERT: D 39 TYR cc_start: 0.7819 (t80) cc_final: 0.7419 (t80) REVERT: D 118 TYR cc_start: 0.8631 (t80) cc_final: 0.8373 (t80) REVERT: E 90 MET cc_start: 0.8405 (mmm) cc_final: 0.8049 (mmm) REVERT: E 125 GLN cc_start: 0.8465 (mp10) cc_final: 0.7908 (mp10) REVERT: G 36 LYS cc_start: 0.8426 (tptp) cc_final: 0.8055 (tptp) REVERT: G 91 GLU cc_start: 0.8359 (tm-30) cc_final: 0.7740 (tm-30) REVERT: G 95 LYS cc_start: 0.9120 (ttmm) cc_final: 0.8695 (mttp) REVERT: H 76 ARG cc_start: 0.7820 (mtm-85) cc_final: 0.7542 (ttp-110) REVERT: H 90 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8136 (mm-30) REVERT: K 5 TYR cc_start: 0.4808 (m-80) cc_final: 0.4243 (m-80) REVERT: K 136 MET cc_start: 0.7822 (mmm) cc_final: 0.7427 (mmm) REVERT: K 262 MET cc_start: 0.8757 (mtp) cc_final: 0.8450 (mtp) outliers start: 21 outliers final: 13 residues processed: 112 average time/residue: 0.3196 time to fit residues: 51.4519 Evaluate side-chains 101 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.486 ------------------------------------------------------------------------------- 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 75 SER Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 212 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 106 optimal weight: 0.7980 chunk 1 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 122 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** K 242 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 = 0.3935 r_free = 0.3935 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.058657 restraints weight = 64871.152| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.80 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 15269 Z= 0.215 Angle : 0.640 26.957 21909 Z= 0.353 Chirality : 0.054 1.988 2495 Planarity : 0.005 0.128 1751 Dihedral : 29.036 174.301 4460 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.57 % Favored : 96.23 % Rotamer: Outliers : 2.41 % Allowed : 22.36 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1035 helix: 2.50 (0.21), residues: 611 sheet: -1.99 (0.89), residues: 34 loop : -1.57 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 188 HIS 0.006 0.001 HIS A 113 PHE 0.074 0.002 PHE K 64 TYR 0.011 0.001 TYR B 98 ARG 0.008 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 841) hydrogen bonds : angle 3.10872 ( 2126) metal coordination : bond 0.01287 ( 4) metal coordination : angle 2.64279 ( 6) covalent geometry : bond 0.00483 (15264) covalent geometry : angle 0.63820 (21903) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8100.32 seconds wall clock time: 143 minutes 22.29 seconds (8602.29 seconds total)