Starting phenix.real_space_refine on Mon Dec 30 22:38:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f86_28915/12_2024/8f86_28915.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f86_28915/12_2024/8f86_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_28915/12_2024/8f86_28915.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f86_28915/12_2024/8f86_28915.map" model { file = "/net/cci-nas-00/data/ceres_data/8f86_28915/12_2024/8f86_28915.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f86_28915/12_2024/8f86_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-5532/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: 9.21, per 1000 atoms: 0.64 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: 3.70 Conformation dependent library (CDL) restraints added in 1.5 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: 6.59 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: 6.32 Time building geometry restraints manager: 4.26 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.150 Process input model: 42.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.680 ------------------------------------------------------------------------------- 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 15264 Z= 0.249 Angle : 0.664 27.343 21903 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 *********************** 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 : 1.233 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: 0.3608 time to fit residues: 56.8611 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 : 1.197 ------------------------------------------------------------------------------- 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: 3.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 117 optimal weight: 3.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 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 15264 Z= 0.221 Angle : 0.640 26.977 21903 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 *********************** 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 : 1.280 Fit side-chains revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 84 MET cc_start: 0.7920 (mmm) cc_final: 0.7709 (mmm) REVERT: C 59 THR cc_start: 0.7654 (OUTLIER) cc_final: 0.7090 (m) REVERT: C 92 GLU cc_start: 0.8533 (mp0) cc_final: 0.7692 (mp0) REVERT: D 56 MET cc_start: 0.8577 (tpp) cc_final: 0.8346 (tpp) REVERT: D 118 TYR cc_start: 0.8637 (t80) cc_final: 0.8273 (t80) REVERT: F 77 LYS cc_start: 0.8755 (mttp) cc_final: 0.8447 (mmmt) REVERT: G 36 LYS cc_start: 0.8473 (tptp) cc_final: 0.8060 (tppt) REVERT: G 39 TYR cc_start: 0.8407 (m-80) cc_final: 0.8033 (m-80) REVERT: G 90 ASP cc_start: 0.7352 (t0) cc_final: 0.7051 (m-30) REVERT: G 93 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8432 (mp) REVERT: H 110 GLU cc_start: 0.7809 (tt0) cc_final: 0.7586 (mm-30) REVERT: K 5 TYR cc_start: 0.5146 (m-80) cc_final: 0.4723 (m-80) REVERT: K 35 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6433 (m-90) REVERT: K 93 GLN cc_start: 0.8120 (tp40) cc_final: 0.7877 (tp-100) REVERT: K 136 MET cc_start: 0.7744 (mmm) cc_final: 0.7372 (mmm) REVERT: K 262 MET cc_start: 0.8983 (mtp) cc_final: 0.8701 (mtp) outliers start: 18 outliers final: 6 residues processed: 127 average time/residue: 0.3092 time to fit residues: 56.2311 Evaluate side-chains 105 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 1.177 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 126 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 64 ASN K 100 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 15264 Z= 0.250 Angle : 0.623 26.998 21903 Z= 0.347 Chirality : 0.055 2.023 2495 Planarity : 0.005 0.116 1751 Dihedral : 28.859 175.966 4460 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.48 % Favored : 96.33 % Rotamer: Outliers : 3.33 % Allowed : 18.46 % Favored : 78.21 % 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: 1.29 (0.27), residues: 1035 helix: 2.40 (0.21), residues: 613 sheet: -1.82 (1.06), residues: 24 loop : -1.57 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 71 HIS 0.007 0.001 HIS K 133 PHE 0.020 0.002 PHE E 78 TYR 0.012 0.001 TYR C 57 ARG 0.003 0.000 ARG K 175 *********************** 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 92 time to evaluate : 1.433 Fit side-chains REVERT: A 122 LYS cc_start: 0.8188 (pttt) cc_final: 0.7537 (ptpp) REVERT: B 63 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 84 MET cc_start: 0.8015 (mmm) cc_final: 0.7775 (mmm) REVERT: C 59 THR cc_start: 0.7718 (OUTLIER) cc_final: 0.7120 (m) REVERT: C 92 GLU cc_start: 0.8562 (mp0) cc_final: 0.7744 (mp0) REVERT: D 118 TYR cc_start: 0.8669 (t80) cc_final: 0.8340 (t80) REVERT: E 125 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: F 77 LYS cc_start: 0.8774 (mttp) cc_final: 0.8477 (mmmt) REVERT: G 36 LYS cc_start: 0.8405 (tptp) cc_final: 0.8016 (tppt) REVERT: G 39 TYR cc_start: 0.8387 (m-80) cc_final: 0.8010 (m-80) REVERT: G 90 ASP cc_start: 0.7364 (t0) cc_final: 0.7115 (m-30) REVERT: G 91 GLU cc_start: 0.8270 (tm-30) cc_final: 0.7735 (tm-30) REVERT: G 93 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8403 (mp) REVERT: H 98 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7309 (mm) REVERT: K 5 TYR cc_start: 0.5239 (m-80) cc_final: 0.4498 (m-80) REVERT: K 93 GLN cc_start: 0.8104 (tp40) cc_final: 0.7901 (tp-100) REVERT: K 136 MET cc_start: 0.7791 (mmm) cc_final: 0.7264 (mmm) REVERT: K 262 MET cc_start: 0.8993 (mtp) cc_final: 0.8784 (mtp) outliers start: 29 outliers final: 9 residues processed: 117 average time/residue: 0.3267 time to fit residues: 54.5487 Evaluate side-chains 103 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 1.228 ------------------------------------------------------------------------------- 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 75 SER 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 48 ASP Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 VAL 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 115 optimal weight: 2.9990 chunk 88 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN K 224 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 15264 Z= 0.359 Angle : 0.667 26.799 21903 Z= 0.371 Chirality : 0.057 2.020 2495 Planarity : 0.005 0.120 1751 Dihedral : 29.157 175.349 4460 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.15 % Favored : 95.65 % Rotamer: Outliers : 3.44 % Allowed : 19.50 % 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: 0.85 (0.26), residues: 1035 helix: 2.10 (0.21), residues: 611 sheet: -2.68 (0.78), residues: 34 loop : -1.76 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 71 HIS 0.007 0.001 HIS K 133 PHE 0.023 0.002 PHE E 78 TYR 0.017 0.002 TYR E 54 ARG 0.012 0.001 ARG K 172 *********************** 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 127 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 97 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8208 (pttt) cc_final: 0.7571 (ptpp) REVERT: C 59 THR cc_start: 0.7756 (OUTLIER) cc_final: 0.7524 (t) REVERT: C 92 GLU cc_start: 0.8597 (mp0) cc_final: 0.7778 (mp0) REVERT: D 118 TYR cc_start: 0.8693 (t80) cc_final: 0.8350 (t80) REVERT: E 90 MET cc_start: 0.8289 (mmm) cc_final: 0.8006 (mmm) REVERT: E 125 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: F 31 LYS cc_start: 0.8630 (mtmt) cc_final: 0.8321 (mtpp) REVERT: G 36 LYS cc_start: 0.8444 (tptp) cc_final: 0.8070 (tppt) REVERT: G 41 GLU cc_start: 0.7492 (mp0) cc_final: 0.7051 (mp0) REVERT: G 91 GLU cc_start: 0.8267 (tm-30) cc_final: 0.7786 (tm-30) REVERT: H 98 LEU cc_start: 0.7494 (OUTLIER) cc_final: 0.7250 (mm) REVERT: K 5 TYR cc_start: 0.5245 (m-80) cc_final: 0.4564 (m-80) REVERT: K 93 GLN cc_start: 0.8087 (tp40) cc_final: 0.7825 (tp-100) REVERT: K 136 MET cc_start: 0.7820 (mmm) cc_final: 0.7239 (mmm) REVERT: K 213 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6410 (mt) outliers start: 30 outliers final: 16 residues processed: 122 average time/residue: 0.3094 time to fit residues: 53.1920 Evaluate side-chains 112 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 D residue 87 THR 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 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 213 LEU Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 1 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 106 optimal weight: 0.0010 chunk 86 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 overall best weight: 1.9590 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 15264 Z= 0.253 Angle : 0.626 26.880 21903 Z= 0.347 Chirality : 0.054 2.021 2495 Planarity : 0.005 0.120 1751 Dihedral : 29.092 175.032 4460 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.38 % Favored : 96.43 % Rotamer: Outliers : 2.98 % Allowed : 20.53 % 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: 1.04 (0.27), residues: 1035 helix: 2.32 (0.21), residues: 611 sheet: -3.01 (0.68), residues: 41 loop : -1.72 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.015 0.002 PHE E 78 TYR 0.013 0.001 TYR G 39 ARG 0.004 0.000 ARG K 172 *********************** 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 121 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8199 (pttt) cc_final: 0.7570 (ptpp) REVERT: B 77 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8697 (mmtm) REVERT: B 96 THR cc_start: 0.8539 (p) cc_final: 0.8264 (t) REVERT: C 59 THR cc_start: 0.7706 (OUTLIER) cc_final: 0.7109 (m) REVERT: C 92 GLU cc_start: 0.8551 (mp0) cc_final: 0.7715 (mp0) REVERT: D 56 MET cc_start: 0.8581 (tpp) cc_final: 0.8284 (tpp) REVERT: D 118 TYR cc_start: 0.8665 (t80) cc_final: 0.8345 (t80) REVERT: E 90 MET cc_start: 0.8295 (mmm) cc_final: 0.7940 (mmm) REVERT: E 125 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: F 31 LYS cc_start: 0.8600 (mtmt) cc_final: 0.8293 (mtpp) REVERT: G 36 LYS cc_start: 0.8400 (tptp) cc_final: 0.8016 (tppt) REVERT: G 90 ASP cc_start: 0.7392 (t0) cc_final: 0.7187 (m-30) REVERT: G 91 GLU cc_start: 0.8276 (tm-30) cc_final: 0.7546 (tm-30) REVERT: G 95 LYS cc_start: 0.9129 (ttmm) cc_final: 0.8615 (mtmt) REVERT: H 98 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.7272 (mm) REVERT: K 5 TYR cc_start: 0.5261 (m-80) cc_final: 0.4590 (m-80) REVERT: K 93 GLN cc_start: 0.8117 (tp40) cc_final: 0.7744 (tp-100) REVERT: K 136 MET cc_start: 0.7817 (mmm) cc_final: 0.7281 (mmm) REVERT: K 206 ASN cc_start: 0.8777 (t0) cc_final: 0.8467 (t0) REVERT: K 262 MET cc_start: 0.9000 (mtp) cc_final: 0.8637 (mtp) outliers start: 26 outliers final: 14 residues processed: 115 average time/residue: 0.3075 time to fit residues: 50.4151 Evaluate side-chains 106 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 1.141 ------------------------------------------------------------------------------- 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 93 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 98 LEU 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 41 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 overall best weight: 1.6166 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 15264 Z= 0.228 Angle : 0.616 26.997 21903 Z= 0.342 Chirality : 0.054 2.010 2495 Planarity : 0.005 0.121 1751 Dihedral : 29.040 174.875 4460 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 2.87 % Allowed : 20.76 % Favored : 76.38 % 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: 1.18 (0.27), residues: 1035 helix: 2.45 (0.21), residues: 611 sheet: -2.86 (0.70), residues: 41 loop : -1.69 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.019 0.002 PHE K 49 TYR 0.014 0.001 TYR E 54 ARG 0.003 0.000 ARG F 92 *********************** 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 123 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8205 (pttt) cc_final: 0.7935 (pttp) REVERT: B 77 LYS cc_start: 0.9014 (mmmt) cc_final: 0.8727 (mmtm) REVERT: B 96 THR cc_start: 0.8533 (p) cc_final: 0.8266 (t) REVERT: C 59 THR cc_start: 0.7693 (OUTLIER) cc_final: 0.7102 (m) REVERT: C 92 GLU cc_start: 0.8545 (mp0) cc_final: 0.8194 (mp0) REVERT: D 56 MET cc_start: 0.8550 (tpp) cc_final: 0.8197 (tpp) REVERT: D 118 TYR cc_start: 0.8649 (t80) cc_final: 0.8353 (t80) REVERT: E 90 MET cc_start: 0.8286 (mmm) cc_final: 0.7925 (mmm) REVERT: E 125 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: F 31 LYS cc_start: 0.8594 (mtmt) cc_final: 0.8300 (mtpp) REVERT: G 36 LYS cc_start: 0.8463 (tptp) cc_final: 0.8041 (tppt) REVERT: G 90 ASP cc_start: 0.7430 (t0) cc_final: 0.7213 (m-30) REVERT: G 91 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7501 (tm-30) REVERT: G 95 LYS cc_start: 0.9146 (ttmm) cc_final: 0.8669 (mtmt) REVERT: H 90 GLU cc_start: 0.8224 (mm-30) cc_final: 0.8023 (mm-30) REVERT: K 5 TYR cc_start: 0.5278 (m-80) cc_final: 0.4631 (m-80) REVERT: K 136 MET cc_start: 0.7819 (mmm) cc_final: 0.7313 (mmm) REVERT: K 206 ASN cc_start: 0.8799 (t0) cc_final: 0.8500 (t0) REVERT: K 262 MET cc_start: 0.8999 (mtp) cc_final: 0.8784 (mtp) outliers start: 25 outliers final: 16 residues processed: 118 average time/residue: 0.2953 time to fit residues: 49.7150 Evaluate side-chains 111 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 124 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 15264 Z= 0.294 Angle : 0.638 27.038 21903 Z= 0.354 Chirality : 0.055 2.005 2495 Planarity : 0.005 0.124 1751 Dihedral : 29.142 174.545 4460 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.86 % Favored : 95.94 % 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: 1.03 (0.26), residues: 1035 helix: 2.29 (0.21), residues: 611 sheet: -2.83 (0.71), residues: 41 loop : -1.69 (0.29), residues: 383 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 0.015 0.002 PHE A 67 TYR 0.013 0.001 TYR F 88 ARG 0.004 0.000 ARG F 92 *********************** 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: 30 poor density : 93 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8227 (pttt) cc_final: 0.7796 (pttp) REVERT: B 77 LYS cc_start: 0.9011 (mmmt) cc_final: 0.8742 (mmtm) REVERT: B 96 THR cc_start: 0.8497 (p) cc_final: 0.8219 (t) REVERT: C 59 THR cc_start: 0.7759 (OUTLIER) cc_final: 0.7459 (t) REVERT: C 92 GLU cc_start: 0.8561 (mp0) cc_final: 0.8241 (mp0) REVERT: D 118 TYR cc_start: 0.8662 (t80) cc_final: 0.8359 (t80) REVERT: E 90 MET cc_start: 0.8287 (mmm) cc_final: 0.8056 (mmm) REVERT: E 125 GLN cc_start: 0.8261 (OUTLIER) cc_final: 0.7814 (mp10) REVERT: F 31 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8327 (mtpp) REVERT: G 36 LYS cc_start: 0.8481 (tptp) cc_final: 0.8079 (tppt) REVERT: G 90 ASP cc_start: 0.7436 (t0) cc_final: 0.7226 (m-30) REVERT: G 91 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7484 (tm-30) REVERT: G 95 LYS cc_start: 0.9158 (ttmm) cc_final: 0.8673 (mtmt) REVERT: H 98 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7284 (mm) REVERT: K 5 TYR cc_start: 0.5248 (m-80) cc_final: 0.4528 (m-80) REVERT: K 93 GLN cc_start: 0.7839 (tp-100) cc_final: 0.7589 (tp-100) REVERT: K 136 MET cc_start: 0.7830 (mmm) cc_final: 0.7308 (mmm) REVERT: K 206 ASN cc_start: 0.8805 (t0) cc_final: 0.8481 (t0) REVERT: K 262 MET cc_start: 0.8988 (mtp) cc_final: 0.8747 (mtp) outliers start: 30 outliers final: 21 residues processed: 117 average time/residue: 0.3190 time to fit residues: 53.0136 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 : 1.239 ------------------------------------------------------------------------------- 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 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 50 ILE Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU 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 177 CYS Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15264 Z= 0.272 Angle : 0.634 27.015 21903 Z= 0.352 Chirality : 0.054 2.004 2495 Planarity : 0.005 0.124 1751 Dihedral : 29.116 174.363 4460 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.67 % Favored : 96.14 % Rotamer: Outliers : 3.33 % Allowed : 21.56 % Favored : 75.11 % 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: 1.10 (0.26), residues: 1035 helix: 2.32 (0.21), residues: 612 sheet: -2.73 (0.74), residues: 41 loop : -1.63 (0.30), residues: 382 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 0.015 0.002 PHE A 67 TYR 0.017 0.001 TYR E 54 ARG 0.004 0.000 ARG F 92 *********************** 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 : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8212 (pttt) cc_final: 0.7915 (pttp) REVERT: B 77 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8743 (mmtm) REVERT: B 96 THR cc_start: 0.8553 (p) cc_final: 0.8279 (t) REVERT: C 59 THR cc_start: 0.7763 (OUTLIER) cc_final: 0.7182 (m) REVERT: C 92 GLU cc_start: 0.8545 (mp0) cc_final: 0.8208 (mp0) REVERT: D 56 MET cc_start: 0.8622 (tpp) cc_final: 0.8371 (tpp) REVERT: D 118 TYR cc_start: 0.8663 (t80) cc_final: 0.8367 (t80) REVERT: E 90 MET cc_start: 0.8281 (mmm) cc_final: 0.8027 (mmm) REVERT: E 125 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7721 (mp10) REVERT: F 31 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8311 (mtpp) REVERT: G 36 LYS cc_start: 0.8488 (tptp) cc_final: 0.8086 (tptp) REVERT: G 91 GLU cc_start: 0.8257 (tm-30) cc_final: 0.7477 (tm-30) REVERT: G 95 LYS cc_start: 0.9154 (ttmm) cc_final: 0.8671 (mtmt) REVERT: H 90 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8004 (mm-30) REVERT: H 98 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7277 (mm) REVERT: K 5 TYR cc_start: 0.5218 (m-80) cc_final: 0.4379 (m-80) REVERT: K 136 MET cc_start: 0.7809 (mmm) cc_final: 0.7303 (mmm) REVERT: K 206 ASN cc_start: 0.8802 (t0) cc_final: 0.8499 (t0) REVERT: K 262 MET cc_start: 0.8984 (mtp) cc_final: 0.8760 (mtp) outliers start: 29 outliers final: 22 residues processed: 114 average time/residue: 0.3049 time to fit residues: 49.3484 Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 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 G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU 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 177 CYS Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 215 THR Chi-restraints excluded: chain K residue 273 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 69 optimal weight: 8.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 15264 Z= 0.222 Angle : 0.619 26.968 21903 Z= 0.343 Chirality : 0.053 2.006 2495 Planarity : 0.005 0.124 1751 Dihedral : 29.028 174.409 4460 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.29 % Favored : 96.52 % Rotamer: Outliers : 3.56 % Allowed : 21.10 % Favored : 75.34 % 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: 1.29 (0.27), residues: 1035 helix: 2.48 (0.21), residues: 611 sheet: -2.51 (0.77), residues: 41 loop : -1.58 (0.29), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.014 0.002 PHE A 67 TYR 0.014 0.001 TYR B 98 ARG 0.004 0.000 ARG K 65 *********************** 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 120 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8189 (pttt) cc_final: 0.7918 (pttp) REVERT: B 77 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8749 (mmtm) REVERT: B 96 THR cc_start: 0.8538 (p) cc_final: 0.8277 (t) REVERT: C 59 THR cc_start: 0.7702 (OUTLIER) cc_final: 0.7358 (m) REVERT: C 92 GLU cc_start: 0.8550 (mp0) cc_final: 0.8221 (mp0) REVERT: D 56 MET cc_start: 0.8566 (tpp) cc_final: 0.8300 (tpp) REVERT: D 118 TYR cc_start: 0.8655 (t80) cc_final: 0.8361 (t80) REVERT: E 90 MET cc_start: 0.8285 (mmm) cc_final: 0.8020 (mmm) REVERT: E 125 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7617 (mp10) REVERT: G 36 LYS cc_start: 0.8479 (tptp) cc_final: 0.8080 (tptp) REVERT: G 91 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7616 (tm-30) REVERT: H 98 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7271 (mm) REVERT: K 5 TYR cc_start: 0.5102 (m-80) cc_final: 0.4421 (m-80) REVERT: K 136 MET cc_start: 0.7796 (mmm) cc_final: 0.7318 (mmm) REVERT: K 182 ARG cc_start: 0.8218 (OUTLIER) cc_final: 0.7738 (mtt90) REVERT: K 206 ASN cc_start: 0.8813 (t0) cc_final: 0.8542 (t0) REVERT: K 262 MET cc_start: 0.8960 (mtp) cc_final: 0.8759 (mtp) REVERT: K 273 ILE cc_start: 0.6666 (OUTLIER) cc_final: 0.6371 (mt) outliers start: 31 outliers final: 21 residues processed: 113 average time/residue: 0.2946 time to fit residues: 47.4192 Evaluate side-chains 114 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 88 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 46 VAL 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 F residue 29 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 23 ILE Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 128 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 102 optimal weight: 0.0170 chunk 10 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.6024 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 15264 Z= 0.297 Angle : 0.647 27.054 21903 Z= 0.360 Chirality : 0.055 1.996 2495 Planarity : 0.005 0.127 1751 Dihedral : 29.126 174.248 4460 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.25 % Favored : 95.56 % Rotamer: Outliers : 3.10 % Allowed : 21.79 % Favored : 75.11 % 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: 1.12 (0.26), residues: 1035 helix: 2.31 (0.21), residues: 612 sheet: -2.61 (0.77), residues: 41 loop : -1.59 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.016 0.002 PHE K 64 TYR 0.016 0.002 TYR E 54 ARG 0.004 0.000 ARG F 92 ********************** 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: 27 poor density : 88 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.8223 (pttt) cc_final: 0.7937 (pttp) REVERT: B 77 LYS cc_start: 0.8990 (mmmt) cc_final: 0.8733 (mmtm) REVERT: B 96 THR cc_start: 0.8519 (p) cc_final: 0.8257 (t) REVERT: C 59 THR cc_start: 0.7745 (OUTLIER) cc_final: 0.7445 (t) REVERT: C 92 GLU cc_start: 0.8579 (mp0) cc_final: 0.8286 (mp0) REVERT: D 56 MET cc_start: 0.8562 (tpp) cc_final: 0.8253 (tpp) REVERT: D 118 TYR cc_start: 0.8662 (t80) cc_final: 0.8373 (t80) REVERT: E 90 MET cc_start: 0.8294 (mmm) cc_final: 0.8033 (mmm) REVERT: E 125 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7800 (mp10) REVERT: F 92 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8208 (ttp80) REVERT: G 36 LYS cc_start: 0.8486 (tptp) cc_final: 0.8091 (tptp) REVERT: G 91 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7522 (tm-30) REVERT: G 95 LYS cc_start: 0.9077 (ttmm) cc_final: 0.8574 (mttp) REVERT: H 98 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7257 (mm) REVERT: K 5 TYR cc_start: 0.5152 (m-80) cc_final: 0.4496 (m-80) REVERT: K 136 MET cc_start: 0.7817 (mmm) cc_final: 0.7339 (mmm) REVERT: K 182 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7762 (mtt90) REVERT: K 206 ASN cc_start: 0.8825 (t0) cc_final: 0.8546 (t0) REVERT: K 262 MET cc_start: 0.8968 (mtp) cc_final: 0.8757 (mtp) REVERT: K 273 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6407 (mt) outliers start: 27 outliers final: 20 residues processed: 110 average time/residue: 0.3186 time to fit residues: 49.6757 Evaluate side-chains 113 residues out of total 875 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET 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 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 G residue 108 LEU 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 23 ILE Chi-restraints excluded: chain K residue 177 CYS Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 212 THR Chi-restraints excluded: chain K residue 273 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 28 optimal weight: 0.9980 chunk 102 optimal weight: 0.0970 chunk 42 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 5 optimal weight: 7.9990 overall best weight: 2.1782 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.078499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058768 restraints weight = 64064.205| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 2.79 r_work: 0.3266 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15264 Z= 0.265 Angle : 0.636 27.004 21903 Z= 0.354 Chirality : 0.054 2.001 2495 Planarity : 0.005 0.127 1751 Dihedral : 29.140 174.200 4460 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.96 % Favored : 95.85 % Rotamer: Outliers : 3.21 % Allowed : 21.79 % Favored : 75.00 % 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: 1.18 (0.26), residues: 1035 helix: 2.35 (0.21), residues: 612 sheet: -2.54 (0.78), residues: 41 loop : -1.57 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 71 HIS 0.006 0.001 HIS A 113 PHE 0.020 0.002 PHE K 64 TYR 0.012 0.001 TYR B 98 ARG 0.004 0.000 ARG F 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2698.84 seconds wall clock time: 50 minutes 14.47 seconds (3014.47 seconds total)