Starting phenix.real_space_refine on Fri Feb 14 10:50:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.cif Found real_map, /net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.map" model { file = "/net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6t7c_10393/02_2025/6t7c_10393.cif" } resolution = 4.0 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= 0.004 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 190 5.49 5 S 10 5.16 5 C 6021 2.51 5 N 2026 2.21 5 O 2359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10606 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 809 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 1936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1936 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "J" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1959 Classifications: {'DNA': 95} Link IDs: {'rna3p': 94} Chain: "K" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 307 Classifications: {'peptide': 77} Incomplete info: {'backbone_only': 74, 'n_c_alpha_c_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 71} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 374 Unresolved non-hydrogen angles: 517 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 86 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 178 Chain: "L" Number of atoms: 288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 288 Classifications: {'peptide': 72} Incomplete info: {'backbone_only': 70} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 341 Unresolved non-hydrogen angles: 473 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 160 Time building chain proxies: 5.82, per 1000 atoms: 0.55 Number of scatterers: 10606 At special positions: 0 Unit cell: (89.25, 115.5, 142.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 190 15.00 O 2359 8.00 N 2026 7.00 C 6021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 847.9 milliseconds 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1434 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 9 sheets defined 69.2% alpha, 2.0% beta 94 base pairs and 159 stacking pairs defined. Time for finding SS restraints: 4.42 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.966A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.530A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 28 removed outlier: 3.765A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 4.286A pdb=" N ARG B 36 " --> pdb=" O PRO B 32 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.129A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.862A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.127A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.507A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TYR D 39 " --> pdb=" O SER D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.576A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 4.227A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.637A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 31 through 41 removed outlier: 4.059A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.352A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.838A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.127A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.535A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.507A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR H 39 " --> pdb=" O SER H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.576A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.226A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 71 removed outlier: 3.615A pdb=" N VAL K 58 " --> pdb=" O ASN K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 90 Processing helix chain 'K' and resid 91 through 94 Processing helix chain 'K' and resid 95 through 113 Processing helix chain 'L' and resid 54 through 71 removed outlier: 3.603A pdb=" N VAL L 58 " --> pdb=" O ASN L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 75 through 90 Processing helix chain 'L' and resid 91 through 94 Processing helix chain 'L' and resid 95 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.879A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.313A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.427A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.480A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.313A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 451 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 218 hydrogen bonds 436 hydrogen bond angles 0 basepair planarities 94 basepair parallelities 159 stacking parallelities Total time for adding SS restraints: 3.46 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2624 1.33 - 1.45: 2884 1.45 - 1.57: 5253 1.57 - 1.69: 378 1.69 - 1.81: 20 Bond restraints: 11159 Sorted by residual: bond pdb=" CB LYS G 118 " pdb=" CG LYS G 118 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.52e+00 bond pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.30e+00 bond pdb=" CA ARG B 95 " pdb=" CB ARG B 95 " ideal model delta sigma weight residual 1.539 1.461 0.079 4.88e-02 4.20e+02 2.59e+00 bond pdb=" CB VAL B 81 " pdb=" CG2 VAL B 81 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.36e+00 bond pdb=" CB ILE A 130 " pdb=" CG2 ILE A 130 " ideal model delta sigma weight residual 1.521 1.471 0.050 3.30e-02 9.18e+02 2.32e+00 ... (remaining 11154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.73: 15782 5.73 - 11.46: 10 11.46 - 17.20: 2 17.20 - 22.93: 0 22.93 - 28.66: 2 Bond angle restraints: 15796 Sorted by residual: angle pdb=" CD LYS H 31 " pdb=" CE LYS H 31 " pdb=" NZ LYS H 31 " ideal model delta sigma weight residual 111.90 83.24 28.66 3.20e+00 9.77e-02 8.02e+01 angle pdb=" CD LYS D 31 " pdb=" CE LYS D 31 " pdb=" NZ LYS D 31 " ideal model delta sigma weight residual 111.90 83.26 28.64 3.20e+00 9.77e-02 8.01e+01 angle pdb=" CB LYS G 95 " pdb=" CG LYS G 95 " pdb=" CD LYS G 95 " ideal model delta sigma weight residual 111.30 125.49 -14.19 2.30e+00 1.89e-01 3.81e+01 angle pdb=" CB LYS C 95 " pdb=" CG LYS C 95 " pdb=" CD LYS C 95 " ideal model delta sigma weight residual 111.30 125.38 -14.08 2.30e+00 1.89e-01 3.75e+01 angle pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " pdb=" CG LYS H 31 " ideal model delta sigma weight residual 114.10 122.79 -8.69 2.00e+00 2.50e-01 1.89e+01 ... (remaining 15791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 4370 19.65 - 39.29: 916 39.29 - 58.94: 797 58.94 - 78.58: 50 78.58 - 98.23: 18 Dihedral angle restraints: 6151 sinusoidal: 3780 harmonic: 2371 Sorted by residual: dihedral pdb=" CA LYS D 27 " pdb=" C LYS D 27 " pdb=" N ARG D 28 " pdb=" CA ARG D 28 " ideal model delta harmonic sigma weight residual 180.00 153.88 26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA LYS H 27 " pdb=" C LYS H 27 " pdb=" N ARG H 28 " pdb=" CA ARG H 28 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" C ASN F 25 " pdb=" N ASN F 25 " pdb=" CA ASN F 25 " pdb=" CB ASN F 25 " ideal model delta harmonic sigma weight residual -122.60 -133.49 10.89 0 2.50e+00 1.60e-01 1.90e+01 ... (remaining 6148 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1594 0.084 - 0.167: 116 0.167 - 0.251: 2 0.251 - 0.334: 0 0.334 - 0.418: 1 Chirality restraints: 1713 Sorted by residual: chirality pdb=" CA ASN F 25 " pdb=" N ASN F 25 " pdb=" C ASN F 25 " pdb=" CB ASN F 25 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" CA PRO C 80 " pdb=" N PRO C 80 " pdb=" C PRO C 80 " pdb=" CB PRO C 80 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.32e-01 chirality pdb=" CA PRO G 80 " pdb=" N PRO G 80 " pdb=" C PRO G 80 " pdb=" CB PRO G 80 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.25e-01 ... (remaining 1710 not shown) Planarity restraints: 1395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 114 " 0.027 2.00e-02 2.50e+03 2.87e-02 1.85e+01 pdb=" N1 DC J 114 " -0.068 2.00e-02 2.50e+03 pdb=" C2 DC J 114 " 0.043 2.00e-02 2.50e+03 pdb=" O2 DC J 114 " -0.012 2.00e-02 2.50e+03 pdb=" N3 DC J 114 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 114 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC J 114 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DC J 114 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 114 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 32 " 0.019 2.00e-02 2.50e+03 2.62e-02 1.71e+01 pdb=" N1 DT J 32 " -0.064 2.00e-02 2.50e+03 pdb=" C2 DT J 32 " 0.046 2.00e-02 2.50e+03 pdb=" O2 DT J 32 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT J 32 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DT J 32 " -0.001 2.00e-02 2.50e+03 pdb=" O4 DT J 32 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DT J 32 " 0.005 2.00e-02 2.50e+03 pdb=" C7 DT J 32 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT J 32 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 25 " 0.020 2.00e-02 2.50e+03 3.97e-02 1.57e+01 pdb=" CG ASN F 25 " -0.069 2.00e-02 2.50e+03 pdb=" OD1 ASN F 25 " 0.025 2.00e-02 2.50e+03 pdb=" ND2 ASN F 25 " 0.024 2.00e-02 2.50e+03 ... (remaining 1392 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 230 2.65 - 3.21: 9122 3.21 - 3.77: 19377 3.77 - 4.34: 24506 4.34 - 4.90: 35814 Nonbonded interactions: 89049 Sorted by model distance: nonbonded pdb=" NH1 ARG D 28 " pdb=" OP1 DC J 48 " model vdw 2.081 3.120 nonbonded pdb=" O THR A 58 " pdb=" OE1 GLN G 104 " model vdw 2.110 3.040 nonbonded pdb=" NH2 ARG D 30 " pdb=" OP1 DT I 27 " model vdw 2.208 3.120 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.266 3.120 nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.292 3.120 ... (remaining 89044 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 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'K' and resid 46 through 117) selection = chain 'L' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.110 Find NCS groups from input model: 0.550 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 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 : 0.008 0.079 11159 Z= 0.505 Angle : 0.881 28.661 15796 Z= 0.503 Chirality : 0.046 0.418 1713 Planarity : 0.006 0.052 1395 Dihedral : 26.054 98.228 4717 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.67 % Favored : 98.22 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.14 % 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: -2.97 (0.22), residues: 897 helix: -1.88 (0.16), residues: 623 sheet: None (None), residues: 0 loop : -1.71 (0.33), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 39 PHE 0.012 0.002 PHE A 78 TYR 0.016 0.003 TYR E 99 ARG 0.007 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 76 GLN cc_start: 0.8598 (mt0) cc_final: 0.8353 (mt0) REVERT: A 81 ASP cc_start: 0.8102 (t0) cc_final: 0.7886 (t0) REVERT: A 90 MET cc_start: 0.8774 (mmm) cc_final: 0.8438 (mmm) REVERT: A 99 TYR cc_start: 0.8615 (t80) cc_final: 0.8415 (t80) REVERT: A 118 THR cc_start: 0.9225 (m) cc_final: 0.8876 (p) REVERT: B 21 VAL cc_start: 0.6586 (p) cc_final: 0.6036 (m) REVERT: B 24 ASP cc_start: 0.8317 (t70) cc_final: 0.7864 (t70) REVERT: B 31 LYS cc_start: 0.8545 (tttt) cc_final: 0.8344 (ttpt) REVERT: B 59 LYS cc_start: 0.9325 (mtpt) cc_final: 0.9013 (tptp) REVERT: B 64 ASN cc_start: 0.9153 (m110) cc_final: 0.8902 (m110) REVERT: B 88 TYR cc_start: 0.7876 (m-10) cc_final: 0.7273 (m-10) REVERT: C 32 ARG cc_start: 0.9248 (ttp80) cc_final: 0.8981 (ttp-110) REVERT: C 56 GLU cc_start: 0.8415 (tt0) cc_final: 0.7870 (tt0) REVERT: C 89 ASN cc_start: 0.9065 (m-40) cc_final: 0.8653 (m110) REVERT: C 92 GLU cc_start: 0.8293 (mp0) cc_final: 0.8041 (mt-10) REVERT: C 95 LYS cc_start: 0.9350 (mttt) cc_final: 0.8911 (tppt) REVERT: C 104 GLN cc_start: 0.8463 (mm110) cc_final: 0.8226 (mm-40) REVERT: C 108 LEU cc_start: 0.9263 (tp) cc_final: 0.8796 (tp) REVERT: D 34 TYR cc_start: 0.8586 (m-80) cc_final: 0.8269 (m-80) REVERT: D 65 ASP cc_start: 0.9150 (t70) cc_final: 0.8819 (t0) REVERT: D 76 ARG cc_start: 0.8219 (ptp-170) cc_final: 0.7934 (ptm160) REVERT: D 89 ARG cc_start: 0.8452 (mtp180) cc_final: 0.8248 (mmm-85) REVERT: D 99 LEU cc_start: 0.9089 (mt) cc_final: 0.8841 (mp) REVERT: D 117 LYS cc_start: 0.9244 (tptm) cc_final: 0.8478 (tptm) REVERT: E 41 TYR cc_start: 0.8893 (m-80) cc_final: 0.7940 (m-10) REVERT: E 60 LEU cc_start: 0.8342 (mt) cc_final: 0.7523 (mt) REVERT: E 73 GLU cc_start: 0.9272 (tm-30) cc_final: 0.8776 (tm-30) REVERT: E 78 PHE cc_start: 0.8518 (m-80) cc_final: 0.7676 (m-10) REVERT: E 94 GLU cc_start: 0.8653 (tp30) cc_final: 0.8263 (mm-30) REVERT: E 125 GLN cc_start: 0.8694 (mt0) cc_final: 0.8446 (mt0) REVERT: F 68 ASP cc_start: 0.9071 (m-30) cc_final: 0.8857 (m-30) REVERT: F 88 TYR cc_start: 0.8663 (m-10) cc_final: 0.8299 (m-10) REVERT: G 39 TYR cc_start: 0.8215 (m-80) cc_final: 0.7398 (m-80) REVERT: G 64 GLU cc_start: 0.8382 (tp30) cc_final: 0.7714 (tm-30) REVERT: G 68 ASN cc_start: 0.9213 (m-40) cc_final: 0.8390 (m-40) REVERT: G 71 ARG cc_start: 0.9349 (ttp-170) cc_final: 0.9019 (ttp80) REVERT: H 32 GLU cc_start: 0.7002 (tp30) cc_final: 0.6577 (mp0) REVERT: H 68 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8569 (tp30) REVERT: H 77 LEU cc_start: 0.9065 (mt) cc_final: 0.8862 (mm) REVERT: H 80 TYR cc_start: 0.8342 (m-10) cc_final: 0.8059 (m-10) REVERT: H 90 GLU cc_start: 0.9098 (mp0) cc_final: 0.8726 (mp0) REVERT: H 103 LEU cc_start: 0.9590 (mt) cc_final: 0.9359 (mt) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.3149 time to fit residues: 134.4773 Evaluate side-chains 241 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 30.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 HIS ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN E 76 GLN E 85 GLN E 93 GLN F 64 ASN G 31 HIS G 38 ASN G 110 ASN H 92 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.074250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053682 restraints weight = 39915.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.055364 restraints weight = 22247.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.056482 restraints weight = 15570.450| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11159 Z= 0.239 Angle : 0.635 8.521 15796 Z= 0.371 Chirality : 0.037 0.136 1713 Planarity : 0.004 0.040 1395 Dihedral : 28.950 85.950 3177 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.43 % Allowed : 16.22 % Favored : 80.34 % 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: -0.15 (0.26), residues: 897 helix: 0.39 (0.19), residues: 633 sheet: None (None), residues: 0 loop : -1.09 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS G 31 PHE 0.007 0.001 PHE F 100 TYR 0.020 0.002 TYR B 98 ARG 0.004 0.000 ARG H 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 281 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8236 (mt-10) REVERT: B 46 ILE cc_start: 0.9248 (mm) cc_final: 0.8988 (mm) REVERT: B 88 TYR cc_start: 0.7828 (m-10) cc_final: 0.7270 (m-10) REVERT: B 91 LYS cc_start: 0.9191 (ttmm) cc_final: 0.8752 (tmmt) REVERT: B 98 TYR cc_start: 0.8968 (m-10) cc_final: 0.8607 (m-80) REVERT: C 32 ARG cc_start: 0.9236 (ttp80) cc_final: 0.9029 (ttp-110) REVERT: C 56 GLU cc_start: 0.8600 (tt0) cc_final: 0.7834 (tt0) REVERT: C 89 ASN cc_start: 0.9090 (m-40) cc_final: 0.8694 (m-40) REVERT: C 95 LYS cc_start: 0.9291 (tttt) cc_final: 0.8821 (tppt) REVERT: D 65 ASP cc_start: 0.9242 (t70) cc_final: 0.9008 (t0) REVERT: E 78 PHE cc_start: 0.9129 (m-80) cc_final: 0.8842 (m-10) REVERT: E 90 MET cc_start: 0.8937 (tpp) cc_final: 0.8668 (tpp) REVERT: F 25 ASN cc_start: 0.9098 (m-40) cc_final: 0.7664 (m-40) REVERT: F 98 TYR cc_start: 0.8256 (m-10) cc_final: 0.8039 (m-80) REVERT: G 39 TYR cc_start: 0.8230 (m-80) cc_final: 0.6917 (m-80) REVERT: G 58 LEU cc_start: 0.9632 (mt) cc_final: 0.9407 (mt) REVERT: G 62 ILE cc_start: 0.9354 (mm) cc_final: 0.9081 (tp) REVERT: G 64 GLU cc_start: 0.8062 (tp30) cc_final: 0.7517 (tm-30) REVERT: G 68 ASN cc_start: 0.9081 (m-40) cc_final: 0.7870 (m-40) REVERT: G 95 LYS cc_start: 0.9356 (mmmt) cc_final: 0.9113 (mmmm) REVERT: H 68 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8593 (tp30) REVERT: H 80 TYR cc_start: 0.8125 (m-10) cc_final: 0.7852 (m-10) REVERT: H 118 TYR cc_start: 0.9155 (t80) cc_final: 0.8933 (t80) outliers start: 22 outliers final: 12 residues processed: 291 average time/residue: 0.2616 time to fit residues: 101.3848 Evaluate side-chains 246 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 234 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 7.9990 chunk 81 optimal weight: 30.0000 chunk 96 optimal weight: 5.9990 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 0.0170 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 92 optimal weight: 50.0000 chunk 23 optimal weight: 0.0670 chunk 21 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN D 106 HIS E 125 GLN F 75 HIS G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.073349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.053163 restraints weight = 40136.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054876 restraints weight = 21776.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.056016 restraints weight = 14959.681| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11159 Z= 0.223 Angle : 0.626 8.009 15796 Z= 0.366 Chirality : 0.037 0.171 1713 Planarity : 0.004 0.040 1395 Dihedral : 28.874 85.869 3177 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.96 % Allowed : 19.50 % Favored : 77.54 % 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: 1.09 (0.27), residues: 897 helix: 1.38 (0.20), residues: 629 sheet: None (None), residues: 0 loop : -0.79 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.002 HIS D 79 PHE 0.006 0.001 PHE F 100 TYR 0.017 0.002 TYR H 37 ARG 0.008 0.000 ARG C 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8456 (mp0) REVERT: A 105 GLU cc_start: 0.8103 (tp30) cc_final: 0.7771 (mm-30) REVERT: B 49 LEU cc_start: 0.9024 (mt) cc_final: 0.8584 (mt) REVERT: B 59 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9190 (mmmm) REVERT: B 88 TYR cc_start: 0.7774 (m-10) cc_final: 0.7182 (m-10) REVERT: B 91 LYS cc_start: 0.9151 (ttmm) cc_final: 0.8663 (tmmt) REVERT: B 98 TYR cc_start: 0.9049 (m-10) cc_final: 0.8765 (m-10) REVERT: C 32 ARG cc_start: 0.9263 (ttp80) cc_final: 0.9020 (ttp-110) REVERT: C 42 ARG cc_start: 0.8733 (mtp180) cc_final: 0.8373 (mtp-110) REVERT: C 56 GLU cc_start: 0.8629 (tt0) cc_final: 0.8090 (tt0) REVERT: C 64 GLU cc_start: 0.8429 (tt0) cc_final: 0.8024 (tm-30) REVERT: C 89 ASN cc_start: 0.9081 (m-40) cc_final: 0.8870 (m-40) REVERT: C 92 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 95 LYS cc_start: 0.9251 (tttt) cc_final: 0.8775 (tppt) REVERT: D 65 ASP cc_start: 0.9210 (t70) cc_final: 0.8992 (t0) REVERT: E 85 GLN cc_start: 0.8225 (tp-100) cc_final: 0.7999 (tp-100) REVERT: E 90 MET cc_start: 0.8947 (tpp) cc_final: 0.8584 (tpp) REVERT: F 88 TYR cc_start: 0.8693 (m-10) cc_final: 0.8028 (m-10) REVERT: G 40 SER cc_start: 0.8983 (p) cc_final: 0.8768 (p) REVERT: G 57 TYR cc_start: 0.9549 (t80) cc_final: 0.9310 (t80) REVERT: G 62 ILE cc_start: 0.9381 (mm) cc_final: 0.9093 (tp) REVERT: G 95 LYS cc_start: 0.9344 (mmmt) cc_final: 0.9131 (mmmm) REVERT: H 56 MET cc_start: 0.8891 (tpp) cc_final: 0.8548 (tpp) REVERT: H 68 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8648 (tp30) REVERT: H 110 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7842 (mt-10) REVERT: H 117 LYS cc_start: 0.9572 (mtpp) cc_final: 0.9174 (mtmt) REVERT: H 118 TYR cc_start: 0.9209 (t80) cc_final: 0.8996 (t80) outliers start: 19 outliers final: 11 residues processed: 271 average time/residue: 0.2633 time to fit residues: 95.6753 Evaluate side-chains 263 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 251 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 84 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN H 106 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.072831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.053138 restraints weight = 40797.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.054761 restraints weight = 22929.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.055847 restraints weight = 16050.359| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11159 Z= 0.238 Angle : 0.626 11.884 15796 Z= 0.365 Chirality : 0.037 0.151 1713 Planarity : 0.004 0.039 1395 Dihedral : 28.795 85.769 3177 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.21 % Allowed : 23.09 % Favored : 72.70 % 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: 1.81 (0.27), residues: 897 helix: 1.87 (0.20), residues: 634 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.010 0.001 PHE F 100 TYR 0.021 0.002 TYR H 80 ARG 0.007 0.000 ARG A 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 257 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8455 (mp0) REVERT: A 76 GLN cc_start: 0.8974 (mm-40) cc_final: 0.8534 (mt0) REVERT: A 90 MET cc_start: 0.8730 (mmm) cc_final: 0.8384 (mmm) REVERT: A 94 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8191 (pt0) REVERT: B 49 LEU cc_start: 0.8786 (mt) cc_final: 0.8518 (mt) REVERT: B 88 TYR cc_start: 0.7712 (m-10) cc_final: 0.7336 (m-10) REVERT: B 91 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8834 (ttpp) REVERT: B 98 TYR cc_start: 0.9092 (m-10) cc_final: 0.8732 (m-10) REVERT: C 42 ARG cc_start: 0.8645 (mtp180) cc_final: 0.8155 (mtp180) REVERT: C 56 GLU cc_start: 0.8650 (tt0) cc_final: 0.8180 (tt0) REVERT: C 64 GLU cc_start: 0.8369 (tt0) cc_final: 0.7876 (tm-30) REVERT: C 84 GLN cc_start: 0.8991 (tm-30) cc_final: 0.8721 (tm-30) REVERT: C 92 GLU cc_start: 0.8224 (mt-10) cc_final: 0.8003 (mt-10) REVERT: C 95 LYS cc_start: 0.9240 (tttt) cc_final: 0.8760 (tppt) REVERT: D 44 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8652 (tm-30) REVERT: E 90 MET cc_start: 0.8790 (tpp) cc_final: 0.8488 (tpt) REVERT: E 112 ILE cc_start: 0.9491 (pt) cc_final: 0.9206 (mt) REVERT: E 125 GLN cc_start: 0.8575 (mm110) cc_final: 0.8345 (mm-40) REVERT: F 98 TYR cc_start: 0.8325 (m-80) cc_final: 0.7874 (m-80) REVERT: G 40 SER cc_start: 0.8997 (p) cc_final: 0.8663 (p) REVERT: G 57 TYR cc_start: 0.9357 (t80) cc_final: 0.9110 (t80) REVERT: G 62 ILE cc_start: 0.9319 (mm) cc_final: 0.9007 (tp) REVERT: G 64 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7608 (tm-30) REVERT: G 68 ASN cc_start: 0.8612 (m-40) cc_final: 0.8042 (m-40) REVERT: G 95 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9114 (mmmm) REVERT: H 56 MET cc_start: 0.8963 (tpp) cc_final: 0.8626 (tpp) REVERT: H 113 LYS cc_start: 0.9576 (ttpp) cc_final: 0.9236 (ptmm) outliers start: 27 outliers final: 17 residues processed: 269 average time/residue: 0.2603 time to fit residues: 94.3929 Evaluate side-chains 260 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 243 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 9.9990 chunk 35 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 50.0000 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 40.0000 chunk 29 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.072948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052869 restraints weight = 40444.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054503 restraints weight = 22511.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055629 restraints weight = 15669.938| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11159 Z= 0.230 Angle : 0.626 10.698 15796 Z= 0.364 Chirality : 0.037 0.151 1713 Planarity : 0.003 0.038 1395 Dihedral : 28.749 85.905 3177 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 4.06 % Allowed : 24.18 % Favored : 71.76 % 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: 2.23 (0.28), residues: 897 helix: 2.17 (0.20), residues: 633 sheet: None (None), residues: 0 loop : -0.21 (0.38), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.010 0.001 PHE E 78 TYR 0.027 0.002 TYR F 88 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 259 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8253 (mt-10) REVERT: A 58 THR cc_start: 0.7578 (OUTLIER) cc_final: 0.7033 (t) REVERT: A 76 GLN cc_start: 0.9030 (mm-40) cc_final: 0.8629 (mt0) REVERT: A 90 MET cc_start: 0.8686 (mmm) cc_final: 0.8359 (mmm) REVERT: A 94 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8104 (pt0) REVERT: A 105 GLU cc_start: 0.8210 (tp30) cc_final: 0.7858 (mm-30) REVERT: B 88 TYR cc_start: 0.7604 (m-10) cc_final: 0.7235 (m-10) REVERT: B 91 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8796 (ttpp) REVERT: B 98 TYR cc_start: 0.9158 (m-10) cc_final: 0.8710 (m-10) REVERT: C 42 ARG cc_start: 0.8661 (mtp180) cc_final: 0.8243 (mtp-110) REVERT: C 56 GLU cc_start: 0.8654 (tt0) cc_final: 0.8204 (tt0) REVERT: C 64 GLU cc_start: 0.8408 (tt0) cc_final: 0.7859 (tm-30) REVERT: C 92 GLU cc_start: 0.8262 (mt-10) cc_final: 0.7911 (mt-10) REVERT: C 95 LYS cc_start: 0.9275 (tttt) cc_final: 0.8755 (tppt) REVERT: D 44 GLN cc_start: 0.9092 (tm-30) cc_final: 0.8722 (tm-30) REVERT: E 64 LYS cc_start: 0.8256 (mtmm) cc_final: 0.7755 (ttpt) REVERT: E 90 MET cc_start: 0.8782 (tpp) cc_final: 0.8582 (tpt) REVERT: E 112 ILE cc_start: 0.9487 (pt) cc_final: 0.9176 (mt) REVERT: G 62 ILE cc_start: 0.9308 (mm) cc_final: 0.8985 (tp) REVERT: H 56 MET cc_start: 0.8954 (tpp) cc_final: 0.8607 (tpp) REVERT: H 110 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7545 (mt-10) REVERT: H 113 LYS cc_start: 0.9601 (ttpp) cc_final: 0.9254 (ptmm) outliers start: 26 outliers final: 21 residues processed: 269 average time/residue: 0.2551 time to fit residues: 92.8093 Evaluate side-chains 264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 242 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 72 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 59 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.070804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.049972 restraints weight = 42029.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051543 restraints weight = 24338.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.052580 restraints weight = 17344.658| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11159 Z= 0.316 Angle : 0.683 12.378 15796 Z= 0.394 Chirality : 0.039 0.159 1713 Planarity : 0.004 0.043 1395 Dihedral : 28.801 88.502 3177 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.84 % Allowed : 25.59 % Favored : 69.58 % 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: 2.02 (0.28), residues: 897 helix: 2.01 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.31 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.013 0.001 PHE F 100 TYR 0.026 0.002 TYR H 80 ARG 0.012 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 239 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 76 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8602 (mt0) REVERT: A 81 ASP cc_start: 0.7899 (t0) cc_final: 0.7632 (t70) REVERT: A 90 MET cc_start: 0.8798 (mmm) cc_final: 0.8489 (mmm) REVERT: A 94 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8162 (pt0) REVERT: A 105 GLU cc_start: 0.8118 (tp30) cc_final: 0.7868 (mm-30) REVERT: B 27 GLN cc_start: 0.8774 (mp10) cc_final: 0.8281 (mp10) REVERT: B 49 LEU cc_start: 0.8757 (mt) cc_final: 0.8179 (tt) REVERT: B 88 TYR cc_start: 0.7661 (m-10) cc_final: 0.7143 (m-10) REVERT: B 91 LYS cc_start: 0.9104 (ttmm) cc_final: 0.8800 (ttpp) REVERT: B 98 TYR cc_start: 0.9041 (m-10) cc_final: 0.8496 (m-10) REVERT: C 42 ARG cc_start: 0.8617 (mtp180) cc_final: 0.8166 (mtp180) REVERT: C 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8336 (tt0) REVERT: C 64 GLU cc_start: 0.8456 (tt0) cc_final: 0.7943 (tm-30) REVERT: C 84 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8730 (tm-30) REVERT: C 92 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7903 (mt-10) REVERT: C 95 LYS cc_start: 0.9275 (tttt) cc_final: 0.8842 (tppt) REVERT: D 44 GLN cc_start: 0.9142 (tm-30) cc_final: 0.8810 (tm-30) REVERT: D 56 MET cc_start: 0.8435 (tpp) cc_final: 0.8231 (tpp) REVERT: E 65 LEU cc_start: 0.9315 (mt) cc_final: 0.9115 (mt) REVERT: E 125 GLN cc_start: 0.8489 (mm-40) cc_final: 0.8273 (mm-40) REVERT: G 39 TYR cc_start: 0.8471 (m-80) cc_final: 0.7848 (m-80) REVERT: G 62 ILE cc_start: 0.9315 (mm) cc_final: 0.8998 (tp) REVERT: G 64 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7693 (tm-30) REVERT: G 68 ASN cc_start: 0.8646 (m-40) cc_final: 0.8420 (m-40) REVERT: G 88 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8286 (mpt180) REVERT: H 56 MET cc_start: 0.8979 (tpp) cc_final: 0.8671 (tpp) REVERT: H 113 LYS cc_start: 0.9612 (ttpp) cc_final: 0.9237 (ptmm) REVERT: H 117 LYS cc_start: 0.9587 (mtpp) cc_final: 0.9326 (mttm) outliers start: 31 outliers final: 23 residues processed: 257 average time/residue: 0.2715 time to fit residues: 92.8434 Evaluate side-chains 246 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 223 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 93 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 79 optimal weight: 20.0000 chunk 3 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 31 HIS G 38 ASN H 46 HIS H 79 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.071777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.051437 restraints weight = 41541.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.053055 restraints weight = 23377.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054167 restraints weight = 16360.140| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11159 Z= 0.238 Angle : 0.660 13.063 15796 Z= 0.380 Chirality : 0.037 0.156 1713 Planarity : 0.004 0.040 1395 Dihedral : 28.750 88.819 3177 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.84 % Allowed : 27.30 % Favored : 67.86 % 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: 2.13 (0.28), residues: 897 helix: 2.10 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -0.30 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 106 PHE 0.008 0.001 PHE F 100 TYR 0.043 0.002 TYR H 80 ARG 0.010 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 243 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8393 (mt-10) REVERT: A 76 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8690 (mt0) REVERT: A 81 ASP cc_start: 0.7811 (t0) cc_final: 0.7494 (t70) REVERT: A 90 MET cc_start: 0.8715 (mmm) cc_final: 0.8409 (mmm) REVERT: A 94 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8161 (pt0) REVERT: A 105 GLU cc_start: 0.8157 (tp30) cc_final: 0.7835 (mm-30) REVERT: B 27 GLN cc_start: 0.8852 (mp10) cc_final: 0.8336 (mp10) REVERT: B 34 ILE cc_start: 0.8277 (OUTLIER) cc_final: 0.8008 (tp) REVERT: B 88 TYR cc_start: 0.7548 (m-10) cc_final: 0.7208 (m-10) REVERT: B 91 LYS cc_start: 0.9059 (ttmm) cc_final: 0.8793 (ttpp) REVERT: B 98 TYR cc_start: 0.9027 (m-10) cc_final: 0.8491 (m-10) REVERT: C 42 ARG cc_start: 0.8661 (mtp180) cc_final: 0.8171 (mtp-110) REVERT: C 56 GLU cc_start: 0.8700 (tt0) cc_final: 0.8270 (tt0) REVERT: C 64 GLU cc_start: 0.8461 (tt0) cc_final: 0.7934 (tm-30) REVERT: C 84 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8699 (tm-30) REVERT: C 92 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7978 (mt-10) REVERT: C 95 LYS cc_start: 0.9304 (tttt) cc_final: 0.8755 (tppt) REVERT: E 79 LYS cc_start: 0.8806 (tptp) cc_final: 0.8544 (tptp) REVERT: G 39 TYR cc_start: 0.8604 (m-80) cc_final: 0.7988 (m-80) REVERT: G 62 ILE cc_start: 0.9309 (mm) cc_final: 0.8992 (tp) REVERT: G 64 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 68 ASN cc_start: 0.8710 (m-40) cc_final: 0.8422 (m-40) REVERT: H 56 MET cc_start: 0.8957 (tpp) cc_final: 0.8652 (tpp) REVERT: H 113 LYS cc_start: 0.9626 (ttpp) cc_final: 0.9208 (ptmm) REVERT: H 117 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9334 (mttm) outliers start: 31 outliers final: 23 residues processed: 258 average time/residue: 0.2611 time to fit residues: 90.9239 Evaluate side-chains 260 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 7.9990 chunk 100 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 79 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN G 38 ASN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.070453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050144 restraints weight = 41397.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.051699 restraints weight = 23612.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.052760 restraints weight = 16682.598| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.5489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11159 Z= 0.303 Angle : 0.713 16.518 15796 Z= 0.404 Chirality : 0.039 0.175 1713 Planarity : 0.004 0.042 1395 Dihedral : 28.728 87.945 3177 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 4.84 % Allowed : 27.77 % Favored : 67.39 % 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: 2.03 (0.28), residues: 897 helix: 2.01 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.28 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.015 0.001 PHE E 78 TYR 0.048 0.002 TYR H 80 ARG 0.008 0.001 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 76 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8702 (mt0) REVERT: A 81 ASP cc_start: 0.7885 (t0) cc_final: 0.7577 (t70) REVERT: A 94 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8131 (pt0) REVERT: B 27 GLN cc_start: 0.8877 (mp10) cc_final: 0.8331 (mp10) REVERT: B 34 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8072 (tp) REVERT: B 88 TYR cc_start: 0.7575 (m-10) cc_final: 0.7205 (m-10) REVERT: B 91 LYS cc_start: 0.9065 (ttmm) cc_final: 0.8809 (ttpp) REVERT: B 98 TYR cc_start: 0.9050 (m-10) cc_final: 0.8510 (m-10) REVERT: C 42 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8397 (mtp85) REVERT: C 56 GLU cc_start: 0.8767 (tt0) cc_final: 0.8292 (tt0) REVERT: C 64 GLU cc_start: 0.8497 (tt0) cc_final: 0.7953 (tm-30) REVERT: C 92 GLU cc_start: 0.8386 (mt-10) cc_final: 0.8002 (mt-10) REVERT: C 95 LYS cc_start: 0.9315 (tttt) cc_final: 0.8811 (tppt) REVERT: D 43 LYS cc_start: 0.9396 (tppt) cc_final: 0.9090 (tppt) REVERT: D 56 MET cc_start: 0.8558 (tpp) cc_final: 0.8154 (tpp) REVERT: E 64 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7691 (ttpt) REVERT: G 57 TYR cc_start: 0.9540 (t80) cc_final: 0.9194 (t80) REVERT: G 62 ILE cc_start: 0.9257 (mm) cc_final: 0.8937 (tp) REVERT: G 64 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7803 (tm-30) REVERT: G 68 ASN cc_start: 0.8744 (m-40) cc_final: 0.8464 (m-40) REVERT: H 56 MET cc_start: 0.8986 (tpp) cc_final: 0.8713 (tpp) REVERT: H 113 LYS cc_start: 0.9610 (ttpp) cc_final: 0.9326 (ttpp) outliers start: 31 outliers final: 28 residues processed: 246 average time/residue: 0.2696 time to fit residues: 88.7257 Evaluate side-chains 256 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 112 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 53 optimal weight: 0.3980 chunk 58 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 20.0000 chunk 92 optimal weight: 50.0000 chunk 9 optimal weight: 0.7980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 92 GLN G 73 ASN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.073347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052329 restraints weight = 41899.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053971 restraints weight = 23841.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055088 restraints weight = 16824.392| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.5664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11159 Z= 0.204 Angle : 0.700 14.371 15796 Z= 0.394 Chirality : 0.038 0.158 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.633 86.943 3177 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.12 % Allowed : 30.27 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.12 (0.28), residues: 897 helix: 2.06 (0.20), residues: 637 sheet: None (None), residues: 0 loop : -0.21 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 79 PHE 0.015 0.001 PHE E 78 TYR 0.029 0.002 TYR H 80 ARG 0.008 0.000 ARG G 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 THR cc_start: 0.7925 (OUTLIER) cc_final: 0.7668 (t) REVERT: A 76 GLN cc_start: 0.9046 (mm-40) cc_final: 0.8717 (mt0) REVERT: A 81 ASP cc_start: 0.7889 (t0) cc_final: 0.7611 (t70) REVERT: A 90 MET cc_start: 0.8611 (mmm) cc_final: 0.8384 (mmm) REVERT: A 94 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8030 (pt0) REVERT: A 105 GLU cc_start: 0.8047 (tp30) cc_final: 0.7768 (mm-30) REVERT: B 27 GLN cc_start: 0.8896 (mp10) cc_final: 0.8316 (mp10) REVERT: B 88 TYR cc_start: 0.7527 (m-10) cc_final: 0.7256 (m-10) REVERT: B 91 LYS cc_start: 0.9070 (ttmm) cc_final: 0.8838 (ttpp) REVERT: B 97 LEU cc_start: 0.9066 (tp) cc_final: 0.8698 (tp) REVERT: B 98 TYR cc_start: 0.9054 (m-10) cc_final: 0.8472 (m-10) REVERT: C 29 ARG cc_start: 0.8613 (mtp180) cc_final: 0.8164 (ttt180) REVERT: C 42 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8098 (mtp-110) REVERT: C 56 GLU cc_start: 0.8608 (tt0) cc_final: 0.8149 (tt0) REVERT: C 64 GLU cc_start: 0.8436 (tt0) cc_final: 0.7868 (tm-30) REVERT: C 92 GLU cc_start: 0.8345 (mt-10) cc_final: 0.8020 (mt-10) REVERT: C 95 LYS cc_start: 0.9278 (tttt) cc_final: 0.8728 (tppt) REVERT: D 43 LYS cc_start: 0.9363 (tppt) cc_final: 0.9043 (tppt) REVERT: D 56 MET cc_start: 0.8464 (tpp) cc_final: 0.8077 (tpp) REVERT: D 102 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8275 (tm-30) REVERT: E 90 MET cc_start: 0.8923 (tpt) cc_final: 0.8611 (tpp) REVERT: E 112 ILE cc_start: 0.9534 (pt) cc_final: 0.9231 (mt) REVERT: G 39 TYR cc_start: 0.8768 (m-80) cc_final: 0.8460 (m-80) REVERT: G 57 TYR cc_start: 0.9368 (t80) cc_final: 0.9049 (t80) REVERT: G 62 ILE cc_start: 0.9247 (mm) cc_final: 0.8880 (tp) REVERT: G 64 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7706 (tm-30) REVERT: G 68 ASN cc_start: 0.8612 (m-40) cc_final: 0.8386 (m-40) REVERT: H 49 THR cc_start: 0.8334 (m) cc_final: 0.8133 (p) REVERT: H 56 MET cc_start: 0.8960 (tpp) cc_final: 0.8672 (tpp) REVERT: H 113 LYS cc_start: 0.9570 (ttpp) cc_final: 0.9319 (ttpp) outliers start: 20 outliers final: 17 residues processed: 264 average time/residue: 0.2728 time to fit residues: 95.8641 Evaluate side-chains 257 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN H 79 HIS H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.072430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052158 restraints weight = 41416.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.053779 restraints weight = 23455.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.054886 restraints weight = 16462.512| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11159 Z= 0.230 Angle : 0.725 15.815 15796 Z= 0.401 Chirality : 0.038 0.199 1713 Planarity : 0.004 0.041 1395 Dihedral : 28.613 87.034 3177 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.59 % Allowed : 29.80 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.08 (0.28), residues: 897 helix: 2.00 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -0.16 (0.39), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.012 0.001 PHE E 78 TYR 0.036 0.002 TYR H 80 ARG 0.007 0.000 ARG G 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1794 Ramachandran restraints generated. 897 Oldfield, 0 Emsley, 897 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 241 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8739 (mt0) REVERT: A 81 ASP cc_start: 0.7873 (t0) cc_final: 0.7601 (t70) REVERT: A 90 MET cc_start: 0.8656 (mmm) cc_final: 0.8391 (mmm) REVERT: A 94 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8102 (pt0) REVERT: A 105 GLU cc_start: 0.8076 (tp30) cc_final: 0.7799 (mm-30) REVERT: B 27 GLN cc_start: 0.8910 (mp10) cc_final: 0.8289 (mp10) REVERT: B 34 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7984 (tp) REVERT: B 88 TYR cc_start: 0.7505 (m-10) cc_final: 0.7193 (m-10) REVERT: B 91 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8872 (ttpp) REVERT: B 97 LEU cc_start: 0.9074 (tp) cc_final: 0.8706 (tp) REVERT: B 98 TYR cc_start: 0.9104 (m-10) cc_final: 0.8585 (m-10) REVERT: C 42 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.8315 (mtp85) REVERT: C 56 GLU cc_start: 0.8638 (tt0) cc_final: 0.8167 (tt0) REVERT: C 64 GLU cc_start: 0.8443 (tt0) cc_final: 0.7875 (tm-30) REVERT: C 92 GLU cc_start: 0.8403 (mt-10) cc_final: 0.8029 (mt-10) REVERT: C 95 LYS cc_start: 0.9297 (tttt) cc_final: 0.8764 (tppt) REVERT: D 43 LYS cc_start: 0.9371 (tppt) cc_final: 0.9079 (tppt) REVERT: D 56 MET cc_start: 0.8483 (tpp) cc_final: 0.8199 (tpp) REVERT: D 117 LYS cc_start: 0.9453 (tptm) cc_final: 0.9122 (tttm) REVERT: E 90 MET cc_start: 0.8934 (tpt) cc_final: 0.8636 (tpp) REVERT: E 112 ILE cc_start: 0.9506 (pt) cc_final: 0.9213 (mt) REVERT: E 125 GLN cc_start: 0.8787 (mm110) cc_final: 0.8574 (mm-40) REVERT: G 62 ILE cc_start: 0.9238 (mm) cc_final: 0.8909 (tp) REVERT: G 64 GLU cc_start: 0.8043 (tm-30) cc_final: 0.7694 (tm-30) REVERT: G 68 ASN cc_start: 0.8625 (m-40) cc_final: 0.8276 (m-40) REVERT: H 56 MET cc_start: 0.8946 (tpp) cc_final: 0.8682 (tpp) REVERT: H 83 ARG cc_start: 0.8817 (mmt-90) cc_final: 0.8243 (mmt-90) REVERT: H 113 LYS cc_start: 0.9593 (ttpp) cc_final: 0.9364 (ttpp) REVERT: H 117 LYS cc_start: 0.9525 (mtpp) cc_final: 0.9111 (ptmt) outliers start: 23 outliers final: 18 residues processed: 251 average time/residue: 0.2660 time to fit residues: 88.8721 Evaluate side-chains 252 residues out of total 778 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 232 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 31 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN G 73 ASN H 79 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.070477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050149 restraints weight = 42074.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.051704 restraints weight = 24182.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.052768 restraints weight = 17144.082| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.5998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 11159 Z= 0.326 Angle : 0.760 15.454 15796 Z= 0.422 Chirality : 0.040 0.213 1713 Planarity : 0.004 0.042 1395 Dihedral : 28.614 87.841 3177 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.21 % Allowed : 29.64 % Favored : 66.15 % 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: 1.88 (0.28), residues: 897 helix: 1.90 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -0.35 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.012 0.002 PHE E 78 TYR 0.033 0.002 TYR G 57 ARG 0.007 0.001 ARG D 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3108.51 seconds wall clock time: 56 minutes 28.42 seconds (3388.42 seconds total)