Starting phenix.real_space_refine on Fri Mar 15 04:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_10393.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_10393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_10393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_10393.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t7c_10393/03_2024/6t7c_10393.pdb" } 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 Residue "C GLU 64": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.76, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 5.15 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.59 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: 3.51 Time building geometry restraints manager: 5.47 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: 83.24 - 93.14: 2 93.14 - 103.04: 390 103.04 - 112.94: 6635 112.94 - 122.84: 7447 122.84 - 132.74: 1322 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 2.520 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 2.520 nonbonded pdb=" O LEU A 61 " pdb=" NH2 ARG B 36 " model vdw 2.266 2.520 nonbonded pdb=" N GLU F 53 " pdb=" OE1 GLU F 53 " model vdw 2.292 2.520 ... (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 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: 0.180 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: 1.200 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 34.310 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 333 time to evaluate : 0.853 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: 0.2985 time to fit residues: 127.5926 Evaluate side-chains 241 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 241 time to evaluate : 0.992 ------------------------------------------------------------------------------- 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: 5.9990 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 0.0060 chunk 42 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 92 GLN E 68 GLN ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 GLN E 93 GLN F 64 ASN G 31 HIS H 92 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11159 Z= 0.222 Angle : 0.626 8.782 15796 Z= 0.367 Chirality : 0.036 0.137 1713 Planarity : 0.004 0.037 1395 Dihedral : 28.869 85.526 3177 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.06 % Allowed : 15.44 % Favored : 80.50 % 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: 0.01 (0.26), residues: 897 helix: 0.57 (0.19), residues: 621 sheet: None (None), residues: 0 loop : -1.15 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS G 31 PHE 0.005 0.001 PHE F 100 TYR 0.025 0.002 TYR B 98 ARG 0.004 0.000 ARG D 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 308 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 282 time to evaluate : 0.981 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: 0.8890 (mt-10) cc_final: 0.8248 (mt-10) REVERT: A 61 LEU cc_start: 0.9109 (mp) cc_final: 0.8365 (mt) REVERT: A 81 ASP cc_start: 0.8134 (t0) cc_final: 0.7897 (t0) REVERT: A 93 GLN cc_start: 0.8765 (tt0) cc_final: 0.8561 (tp40) REVERT: A 97 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7758 (pt0) REVERT: B 37 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8830 (tt) REVERT: B 46 ILE cc_start: 0.9095 (mm) cc_final: 0.8822 (mm) REVERT: B 49 LEU cc_start: 0.9165 (mt) cc_final: 0.8401 (mp) REVERT: B 91 LYS cc_start: 0.9103 (ttmm) cc_final: 0.8630 (ttpt) REVERT: B 98 TYR cc_start: 0.8935 (m-10) cc_final: 0.8662 (m-80) REVERT: C 32 ARG cc_start: 0.9296 (ttp80) cc_final: 0.9079 (ttp-110) REVERT: C 42 ARG cc_start: 0.8887 (mtt-85) cc_final: 0.8610 (mtp180) REVERT: C 56 GLU cc_start: 0.8550 (tt0) cc_final: 0.8003 (tt0) REVERT: C 89 ASN cc_start: 0.9146 (m-40) cc_final: 0.8691 (m-40) REVERT: C 95 LYS cc_start: 0.9285 (tttt) cc_final: 0.8744 (tppt) REVERT: C 99 ARG cc_start: 0.7981 (mmp-170) cc_final: 0.7740 (mmp-170) REVERT: C 108 LEU cc_start: 0.9319 (tp) cc_final: 0.8981 (tp) REVERT: D 65 ASP cc_start: 0.9196 (t70) cc_final: 0.8886 (t0) REVERT: D 76 ARG cc_start: 0.8099 (ptp-170) cc_final: 0.7763 (ptp90) REVERT: E 90 MET cc_start: 0.9186 (tpp) cc_final: 0.8867 (tpp) REVERT: E 125 GLN cc_start: 0.8682 (mt0) cc_final: 0.8474 (mm110) REVERT: F 25 ASN cc_start: 0.9146 (m-40) cc_final: 0.7928 (m-40) REVERT: F 68 ASP cc_start: 0.9134 (m-30) cc_final: 0.8860 (m-30) REVERT: G 56 GLU cc_start: 0.9187 (tt0) cc_final: 0.8921 (tt0) REVERT: G 58 LEU cc_start: 0.9602 (mt) cc_final: 0.9390 (mt) REVERT: G 64 GLU cc_start: 0.8280 (tp30) cc_final: 0.7681 (tm-30) REVERT: G 68 ASN cc_start: 0.9139 (m-40) cc_final: 0.8513 (m-40) REVERT: G 95 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9088 (mmmm) REVERT: H 68 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8547 (tp30) REVERT: H 80 TYR cc_start: 0.8168 (m-10) cc_final: 0.7836 (m-10) REVERT: H 118 TYR cc_start: 0.9276 (t80) cc_final: 0.8910 (t80) outliers start: 26 outliers final: 15 residues processed: 293 average time/residue: 0.2527 time to fit residues: 99.0390 Evaluate side-chains 254 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 238 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain D residue 49 THR 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 Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN D 79 HIS D 106 HIS ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11159 Z= 0.369 Angle : 0.710 6.774 15796 Z= 0.411 Chirality : 0.040 0.182 1713 Planarity : 0.005 0.049 1395 Dihedral : 29.013 89.659 3177 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 5.30 % Allowed : 20.28 % Favored : 74.41 % 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: 1.02 (0.27), residues: 897 helix: 1.28 (0.20), residues: 626 sheet: None (None), residues: 0 loop : -0.65 (0.36), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS B 75 PHE 0.018 0.002 PHE F 100 TYR 0.024 0.003 TYR D 80 ARG 0.007 0.001 ARG G 35 *********************** 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 276 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 0.911 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: 0.8927 (mt-10) cc_final: 0.8482 (mp0) REVERT: A 61 LEU cc_start: 0.9181 (mp) cc_final: 0.8780 (mt) REVERT: A 81 ASP cc_start: 0.8035 (t0) cc_final: 0.7757 (t0) REVERT: A 93 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8520 (tp40) REVERT: A 97 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8005 (mt-10) REVERT: B 27 GLN cc_start: 0.9084 (mm110) cc_final: 0.8806 (mp10) REVERT: B 59 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9264 (mmmm) REVERT: B 63 GLU cc_start: 0.9197 (mt-10) cc_final: 0.8938 (mt-10) REVERT: B 88 TYR cc_start: 0.7636 (m-10) cc_final: 0.6975 (m-10) REVERT: B 91 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8362 (tmmt) REVERT: C 29 ARG cc_start: 0.8756 (mtp180) cc_final: 0.8177 (ttt180) REVERT: C 32 ARG cc_start: 0.9353 (ttp80) cc_final: 0.9139 (ttp-110) REVERT: C 56 GLU cc_start: 0.8692 (tt0) cc_final: 0.8165 (tt0) REVERT: C 64 GLU cc_start: 0.8527 (tt0) cc_final: 0.7902 (tm-30) REVERT: C 92 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7908 (mt-10) REVERT: C 95 LYS cc_start: 0.9375 (tttt) cc_final: 0.8826 (tppt) REVERT: C 108 LEU cc_start: 0.9501 (tp) cc_final: 0.9210 (tp) REVERT: D 65 ASP cc_start: 0.9192 (t70) cc_final: 0.8907 (t0) REVERT: D 76 ARG cc_start: 0.8396 (ptp-170) cc_final: 0.7708 (ptp90) REVERT: D 90 GLU cc_start: 0.8855 (mp0) cc_final: 0.8340 (mp0) REVERT: E 64 LYS cc_start: 0.8551 (mtmm) cc_final: 0.8072 (ttpt) REVERT: E 125 GLN cc_start: 0.8739 (mt0) cc_final: 0.8459 (mm110) REVERT: F 68 ASP cc_start: 0.9171 (m-30) cc_final: 0.8909 (m-30) REVERT: F 93 GLN cc_start: 0.8139 (mp10) cc_final: 0.7854 (mp10) REVERT: F 98 TYR cc_start: 0.8413 (m-80) cc_final: 0.8125 (m-80) REVERT: G 25 PHE cc_start: 0.8590 (m-80) cc_final: 0.8342 (m-80) REVERT: G 39 TYR cc_start: 0.8604 (m-80) cc_final: 0.7775 (m-80) REVERT: G 56 GLU cc_start: 0.9236 (tt0) cc_final: 0.8755 (tt0) REVERT: H 56 MET cc_start: 0.8808 (tpp) cc_final: 0.8590 (tpp) REVERT: H 68 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8626 (tp30) REVERT: H 110 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8255 (mt-10) REVERT: H 117 LYS cc_start: 0.9708 (mtpt) cc_final: 0.9380 (ptmm) outliers start: 34 outliers final: 20 residues processed: 260 average time/residue: 0.2400 time to fit residues: 84.3602 Evaluate side-chains 243 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 221 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 107 THR 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 49 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 63 optimal weight: 0.0570 chunk 94 optimal weight: 20.0000 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 overall best weight: 2.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11159 Z= 0.202 Angle : 0.618 12.100 15796 Z= 0.359 Chirality : 0.036 0.165 1713 Planarity : 0.003 0.037 1395 Dihedral : 28.827 86.377 3177 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 4.37 % Allowed : 22.62 % Favored : 73.01 % 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: 1.96 (0.28), residues: 897 helix: 2.00 (0.20), residues: 624 sheet: None (None), residues: 0 loop : -0.31 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.007 0.001 PHE C 25 TYR 0.029 0.002 TYR H 80 ARG 0.007 0.000 ARG G 35 *********************** 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 277 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 249 time to evaluate : 0.998 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: A 41 TYR cc_start: 0.7876 (m-80) cc_final: 0.7565 (m-80) REVERT: A 50 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8442 (mp0) REVERT: A 61 LEU cc_start: 0.9141 (mp) cc_final: 0.8686 (mt) REVERT: A 81 ASP cc_start: 0.7942 (t0) cc_final: 0.7667 (t0) REVERT: A 90 MET cc_start: 0.8852 (mmm) cc_final: 0.8437 (mmm) REVERT: A 93 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8586 (tp40) REVERT: A 97 GLU cc_start: 0.8512 (mt-10) cc_final: 0.8070 (mt-10) REVERT: B 59 LYS cc_start: 0.9495 (OUTLIER) cc_final: 0.9228 (mmmm) REVERT: B 63 GLU cc_start: 0.9175 (mt-10) cc_final: 0.8949 (mt-10) REVERT: B 88 TYR cc_start: 0.7640 (m-10) cc_final: 0.7099 (m-10) REVERT: B 91 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8479 (tmmt) REVERT: B 98 TYR cc_start: 0.9015 (m-10) cc_final: 0.8699 (m-80) REVERT: C 56 GLU cc_start: 0.8623 (tt0) cc_final: 0.8067 (tt0) REVERT: C 84 GLN cc_start: 0.8562 (tm-30) cc_final: 0.8205 (tm-30) REVERT: C 92 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7948 (mt-10) REVERT: C 95 LYS cc_start: 0.9304 (tttt) cc_final: 0.8718 (tppt) REVERT: C 108 LEU cc_start: 0.9489 (tp) cc_final: 0.9086 (tp) REVERT: D 56 MET cc_start: 0.8082 (tpp) cc_final: 0.7860 (tpp) REVERT: D 65 ASP cc_start: 0.9097 (t70) cc_final: 0.8846 (t0) REVERT: D 90 GLU cc_start: 0.8721 (mp0) cc_final: 0.8189 (mp0) REVERT: E 90 MET cc_start: 0.9192 (tpp) cc_final: 0.8922 (tpp) REVERT: E 125 GLN cc_start: 0.8679 (mt0) cc_final: 0.8413 (mm110) REVERT: F 59 LYS cc_start: 0.9500 (tttm) cc_final: 0.9194 (tptm) REVERT: F 68 ASP cc_start: 0.9143 (m-30) cc_final: 0.8880 (m-30) REVERT: F 93 GLN cc_start: 0.8196 (mp10) cc_final: 0.7888 (mp10) REVERT: F 98 TYR cc_start: 0.7941 (m-10) cc_final: 0.7656 (m-80) REVERT: G 25 PHE cc_start: 0.8516 (m-80) cc_final: 0.8283 (m-80) REVERT: G 39 TYR cc_start: 0.8408 (m-80) cc_final: 0.7691 (m-80) REVERT: G 56 GLU cc_start: 0.9216 (tt0) cc_final: 0.8663 (tt0) REVERT: H 56 MET cc_start: 0.8801 (tpp) cc_final: 0.8503 (tpp) REVERT: H 68 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8566 (tp30) outliers start: 28 outliers final: 18 residues processed: 257 average time/residue: 0.2202 time to fit residues: 78.3329 Evaluate side-chains 257 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 237 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR 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 G residue 87 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 90 optimal weight: 0.1980 chunk 25 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN H 106 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4699 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= 0.200 Angle : 0.601 10.094 15796 Z= 0.351 Chirality : 0.036 0.158 1713 Planarity : 0.003 0.037 1395 Dihedral : 28.682 87.247 3177 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.68 % Allowed : 24.49 % Favored : 70.83 % 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: 2.46 (0.28), residues: 897 helix: 2.30 (0.20), residues: 636 sheet: None (None), residues: 0 loop : -0.04 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.001 HIS E 113 PHE 0.007 0.001 PHE E 78 TYR 0.027 0.002 TYR H 80 ARG 0.005 0.000 ARG G 35 *********************** 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 276 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 0.849 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 41 TYR cc_start: 0.7979 (m-80) cc_final: 0.7731 (m-80) REVERT: A 50 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 61 LEU cc_start: 0.9146 (mp) cc_final: 0.8721 (mt) REVERT: A 81 ASP cc_start: 0.7926 (t0) cc_final: 0.7599 (t0) REVERT: A 93 GLN cc_start: 0.8901 (tt0) cc_final: 0.8642 (tp40) REVERT: A 97 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8090 (mt-10) REVERT: B 59 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9173 (mmmm) REVERT: B 63 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8917 (mt-10) REVERT: B 88 TYR cc_start: 0.7593 (m-10) cc_final: 0.7244 (m-10) REVERT: B 91 LYS cc_start: 0.8979 (ttmm) cc_final: 0.8637 (ttpp) REVERT: B 98 TYR cc_start: 0.8954 (m-10) cc_final: 0.8658 (m-10) REVERT: C 42 ARG cc_start: 0.9436 (mmm-85) cc_final: 0.8847 (mmm-85) REVERT: C 56 GLU cc_start: 0.8652 (tt0) cc_final: 0.8105 (tt0) REVERT: C 92 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7990 (mt-10) REVERT: C 95 LYS cc_start: 0.9288 (tttt) cc_final: 0.8721 (tppt) REVERT: C 108 LEU cc_start: 0.9574 (tp) cc_final: 0.9350 (tp) REVERT: D 56 MET cc_start: 0.8094 (tpp) cc_final: 0.7877 (tpp) REVERT: D 65 ASP cc_start: 0.9073 (t70) cc_final: 0.8847 (t0) REVERT: E 90 MET cc_start: 0.9125 (tpp) cc_final: 0.8853 (tpp) REVERT: E 125 GLN cc_start: 0.8699 (mt0) cc_final: 0.8423 (mm110) REVERT: F 68 ASP cc_start: 0.9093 (m-30) cc_final: 0.8862 (m-30) REVERT: F 93 GLN cc_start: 0.8192 (mp10) cc_final: 0.7983 (mp10) REVERT: F 98 TYR cc_start: 0.7728 (m-10) cc_final: 0.7266 (m-80) REVERT: G 25 PHE cc_start: 0.8538 (m-80) cc_final: 0.8272 (m-80) REVERT: G 56 GLU cc_start: 0.9205 (tt0) cc_final: 0.8593 (tt0) REVERT: G 64 GLU cc_start: 0.8479 (tm-30) cc_final: 0.8275 (tm-30) REVERT: G 75 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8883 (mmtp) REVERT: H 56 MET cc_start: 0.8810 (tpp) cc_final: 0.8476 (tpp) REVERT: H 68 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8650 (tp30) REVERT: H 117 LYS cc_start: 0.9527 (mtpp) cc_final: 0.9083 (mtmm) outliers start: 30 outliers final: 25 residues processed: 257 average time/residue: 0.2264 time to fit residues: 80.5295 Evaluate side-chains 258 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain C residue 43 VAL 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 80 THR Chi-restraints excluded: chain E residue 107 THR 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 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 40.0000 chunk 19 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 83 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 8 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 97 optimal weight: 50.0000 overall best weight: 6.3188 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11159 Z= 0.317 Angle : 0.664 12.344 15796 Z= 0.382 Chirality : 0.038 0.151 1713 Planarity : 0.004 0.042 1395 Dihedral : 28.676 89.183 3177 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.77 % Allowed : 25.27 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.28), residues: 897 helix: 2.25 (0.21), residues: 625 sheet: None (None), residues: 0 loop : -0.25 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.010 0.002 PHE F 100 TYR 0.040 0.002 TYR F 88 ARG 0.004 0.000 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 273 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 0.947 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: 0.8946 (mt-10) cc_final: 0.8307 (mt-10) REVERT: A 61 LEU cc_start: 0.9211 (mp) cc_final: 0.8829 (mt) REVERT: A 81 ASP cc_start: 0.7736 (t0) cc_final: 0.7388 (t0) REVERT: A 93 GLN cc_start: 0.8954 (tt0) cc_final: 0.8632 (tp40) REVERT: A 97 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8150 (mt-10) REVERT: B 63 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8960 (mt-10) REVERT: B 88 TYR cc_start: 0.7557 (m-10) cc_final: 0.7208 (m-10) REVERT: B 91 LYS cc_start: 0.8970 (ttmm) cc_final: 0.8621 (ttpp) REVERT: C 56 GLU cc_start: 0.8689 (tt0) cc_final: 0.8248 (tt0) REVERT: C 84 GLN cc_start: 0.8650 (tm-30) cc_final: 0.8256 (tm-30) REVERT: C 92 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7901 (mt-10) REVERT: C 95 LYS cc_start: 0.9318 (tttt) cc_final: 0.8771 (tppt) REVERT: C 108 LEU cc_start: 0.9525 (tp) cc_final: 0.9259 (tp) REVERT: D 56 MET cc_start: 0.8170 (tpp) cc_final: 0.7947 (tpp) REVERT: D 65 ASP cc_start: 0.9146 (t70) cc_final: 0.8944 (t0) REVERT: D 82 LYS cc_start: 0.9377 (mttp) cc_final: 0.9177 (tppt) REVERT: E 125 GLN cc_start: 0.8717 (mt0) cc_final: 0.8446 (mm110) REVERT: F 53 GLU cc_start: 0.7887 (mp0) cc_final: 0.7572 (mp0) REVERT: F 68 ASP cc_start: 0.9170 (m-30) cc_final: 0.8940 (m-30) REVERT: F 98 TYR cc_start: 0.7966 (m-10) cc_final: 0.7666 (m-80) REVERT: G 56 GLU cc_start: 0.9247 (tt0) cc_final: 0.8890 (tt0) REVERT: H 56 MET cc_start: 0.8830 (tpp) cc_final: 0.8520 (tpp) REVERT: H 68 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8686 (tp30) REVERT: H 92 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8692 (pt0) outliers start: 37 outliers final: 28 residues processed: 253 average time/residue: 0.2310 time to fit residues: 80.6329 Evaluate side-chains 253 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 122 LYS 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 G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 7.9990 chunk 57 optimal weight: 0.5980 chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- 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** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.5224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11159 Z= 0.255 Angle : 0.647 12.707 15796 Z= 0.372 Chirality : 0.037 0.154 1713 Planarity : 0.004 0.036 1395 Dihedral : 28.635 87.061 3177 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.77 % Allowed : 24.96 % Favored : 69.27 % 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: 2.43 (0.28), residues: 897 helix: 2.32 (0.21), residues: 624 sheet: None (None), residues: 0 loop : -0.03 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 113 PHE 0.007 0.001 PHE B 100 TYR 0.023 0.002 TYR F 88 ARG 0.003 0.000 ARG H 89 *********************** 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 273 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 236 time to evaluate : 0.945 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: 0.8920 (mt-10) cc_final: 0.8322 (mt-10) REVERT: A 61 LEU cc_start: 0.9173 (mp) cc_final: 0.8772 (mt) REVERT: A 81 ASP cc_start: 0.7715 (t0) cc_final: 0.7351 (t0) REVERT: A 93 GLN cc_start: 0.8894 (OUTLIER) cc_final: 0.8573 (tp40) REVERT: A 97 GLU cc_start: 0.8538 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 63 GLU cc_start: 0.9195 (mt-10) cc_final: 0.8929 (mt-10) REVERT: B 88 TYR cc_start: 0.7518 (m-10) cc_final: 0.6963 (m-10) REVERT: B 91 LYS cc_start: 0.8903 (ttmm) cc_final: 0.8468 (tmmt) REVERT: C 56 GLU cc_start: 0.8674 (tt0) cc_final: 0.8196 (tt0) REVERT: C 84 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8254 (tm-30) REVERT: C 92 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7896 (mt-10) REVERT: C 95 LYS cc_start: 0.9329 (tttt) cc_final: 0.8743 (tppt) REVERT: C 108 LEU cc_start: 0.9536 (tp) cc_final: 0.9296 (tp) REVERT: D 65 ASP cc_start: 0.9130 (t70) cc_final: 0.8925 (t0) REVERT: E 64 LYS cc_start: 0.8386 (mtpp) cc_final: 0.7833 (ttpt) REVERT: E 65 LEU cc_start: 0.9427 (mt) cc_final: 0.9223 (mt) REVERT: E 79 LYS cc_start: 0.7796 (tmtt) cc_final: 0.7536 (tmtt) REVERT: E 125 GLN cc_start: 0.8723 (mt0) cc_final: 0.8452 (mm110) REVERT: F 68 ASP cc_start: 0.9172 (m-30) cc_final: 0.8956 (m-30) REVERT: F 98 TYR cc_start: 0.7780 (m-10) cc_final: 0.7510 (m-80) REVERT: G 56 GLU cc_start: 0.9215 (tt0) cc_final: 0.8886 (tt0) REVERT: G 64 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8514 (tm-30) REVERT: H 56 MET cc_start: 0.8802 (tpp) cc_final: 0.8509 (tpp) REVERT: H 68 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8674 (tp30) REVERT: H 92 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8693 (pt0) outliers start: 37 outliers final: 32 residues processed: 250 average time/residue: 0.2281 time to fit residues: 79.2795 Evaluate side-chains 266 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 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 D residue 41 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 122 LYS 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 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 63 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 96 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11159 Z= 0.313 Angle : 0.684 13.015 15796 Z= 0.391 Chirality : 0.039 0.172 1713 Planarity : 0.004 0.036 1395 Dihedral : 28.615 88.098 3177 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 5.62 % Allowed : 25.59 % Favored : 68.80 % 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: 2.26 (0.28), residues: 897 helix: 2.18 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -0.08 (0.38), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.011 0.001 PHE B 100 TYR 0.031 0.002 TYR H 80 ARG 0.003 0.000 ARG H 96 *********************** 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 271 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 235 time to evaluate : 0.924 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: 0.8954 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 61 LEU cc_start: 0.9183 (mp) cc_final: 0.8763 (mt) REVERT: A 81 ASP cc_start: 0.7662 (t0) cc_final: 0.7303 (t0) REVERT: A 93 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8536 (tp40) REVERT: A 97 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8077 (mt-10) REVERT: B 63 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8939 (mt-10) REVERT: B 88 TYR cc_start: 0.7387 (m-10) cc_final: 0.7143 (m-10) REVERT: B 91 LYS cc_start: 0.8832 (ttmm) cc_final: 0.8524 (tmmt) REVERT: C 56 GLU cc_start: 0.8706 (tt0) cc_final: 0.8279 (tt0) REVERT: C 95 LYS cc_start: 0.9347 (tttt) cc_final: 0.8790 (tppt) REVERT: C 108 LEU cc_start: 0.9540 (tp) cc_final: 0.9049 (tp) REVERT: D 43 LYS cc_start: 0.9381 (tppt) cc_final: 0.9125 (tppt) REVERT: E 64 LYS cc_start: 0.8416 (mtpp) cc_final: 0.7863 (tptp) REVERT: E 65 LEU cc_start: 0.9418 (mt) cc_final: 0.9202 (mt) REVERT: E 73 GLU cc_start: 0.9040 (pt0) cc_final: 0.8806 (pt0) REVERT: E 79 LYS cc_start: 0.7900 (tmtt) cc_final: 0.7644 (tmtt) REVERT: E 125 GLN cc_start: 0.8750 (mt0) cc_final: 0.8472 (mm110) REVERT: F 68 ASP cc_start: 0.9156 (m-30) cc_final: 0.8953 (m-30) REVERT: F 98 TYR cc_start: 0.7822 (m-10) cc_final: 0.7600 (m-80) REVERT: G 25 PHE cc_start: 0.8580 (m-80) cc_final: 0.8251 (m-80) REVERT: G 56 GLU cc_start: 0.9243 (tt0) cc_final: 0.8875 (tt0) REVERT: H 56 MET cc_start: 0.8813 (tpp) cc_final: 0.8522 (tpp) REVERT: H 68 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8729 (tp30) REVERT: H 92 GLN cc_start: 0.9152 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: H 117 LYS cc_start: 0.9575 (mtpp) cc_final: 0.9211 (ptmt) outliers start: 36 outliers final: 34 residues processed: 252 average time/residue: 0.2297 time to fit residues: 79.3221 Evaluate side-chains 267 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 231 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 11159 Z= 0.329 Angle : 0.704 13.591 15796 Z= 0.402 Chirality : 0.039 0.203 1713 Planarity : 0.004 0.046 1395 Dihedral : 28.594 87.194 3177 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 5.93 % Allowed : 25.74 % Favored : 68.33 % 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: 2.15 (0.28), residues: 897 helix: 2.09 (0.21), residues: 626 sheet: None (None), residues: 0 loop : -0.12 (0.38), residues: 271 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 0.042 0.002 TYR B 98 ARG 0.003 0.000 ARG H 76 *********************** 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 272 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 234 time to evaluate : 0.974 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: 0.8945 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 61 LEU cc_start: 0.9172 (mp) cc_final: 0.8796 (mt) REVERT: A 81 ASP cc_start: 0.7627 (t0) cc_final: 0.7314 (t0) REVERT: A 93 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8603 (tp40) REVERT: A 97 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 27 GLN cc_start: 0.8873 (mp10) cc_final: 0.8260 (mp10) REVERT: B 63 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8937 (mt-10) REVERT: B 88 TYR cc_start: 0.7389 (m-10) cc_final: 0.7145 (m-10) REVERT: B 91 LYS cc_start: 0.8901 (ttmm) cc_final: 0.8573 (tmmt) REVERT: C 56 GLU cc_start: 0.8701 (tt0) cc_final: 0.8236 (tt0) REVERT: C 64 GLU cc_start: 0.8596 (tt0) cc_final: 0.7961 (tm-30) REVERT: C 84 GLN cc_start: 0.8656 (tm-30) cc_final: 0.8416 (tm-30) REVERT: C 95 LYS cc_start: 0.9345 (tttt) cc_final: 0.8774 (tppt) REVERT: D 43 LYS cc_start: 0.9408 (tppt) cc_final: 0.9116 (tppt) REVERT: D 56 MET cc_start: 0.8250 (tpp) cc_final: 0.8015 (tpp) REVERT: E 64 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7889 (tptp) REVERT: E 73 GLU cc_start: 0.9057 (pt0) cc_final: 0.8814 (pt0) REVERT: E 79 LYS cc_start: 0.7995 (tmtt) cc_final: 0.7737 (tmtt) REVERT: E 125 GLN cc_start: 0.8738 (mt0) cc_final: 0.8462 (mm110) REVERT: G 56 GLU cc_start: 0.9225 (tt0) cc_final: 0.9004 (tt0) REVERT: H 68 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8752 (tp30) REVERT: H 92 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8612 (pt0) REVERT: H 117 LYS cc_start: 0.9589 (mtpp) cc_final: 0.9174 (ptpp) outliers start: 38 outliers final: 35 residues processed: 251 average time/residue: 0.2413 time to fit residues: 82.8227 Evaluate side-chains 265 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 63 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.5889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 11159 Z= 0.277 Angle : 0.713 14.720 15796 Z= 0.401 Chirality : 0.039 0.202 1713 Planarity : 0.004 0.043 1395 Dihedral : 28.537 87.115 3177 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.46 % Allowed : 27.93 % 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: 2.27 (0.28), residues: 897 helix: 2.13 (0.21), residues: 634 sheet: None (None), residues: 0 loop : -0.01 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.008 0.001 PHE F 100 TYR 0.039 0.002 TYR B 98 ARG 0.005 0.000 ARG D 30 ********************** 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 269 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 234 time to evaluate : 0.840 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: 0.8944 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 61 LEU cc_start: 0.9159 (mp) cc_final: 0.8766 (mt) REVERT: A 81 ASP cc_start: 0.7579 (t0) cc_final: 0.7267 (t0) REVERT: A 93 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8585 (tp40) REVERT: A 97 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8121 (mt-10) REVERT: B 27 GLN cc_start: 0.8896 (mp10) cc_final: 0.8308 (mp10) REVERT: B 63 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8915 (mt-10) REVERT: B 88 TYR cc_start: 0.7402 (m-10) cc_final: 0.7162 (m-10) REVERT: B 91 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8562 (tmmt) REVERT: C 42 ARG cc_start: 0.9390 (mmm-85) cc_final: 0.8972 (mmm-85) REVERT: C 56 GLU cc_start: 0.8649 (tt0) cc_final: 0.7994 (tt0) REVERT: C 61 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8628 (mm-30) REVERT: C 64 GLU cc_start: 0.8593 (tt0) cc_final: 0.7932 (tm-30) REVERT: C 84 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8370 (tm-30) REVERT: C 95 LYS cc_start: 0.9331 (tttt) cc_final: 0.8733 (tppt) REVERT: C 108 LEU cc_start: 0.9362 (tp) cc_final: 0.9037 (tp) REVERT: D 43 LYS cc_start: 0.9376 (tppt) cc_final: 0.9099 (tppt) REVERT: D 56 MET cc_start: 0.8361 (tpp) cc_final: 0.7935 (tpp) REVERT: E 73 GLU cc_start: 0.9050 (pt0) cc_final: 0.8827 (pt0) REVERT: E 79 LYS cc_start: 0.7934 (tmtt) cc_final: 0.7710 (tmtt) REVERT: E 125 GLN cc_start: 0.8710 (mt0) cc_final: 0.8464 (mm110) REVERT: G 56 GLU cc_start: 0.9185 (tt0) cc_final: 0.8931 (tt0) REVERT: H 68 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8734 (tp30) REVERT: H 117 LYS cc_start: 0.9589 (mtpp) cc_final: 0.9204 (ptmt) outliers start: 35 outliers final: 33 residues processed: 249 average time/residue: 0.2373 time to fit residues: 80.4978 Evaluate side-chains 266 residues out of total 778 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 232 time to evaluate : 0.934 ------------------------------------------------------------------------------- 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 A residue 93 GLN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 46 HIS Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 122 LYS 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 34 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 92 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 34 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 72 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS H 92 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.071117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.050703 restraints weight = 41994.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052295 restraints weight = 24184.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.053382 restraints weight = 17238.547| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 11159 Z= 0.250 Angle : 0.702 13.406 15796 Z= 0.394 Chirality : 0.038 0.193 1713 Planarity : 0.004 0.039 1395 Dihedral : 28.457 87.056 3177 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.99 % Allowed : 28.39 % 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: 2.35 (0.28), residues: 897 helix: 2.18 (0.21), residues: 635 sheet: None (None), residues: 0 loop : 0.04 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 113 PHE 0.006 0.001 PHE B 100 TYR 0.027 0.002 TYR B 98 ARG 0.003 0.000 ARG F 55 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1999.31 seconds wall clock time: 36 minutes 38.32 seconds (2198.32 seconds total)