Starting phenix.real_space_refine on Sat Nov 16 23:22:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g6s_29781/11_2024/8g6s_29781.cif" } resolution = 3.47 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= 0.001 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 13 5.16 5 C 6944 2.51 5 N 2330 2.21 5 O 2905 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 12480 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 582 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU K 73 " occ=0.80 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.80 Time building chain proxies: 7.73, per 1000 atoms: 0.62 Number of scatterers: 12480 At special positions: 0 Unit cell: (125.13, 81.48, 132.89, 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 13 16.00 P 288 15.00 O 2905 8.00 N 2330 7.00 C 6944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.0 seconds 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 11 sheets defined 69.5% alpha, 4.6% beta 142 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.996A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.621A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.035A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.549A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 3.583A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.578A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.597A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.774A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.606A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.686A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.677A pdb=" N ARG G 20 " --> pdb=" O THR G 16 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.765A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.644A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.754A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 60 removed outlier: 3.547A pdb=" N TYR K 59 " --> pdb=" O LEU K 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.980A 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 removed outlier: 3.891A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 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: 7.307A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.980A 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 'E' and resid 118 through 119 removed outlier: 3.760A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 12 through 16 removed outlier: 8.767A pdb=" N LEU K 67 " --> pdb=" O GLN K 2 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N PHE K 4 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N LEU K 69 " --> pdb=" O PHE K 4 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LYS K 6 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N LEU K 71 " --> pdb=" O LYS K 6 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 726 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 4.71 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2894 1.34 - 1.46: 4157 1.46 - 1.58: 5637 1.58 - 1.70: 576 1.70 - 1.82: 24 Bond restraints: 13288 Sorted by residual: bond pdb=" N HIS E 113 " pdb=" CA HIS E 113 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.56e+00 bond pdb=" N ALA E 114 " pdb=" CA ALA E 114 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.25e-02 6.40e+03 5.37e+00 bond pdb=" N LYS E 115 " pdb=" CA LYS E 115 " ideal model delta sigma weight residual 1.462 1.490 -0.028 1.50e-02 4.44e+03 3.61e+00 bond pdb=" CA ALA E 114 " pdb=" CB ALA E 114 " ideal model delta sigma weight residual 1.530 1.506 0.024 1.51e-02 4.39e+03 2.47e+00 bond pdb=" CE1 HIS E 113 " pdb=" NE2 HIS E 113 " ideal model delta sigma weight residual 1.321 1.336 -0.015 1.00e-02 1.00e+04 2.39e+00 ... (remaining 13283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 18759 1.79 - 3.58: 397 3.58 - 5.37: 27 5.37 - 7.17: 6 7.17 - 8.96: 3 Bond angle restraints: 19192 Sorted by residual: angle pdb=" CA GLN F 27 " pdb=" CB GLN F 27 " pdb=" CG GLN F 27 " ideal model delta sigma weight residual 114.10 120.72 -6.62 2.00e+00 2.50e-01 1.09e+01 angle pdb=" N GLY H 101 " pdb=" CA GLY H 101 " pdb=" C GLY H 101 " ideal model delta sigma weight residual 113.18 120.59 -7.41 2.37e+00 1.78e-01 9.77e+00 angle pdb=" CA GLU D 68 " pdb=" CB GLU D 68 " pdb=" CG GLU D 68 " ideal model delta sigma weight residual 114.10 119.86 -5.76 2.00e+00 2.50e-01 8.29e+00 angle pdb=" CA GLU C 64 " pdb=" CB GLU C 64 " pdb=" CG GLU C 64 " ideal model delta sigma weight residual 114.10 119.73 -5.63 2.00e+00 2.50e-01 7.93e+00 angle pdb=" CA HIS E 113 " pdb=" C HIS E 113 " pdb=" O HIS E 113 " ideal model delta sigma weight residual 120.55 117.63 2.92 1.06e+00 8.90e-01 7.58e+00 ... (remaining 19187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 5817 34.50 - 69.00: 1426 69.00 - 103.50: 17 103.50 - 138.00: 3 138.00 - 172.50: 1 Dihedral angle restraints: 7264 sinusoidal: 4874 harmonic: 2390 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 47.50 172.50 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 86.15 133.85 1 3.50e+01 8.16e-04 1.33e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 93.09 126.91 1 3.50e+01 8.16e-04 1.25e+01 ... (remaining 7261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1455 0.027 - 0.053: 536 0.053 - 0.080: 131 0.080 - 0.107: 48 0.107 - 0.133: 23 Chirality restraints: 2193 Sorted by residual: chirality pdb=" CB ILE D 86 " pdb=" CA ILE D 86 " pdb=" CG1 ILE D 86 " pdb=" CG2 ILE D 86 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 2190 not shown) Planarity restraints: 1426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE E 112 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.18e+00 pdb=" C ILE E 112 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE E 112 " -0.019 2.00e-02 2.50e+03 pdb=" N HIS E 113 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 80 " 0.012 2.00e-02 2.50e+03 1.24e-02 3.08e+00 pdb=" CG TYR H 80 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 80 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR H 80 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR H 80 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR H 80 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR H 80 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR H 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " -0.022 2.00e-02 2.50e+03 9.22e-03 2.55e+00 pdb=" N9 DG I 26 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.002 2.00e-02 2.50e+03 ... (remaining 1423 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 449 2.70 - 3.25: 10994 3.25 - 3.80: 22410 3.80 - 4.35: 26841 4.35 - 4.90: 39404 Nonbonded interactions: 100098 Sorted by model distance: nonbonded pdb=" N GLU H 102 " pdb=" OE1 GLU H 102 " model vdw 2.149 3.120 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 75 " model vdw 2.212 3.040 nonbonded pdb=" N GLU G 41 " pdb=" OE1 GLU G 41 " model vdw 2.232 3.120 nonbonded pdb=" OG1 THR F 82 " pdb=" OD2 ASP F 85 " model vdw 2.255 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 75 " model vdw 2.258 3.040 ... (remaining 100093 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 29 through 121) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.80 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 34.090 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13288 Z= 0.207 Angle : 0.593 8.958 19192 Z= 0.352 Chirality : 0.033 0.133 2193 Planarity : 0.004 0.034 1426 Dihedral : 27.639 172.505 5720 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.43 % Allowed : 24.86 % Favored : 74.71 % 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: 2.29 (0.30), residues: 806 helix: 2.56 (0.23), residues: 532 sheet: 1.56 (1.03), residues: 26 loop : -0.91 (0.39), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE E 78 TYR 0.029 0.001 TYR H 80 ARG 0.003 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 130 time to evaluate : 0.919 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8514 (tp30) cc_final: 0.8208 (tp30) REVERT: C 64 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8043 (tt0) REVERT: C 99 ARG cc_start: 0.7998 (mmt180) cc_final: 0.7426 (mtp85) REVERT: D 48 ASP cc_start: 0.9145 (p0) cc_final: 0.8562 (p0) REVERT: E 42 ARG cc_start: 0.8779 (mmm-85) cc_final: 0.8303 (mtp85) REVERT: G 95 LYS cc_start: 0.8517 (tptp) cc_final: 0.8116 (ttmm) REVERT: G 99 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.6968 (mtp85) REVERT: K 1 MET cc_start: 0.7299 (ppp) cc_final: 0.6868 (ppp) REVERT: K 48 LYS cc_start: 0.6017 (mmtt) cc_final: 0.5610 (mmtt) outliers start: 3 outliers final: 2 residues processed: 131 average time/residue: 0.3277 time to fit residues: 57.4581 Evaluate side-chains 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 118 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 50 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 0.0670 chunk 54 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 8.9990 overall best weight: 2.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN C 38 ASN E 68 GLN G 73 ASN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13288 Z= 0.281 Angle : 0.595 11.665 19192 Z= 0.352 Chirality : 0.035 0.136 2193 Planarity : 0.004 0.035 1426 Dihedral : 29.660 173.572 4087 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.02 % Allowed : 23.27 % Favored : 74.71 % 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: 2.48 (0.30), residues: 806 helix: 2.74 (0.22), residues: 540 sheet: 1.45 (1.05), residues: 26 loop : -1.03 (0.39), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE H 62 TYR 0.031 0.002 TYR H 80 ARG 0.006 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8576 (tp30) cc_final: 0.8240 (tp30) REVERT: C 64 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8083 (tt0) REVERT: D 48 ASP cc_start: 0.9197 (p0) cc_final: 0.8562 (p0) REVERT: F 27 GLN cc_start: 0.8957 (tp40) cc_final: 0.7961 (tm-30) REVERT: F 47 SER cc_start: 0.8927 (OUTLIER) cc_final: 0.8674 (t) REVERT: G 95 LYS cc_start: 0.8495 (tptp) cc_final: 0.8109 (ttmm) REVERT: G 99 ARG cc_start: 0.7732 (mmt-90) cc_final: 0.6912 (mtp85) REVERT: G 102 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8187 (mt) REVERT: H 117 LYS cc_start: 0.8804 (tptm) cc_final: 0.8348 (ttpt) REVERT: K 67 LEU cc_start: 0.9354 (tt) cc_final: 0.8725 (mp) outliers start: 14 outliers final: 6 residues processed: 134 average time/residue: 0.2782 time to fit residues: 51.9474 Evaluate side-chains 120 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 96 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS F 25 ASN H 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.054 13288 Z= 0.399 Angle : 0.652 11.896 19192 Z= 0.384 Chirality : 0.038 0.141 2193 Planarity : 0.005 0.037 1426 Dihedral : 29.729 175.204 4085 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.06 % Allowed : 21.97 % Favored : 72.98 % 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: 2.01 (0.30), residues: 806 helix: 2.48 (0.22), residues: 533 sheet: 1.26 (1.03), residues: 26 loop : -1.37 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS H 79 PHE 0.013 0.002 PHE H 62 TYR 0.045 0.002 TYR H 80 ARG 0.005 0.001 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 115 time to evaluate : 0.915 Fit side-chains REVERT: A 105 GLU cc_start: 0.8570 (tp30) cc_final: 0.8189 (tp30) REVERT: B 93 GLN cc_start: 0.8301 (OUTLIER) cc_final: 0.7549 (mt0) REVERT: C 64 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8138 (tt0) REVERT: C 91 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7489 (tm-30) REVERT: C 92 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8548 (mm-30) REVERT: D 29 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8553 (p) REVERT: D 39 TYR cc_start: 0.8175 (t80) cc_final: 0.7885 (t80) REVERT: G 95 LYS cc_start: 0.8617 (tptp) cc_final: 0.8259 (ttmm) REVERT: G 99 ARG cc_start: 0.7774 (mmt-90) cc_final: 0.6964 (mtp85) outliers start: 35 outliers final: 21 residues processed: 142 average time/residue: 0.2776 time to fit residues: 54.5738 Evaluate side-chains 133 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 4 PHE Chi-restraints excluded: chain K residue 25 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13288 Z= 0.194 Angle : 0.562 9.384 19192 Z= 0.335 Chirality : 0.033 0.127 2193 Planarity : 0.004 0.036 1426 Dihedral : 29.594 177.034 4085 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.32 % Allowed : 25.58 % Favored : 71.10 % 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: 2.70 (0.30), residues: 806 helix: 2.91 (0.22), residues: 542 sheet: 1.39 (1.06), residues: 26 loop : -0.98 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 79 PHE 0.010 0.001 PHE H 67 TYR 0.027 0.001 TYR H 80 ARG 0.008 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8599 (tp30) cc_final: 0.8214 (tp30) REVERT: B 93 GLN cc_start: 0.7807 (OUTLIER) cc_final: 0.7042 (mt0) REVERT: C 64 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8144 (tt0) REVERT: D 39 TYR cc_start: 0.7912 (t80) cc_final: 0.7704 (t80) REVERT: F 47 SER cc_start: 0.8731 (OUTLIER) cc_final: 0.8454 (t) REVERT: G 95 LYS cc_start: 0.8511 (tptp) cc_final: 0.8125 (ttmm) REVERT: G 99 ARG cc_start: 0.7778 (mmt-90) cc_final: 0.6967 (mtp85) outliers start: 23 outliers final: 11 residues processed: 140 average time/residue: 0.2832 time to fit residues: 54.9099 Evaluate side-chains 128 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 115 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 47 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 115 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 38 ASN H 92 GLN ** K 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 13288 Z= 0.363 Angle : 0.620 10.004 19192 Z= 0.367 Chirality : 0.037 0.138 2193 Planarity : 0.004 0.037 1426 Dihedral : 29.645 179.260 4085 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.05 % Allowed : 25.14 % Favored : 70.81 % 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: 2.31 (0.30), residues: 806 helix: 2.69 (0.22), residues: 539 sheet: 0.74 (1.03), residues: 26 loop : -1.23 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS F 75 PHE 0.012 0.002 PHE H 62 TYR 0.047 0.002 TYR H 80 ARG 0.012 0.001 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 118 time to evaluate : 0.978 Fit side-chains REVERT: A 105 GLU cc_start: 0.8570 (tp30) cc_final: 0.8176 (tp30) REVERT: B 93 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7477 (mt0) REVERT: C 64 GLU cc_start: 0.8508 (tm-30) cc_final: 0.8163 (tt0) REVERT: C 77 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8065 (mtt180) REVERT: C 91 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7417 (tm-30) REVERT: C 92 GLU cc_start: 0.8845 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 99 ARG cc_start: 0.7856 (mmt180) cc_final: 0.7306 (mtp85) REVERT: D 39 TYR cc_start: 0.8122 (t80) cc_final: 0.7800 (t80) REVERT: G 95 LYS cc_start: 0.8608 (tptp) cc_final: 0.8232 (ttmm) REVERT: G 99 ARG cc_start: 0.7779 (mmt-90) cc_final: 0.6970 (mtp85) outliers start: 28 outliers final: 17 residues processed: 136 average time/residue: 0.3147 time to fit residues: 57.8358 Evaluate side-chains 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 102 optimal weight: 0.0070 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN K 31 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13288 Z= 0.180 Angle : 0.551 8.024 19192 Z= 0.329 Chirality : 0.033 0.129 2193 Planarity : 0.004 0.039 1426 Dihedral : 29.546 179.972 4085 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.75 % Allowed : 25.87 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.31), residues: 806 helix: 3.04 (0.22), residues: 545 sheet: 0.48 (0.99), residues: 26 loop : -0.96 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.009 0.001 PHE H 67 TYR 0.022 0.001 TYR F 88 ARG 0.003 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.001 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8573 (tp30) cc_final: 0.8190 (tp30) REVERT: B 93 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: C 64 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8148 (tt0) REVERT: E 73 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8265 (tt0) REVERT: F 84 MET cc_start: 0.8546 (mmm) cc_final: 0.8153 (mmt) REVERT: G 95 LYS cc_start: 0.8536 (tptp) cc_final: 0.8140 (ttmm) REVERT: G 99 ARG cc_start: 0.7813 (mmt-90) cc_final: 0.6992 (mtp85) REVERT: K 1 MET cc_start: 0.7233 (ppp) cc_final: 0.6652 (ppp) outliers start: 19 outliers final: 11 residues processed: 133 average time/residue: 0.2779 time to fit residues: 51.4636 Evaluate side-chains 127 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 115 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 102 optimal weight: 0.3980 chunk 63 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** 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: 0.8336 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13288 Z= 0.252 Angle : 0.573 8.308 19192 Z= 0.341 Chirality : 0.034 0.135 2193 Planarity : 0.004 0.041 1426 Dihedral : 29.549 177.535 4085 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.32 % Allowed : 25.43 % Favored : 71.24 % 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: 2.61 (0.30), residues: 806 helix: 2.92 (0.22), residues: 543 sheet: 0.38 (0.98), residues: 26 loop : -1.11 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.010 0.001 PHE H 62 TYR 0.028 0.002 TYR H 80 ARG 0.002 0.000 ARG K 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.994 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8570 (tp30) cc_final: 0.8184 (tp30) REVERT: B 79 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8005 (mttp) REVERT: B 93 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7220 (mt0) REVERT: C 64 GLU cc_start: 0.8516 (tm-30) cc_final: 0.8188 (tt0) REVERT: C 77 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.7937 (mtm-85) REVERT: C 91 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7435 (tm-30) REVERT: C 92 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8643 (mm-30) REVERT: D 29 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (p) REVERT: E 73 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8276 (tt0) REVERT: G 95 LYS cc_start: 0.8528 (tptp) cc_final: 0.8127 (ttmm) REVERT: G 99 ARG cc_start: 0.7775 (mmt-90) cc_final: 0.6992 (mtp85) REVERT: H 79 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6681 (t-90) REVERT: K 1 MET cc_start: 0.7446 (ppp) cc_final: 0.7066 (ppp) outliers start: 23 outliers final: 15 residues processed: 132 average time/residue: 0.2922 time to fit residues: 52.6171 Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** 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: 0.8283 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13288 Z= 0.185 Angle : 0.554 8.046 19192 Z= 0.330 Chirality : 0.032 0.129 2193 Planarity : 0.004 0.042 1426 Dihedral : 29.477 178.504 4085 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.89 % Allowed : 26.01 % Favored : 71.10 % 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: 2.82 (0.31), residues: 806 helix: 3.08 (0.22), residues: 543 sheet: 0.47 (1.04), residues: 26 loop : -1.02 (0.41), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE K 4 TYR 0.041 0.001 TYR F 88 ARG 0.005 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.903 Fit side-chains REVERT: A 105 GLU cc_start: 0.8567 (tp30) cc_final: 0.8201 (tp30) REVERT: B 79 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7967 (mttp) REVERT: B 93 GLN cc_start: 0.7554 (OUTLIER) cc_final: 0.6856 (mt0) REVERT: C 64 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8151 (tt0) REVERT: C 92 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8606 (mm-30) REVERT: D 29 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8535 (p) REVERT: E 73 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8266 (tt0) REVERT: G 95 LYS cc_start: 0.8484 (tptp) cc_final: 0.8063 (ttmm) REVERT: G 99 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.6968 (mtp85) REVERT: H 79 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.6490 (t-90) REVERT: K 1 MET cc_start: 0.7239 (ppp) cc_final: 0.6654 (ppp) outliers start: 20 outliers final: 14 residues processed: 134 average time/residue: 0.2830 time to fit residues: 52.7674 Evaluate side-chains 134 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 0.1980 chunk 86 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 8.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** 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: 0.8402 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 13288 Z= 0.467 Angle : 0.679 9.530 19192 Z= 0.397 Chirality : 0.040 0.143 2193 Planarity : 0.005 0.036 1426 Dihedral : 29.629 175.565 4085 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.32 % Allowed : 25.43 % Favored : 71.24 % 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: 1.97 (0.30), residues: 806 helix: 2.46 (0.21), residues: 541 sheet: 0.04 (1.03), residues: 26 loop : -1.40 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.015 0.002 PHE H 62 TYR 0.028 0.003 TYR D 80 ARG 0.004 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8550 (tp30) cc_final: 0.8157 (tp30) REVERT: B 79 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8044 (mttp) REVERT: B 93 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7596 (mt0) REVERT: C 64 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8198 (tt0) REVERT: C 77 ARG cc_start: 0.8568 (OUTLIER) cc_final: 0.8036 (mtt180) REVERT: C 91 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 92 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8685 (mm-30) REVERT: C 99 ARG cc_start: 0.7890 (mmt180) cc_final: 0.7308 (mtp85) REVERT: D 29 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8579 (p) REVERT: E 73 GLU cc_start: 0.8690 (tm-30) cc_final: 0.8464 (tm-30) REVERT: G 95 LYS cc_start: 0.8576 (tptp) cc_final: 0.8203 (ttmm) REVERT: G 99 ARG cc_start: 0.7778 (mmt-90) cc_final: 0.6990 (mtp85) REVERT: H 79 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6818 (t-90) REVERT: H 82 LYS cc_start: 0.9124 (tppp) cc_final: 0.8912 (tptp) outliers start: 23 outliers final: 17 residues processed: 131 average time/residue: 0.3136 time to fit residues: 55.1062 Evaluate side-chains 135 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain K residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** 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: 0.8359 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13288 Z= 0.277 Angle : 0.595 8.506 19192 Z= 0.354 Chirality : 0.035 0.137 2193 Planarity : 0.004 0.042 1426 Dihedral : 29.590 178.782 4085 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.32 % Allowed : 25.58 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.30), residues: 806 helix: 2.74 (0.22), residues: 540 sheet: -0.62 (0.98), residues: 27 loop : -1.39 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS F 75 PHE 0.008 0.001 PHE H 62 TYR 0.025 0.002 TYR H 80 ARG 0.001 0.000 ARG G 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1612 Ramachandran restraints generated. 806 Oldfield, 0 Emsley, 806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8555 (tp30) cc_final: 0.8169 (tp30) REVERT: B 79 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7987 (mttp) REVERT: B 93 GLN cc_start: 0.7995 (OUTLIER) cc_final: 0.7303 (mt0) REVERT: C 64 GLU cc_start: 0.8454 (tm-30) cc_final: 0.8151 (tt0) REVERT: C 77 ARG cc_start: 0.8547 (OUTLIER) cc_final: 0.8054 (mtt180) REVERT: C 92 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8643 (mm-30) REVERT: D 29 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8591 (p) REVERT: E 73 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8270 (tt0) REVERT: G 95 LYS cc_start: 0.8560 (tptp) cc_final: 0.8163 (ttmm) REVERT: G 99 ARG cc_start: 0.7827 (mmt-90) cc_final: 0.7018 (mtp85) REVERT: H 79 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6553 (t-90) REVERT: K 1 MET cc_start: 0.7485 (ppp) cc_final: 0.6990 (ppp) outliers start: 23 outliers final: 16 residues processed: 131 average time/residue: 0.3100 time to fit residues: 55.4887 Evaluate side-chains 136 residues out of total 692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain H residue 79 HIS Chi-restraints excluded: chain H residue 80 TYR Chi-restraints excluded: chain K residue 4 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 92 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.097833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.065631 restraints weight = 33665.054| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.32 r_work: 0.2791 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13288 Z= 0.193 Angle : 0.571 9.633 19192 Z= 0.338 Chirality : 0.033 0.129 2193 Planarity : 0.004 0.042 1426 Dihedral : 29.487 178.109 4085 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.60 % Allowed : 26.73 % Favored : 70.66 % 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: 2.60 (0.31), residues: 806 helix: 2.99 (0.22), residues: 541 sheet: -0.32 (1.06), residues: 27 loop : -1.20 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 75 PHE 0.009 0.001 PHE K 4 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG H 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2271.63 seconds wall clock time: 42 minutes 15.53 seconds (2535.53 seconds total)