Starting phenix.real_space_refine on Sat Jul 4 05:34:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afn_11771/07_2026/7afn_11771.map" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 11 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18520 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.15, per 1000 atoms: 0.17 Number of scatterers: 18520 At special positions: 0 Unit cell: (121.52, 146.475, 125.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 11 11.99 O 4730 8.00 N 3449 7.00 C 9845 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: 1.40 Conformation dependent library (CDL) restraints added in 340.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 9 sheets defined 49.7% alpha, 14.1% beta 146 base pairs and 207 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.653A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 25 through 51 removed outlier: 4.288A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA C 50 " --> pdb=" O GLU C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 95 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.541A pdb=" N SER G 41 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL G 43 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.303A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 106 removed outlier: 3.664A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 110 Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.537A pdb=" N ARG G 119 " --> pdb=" O SER G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 135 through 140 Processing helix chain 'G' and resid 140 through 148 removed outlier: 4.629A pdb=" N GLU G 146 " --> pdb=" O HIS G 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 56 removed outlier: 3.855A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 93 through 102 removed outlier: 4.446A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 90 removed outlier: 3.710A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 Processing helix chain 'M' and resid 65 through 83 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.849A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TYR N 20 " --> pdb=" O LEU N 16 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.705A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 70 through 75 removed outlier: 4.323A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 70 through 75' Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.617A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 171 removed outlier: 6.674A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.119A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 40 through 41 Processing sheet with id=AA8, first strand: chain 'J' and resid 45 through 52 Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.326A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 364 hydrogen bonds 578 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 207 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2050 1.31 - 1.43: 7783 1.43 - 1.56: 9000 1.56 - 1.69: 914 1.69 - 1.82: 54 Bond restraints: 19801 Sorted by residual: bond pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 1.607 1.738 -0.131 1.50e-02 4.44e+03 7.57e+01 bond pdb=" N9 A 11188 " pdb=" C4 A 11188 " ideal model delta sigma weight residual 1.374 1.344 0.030 6.00e-03 2.78e+04 2.43e+01 bond pdb=" N PHE S 41 " pdb=" CA PHE S 41 " ideal model delta sigma weight residual 1.455 1.487 -0.032 7.00e-03 2.04e+04 2.03e+01 bond pdb=" CA ALA S 75 " pdb=" C ALA S 75 " ideal model delta sigma weight residual 1.524 1.572 -0.048 1.08e-02 8.57e+03 1.98e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.467 -0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 27519 2.33 - 4.66: 1334 4.66 - 6.99: 76 6.99 - 9.32: 16 9.32 - 11.65: 4 Bond angle restraints: 28949 Sorted by residual: angle pdb=" O2 C 11210 " pdb=" C2 C 11210 " pdb=" N3 C 11210 " ideal model delta sigma weight residual 121.90 116.42 5.48 7.00e-01 2.04e+00 6.13e+01 angle pdb=" C3' G 1 963 " pdb=" O3' G 1 963 " pdb=" P A 1 964 " ideal model delta sigma weight residual 120.20 108.55 11.65 1.50e+00 4.44e-01 6.04e+01 angle pdb=" O3' U 11240 " pdb=" C3' U 11240 " pdb=" C2' U 11240 " ideal model delta sigma weight residual 109.50 119.53 -10.03 1.50e+00 4.44e-01 4.47e+01 angle pdb=" N ARG S 55 " pdb=" CA ARG S 55 " pdb=" C ARG S 55 " ideal model delta sigma weight residual 113.97 106.22 7.75 1.28e+00 6.10e-01 3.67e+01 angle pdb=" CA GLY I 69 " pdb=" C GLY I 69 " pdb=" O GLY I 69 " ideal model delta sigma weight residual 122.29 117.69 4.60 8.10e-01 1.52e+00 3.22e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 11218 35.18 - 70.35: 1261 70.35 - 105.53: 157 105.53 - 140.70: 11 140.70 - 175.88: 4 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 Sorted by residual: dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 5.09 -165.09 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 59.96 140.04 1 1.50e+01 4.44e-03 7.54e+01 dihedral pdb=" O4' U 11168 " pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sinusoidal sigma weight residual 232.00 56.12 175.88 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.119: 3245 0.119 - 0.237: 348 0.237 - 0.355: 15 0.355 - 0.474: 0 0.474 - 0.592: 1 Chirality restraints: 3609 Sorted by residual: chirality pdb=" CA ASN M 105 " pdb=" N ASN M 105 " pdb=" C ASN M 105 " pdb=" CB ASN M 105 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.77e+00 chirality pdb=" CA ILE C 68 " pdb=" N ILE C 68 " pdb=" C ILE C 68 " pdb=" CB ILE C 68 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" C3' A 1 964 " pdb=" C4' A 1 964 " pdb=" O3' A 1 964 " pdb=" C2' A 1 964 " both_signs ideal model delta sigma weight residual False -2.48 -2.80 0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " 0.018 2.00e-02 2.50e+03 2.71e-02 2.39e+01 pdb=" N9 2MG 1 966 " 0.002 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " -0.014 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " -0.019 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " -0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " -0.000 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " -0.015 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " 0.014 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " 0.026 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " 0.039 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " 0.023 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " 0.007 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 59 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO C 60 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 189 " -0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ALA C 189 " 0.069 2.00e-02 2.50e+03 pdb=" O ALA C 189 " -0.026 2.00e-02 2.50e+03 pdb=" N HIS C 190 " -0.023 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 149 2.38 - 3.01: 11542 3.01 - 3.64: 37141 3.64 - 4.27: 54017 4.27 - 4.90: 74306 Nonbonded interactions: 177155 Sorted by model distance: nonbonded pdb=" O5' C 11366 " pdb="MG MG 11606 " model vdw 1.755 2.170 nonbonded pdb=" O2' G 11242 " pdb="MG MG 11610 " model vdw 1.810 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.823 2.170 nonbonded pdb=" O5' A 11238 " pdb="MG MG 11611 " model vdw 1.825 2.170 nonbonded pdb=" OP2 A 11238 " pdb="MG MG 11611 " model vdw 1.856 2.170 ... (remaining 177150 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.680 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.152 19802 Z= 0.696 Angle : 1.024 11.653 28949 Z= 0.813 Chirality : 0.068 0.592 3609 Planarity : 0.006 0.101 1995 Dihedral : 23.442 175.877 10599 Min Nonbonded Distance : 1.755 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 9.45 % Favored : 90.55 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.25), residues: 1092 helix: -0.85 (0.24), residues: 487 sheet: -1.11 (0.39), residues: 160 loop : -1.69 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 138 TYR 0.016 0.002 TYR M 23 PHE 0.025 0.002 PHE S 74 TRP 0.011 0.002 TRP N 101 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00823 / 0.70 (19801) covalent geometry : angle 1.02395 / 0.81 (28949) hydrogen bonds : bond 0.18020 / 18.43 ( 798) hydrogen bonds : angle 7.52815 / 9.51 ( 1823) metal coordination : bond 0.15162 / 7.58 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 282 time to evaluate : 0.359 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 MET cc_start: 0.9303 (mmm) cc_final: 0.8895 (tpp) REVERT: C 153 VAL cc_start: 0.9634 (m) cc_final: 0.9370 (m) REVERT: C 170 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8323 (tm-30) REVERT: C 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8257 (t0) REVERT: G 31 MET cc_start: 0.8782 (ttp) cc_final: 0.8415 (ttp) REVERT: G 38 THR cc_start: 0.9231 (t) cc_final: 0.9029 (t) REVERT: I 7 TYR cc_start: 0.7518 (p90) cc_final: 0.7304 (p90) REVERT: J 10 LEU cc_start: 0.9605 (mt) cc_final: 0.9395 (mm) REVERT: J 19 ASP cc_start: 0.9221 (m-30) cc_final: 0.8885 (m-30) REVERT: J 50 THR cc_start: 0.9396 (m) cc_final: 0.8327 (p) REVERT: J 63 ASP cc_start: 0.9308 (t0) cc_final: 0.8830 (t0) REVERT: M 23 TYR cc_start: 0.8794 (t80) cc_final: 0.8325 (t80) REVERT: M 75 MET cc_start: 0.9398 (mmp) cc_final: 0.9180 (mmm) REVERT: M 78 LYS cc_start: 0.9383 (tptp) cc_final: 0.8379 (tptp) REVERT: N 89 MET cc_start: 0.9440 (mmp) cc_final: 0.9159 (mmm) REVERT: S 66 MET cc_start: 0.9245 (mtp) cc_final: 0.8709 (mtp) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.1483 time to fit residues: 60.4420 Evaluate side-chains 142 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS C 32 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN I 110 GLN J 4 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.028533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.022648 restraints weight = 222093.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.023384 restraints weight = 97708.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.023832 restraints weight = 59464.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.024140 restraints weight = 44399.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.024280 restraints weight = 37246.953| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19802 Z= 0.191 Angle : 0.667 8.733 28949 Z= 0.385 Chirality : 0.043 0.301 3609 Planarity : 0.006 0.063 1995 Dihedral : 24.344 171.323 8374 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.82 % Allowed : 18.02 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.24), residues: 1092 helix: -0.42 (0.22), residues: 507 sheet: -0.74 (0.40), residues: 164 loop : -1.13 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 72 TYR 0.036 0.002 TYR C 42 PHE 0.032 0.003 PHE B 126 TRP 0.014 0.001 TRP C 201 HIS 0.016 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (19801) covalent geometry : angle 0.66657 / 0.38 (28949) hydrogen bonds : bond 0.08996 / 9.12 ( 798) hydrogen bonds : angle 5.23392 / 6.54 ( 1823) metal coordination : bond 0.01231 / 0.62 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 163 time to evaluate : 0.365 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: symmetry clash revert: symmetry clash REVERT: B 91 PHE cc_start: 0.8337 (p90) cc_final: 0.8049 (p90) REVERT: B 122 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8342 (tm-30) REVERT: C 100 GLN cc_start: 0.7864 (tm-30) cc_final: 0.5686 (tm-30) REVERT: C 129 MET cc_start: 0.9287 (mmm) cc_final: 0.8829 (tpp) REVERT: C 134 MET cc_start: 0.9621 (ptp) cc_final: 0.9194 (ppp) REVERT: C 142 MET cc_start: 0.9353 (mmm) cc_final: 0.8562 (mmm) REVERT: C 170 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8682 (tm-30) REVERT: C 183 ASP cc_start: 0.8482 (t0) cc_final: 0.8227 (t0) REVERT: C 211 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.8010 (mmm) REVERT: G 31 MET cc_start: 0.8904 (ttp) cc_final: 0.8430 (ttp) REVERT: G 38 THR cc_start: 0.9194 (t) cc_final: 0.8914 (t) REVERT: I 42 GLU cc_start: 0.8912 (pm20) cc_final: 0.8706 (pp20) REVERT: I 118 LEU cc_start: 0.9459 (mt) cc_final: 0.9205 (mt) REVERT: J 19 ASP cc_start: 0.9193 (m-30) cc_final: 0.8955 (m-30) REVERT: J 46 LYS cc_start: 0.9385 (mptt) cc_final: 0.9137 (mmtm) REVERT: J 63 ASP cc_start: 0.9314 (t0) cc_final: 0.8852 (t0) REVERT: J 66 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8369 (tm-30) REVERT: M 23 TYR cc_start: 0.8813 (t80) cc_final: 0.8353 (t80) REVERT: M 78 LYS cc_start: 0.9367 (tptp) cc_final: 0.8872 (tptp) REVERT: N 82 ILE cc_start: 0.9374 (mt) cc_final: 0.8752 (mm) REVERT: N 89 MET cc_start: 0.9372 (mmp) cc_final: 0.8888 (mmt) REVERT: S 41 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.8781 (m-80) REVERT: S 66 MET cc_start: 0.9366 (mtp) cc_final: 0.8901 (mtp) outliers start: 26 outliers final: 10 residues processed: 177 average time/residue: 0.1178 time to fit residues: 32.5721 Evaluate side-chains 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 134 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain S residue 41 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 118 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 177 ASN B 227 GLN G 52 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN J 56 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.027811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.021989 restraints weight = 226522.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.022731 restraints weight = 99573.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.023189 restraints weight = 60439.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.023458 restraints weight = 44959.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.023629 restraints weight = 37462.861| |-----------------------------------------------------------------------------| r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 19802 Z= 0.196 Angle : 0.594 8.608 28949 Z= 0.345 Chirality : 0.040 0.299 3609 Planarity : 0.005 0.051 1995 Dihedral : 24.155 176.836 8374 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.58 % Allowed : 20.09 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.24), residues: 1092 helix: 0.04 (0.22), residues: 502 sheet: -0.82 (0.39), residues: 165 loop : -0.92 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG S 32 TYR 0.021 0.002 TYR C 168 PHE 0.048 0.002 PHE B 16 TRP 0.011 0.001 TRP C 201 HIS 0.011 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 (19801) covalent geometry : angle 0.59428 / 0.34 (28949) hydrogen bonds : bond 0.08365 / 8.34 ( 798) hydrogen bonds : angle 4.92361 / 6.23 ( 1823) metal coordination : bond 0.00007 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.297 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: B 122 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8396 (tm-30) REVERT: C 29 PHE cc_start: 0.9463 (t80) cc_final: 0.9223 (t80) REVERT: C 129 MET cc_start: 0.9237 (mmm) cc_final: 0.8821 (tpp) REVERT: C 134 MET cc_start: 0.9646 (ptp) cc_final: 0.9224 (ppp) REVERT: C 142 MET cc_start: 0.9395 (mmm) cc_final: 0.8542 (mmp) REVERT: C 170 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8649 (tm-30) REVERT: C 183 ASP cc_start: 0.8609 (t0) cc_final: 0.8374 (t0) REVERT: C 211 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8116 (mmt) REVERT: G 31 MET cc_start: 0.8865 (ttp) cc_final: 0.8330 (ttp) REVERT: G 38 THR cc_start: 0.9353 (t) cc_final: 0.9087 (t) REVERT: G 71 PRO cc_start: 0.9137 (Cg_exo) cc_final: 0.8794 (Cg_endo) REVERT: I 42 GLU cc_start: 0.9062 (pm20) cc_final: 0.8680 (pp20) REVERT: I 46 MET cc_start: 0.9138 (mmm) cc_final: 0.8475 (mmm) REVERT: I 57 MET cc_start: 0.9446 (tpp) cc_final: 0.8984 (tmm) REVERT: J 19 ASP cc_start: 0.9245 (m-30) cc_final: 0.9012 (m-30) REVERT: J 46 LYS cc_start: 0.9388 (mptt) cc_final: 0.9133 (mmtm) REVERT: J 63 ASP cc_start: 0.9273 (t0) cc_final: 0.8849 (t70) REVERT: M 23 TYR cc_start: 0.8823 (t80) cc_final: 0.8229 (t80) REVERT: M 27 LYS cc_start: 0.9624 (tptt) cc_final: 0.9180 (tppt) REVERT: M 31 LYS cc_start: 0.9517 (pttp) cc_final: 0.9224 (mtmm) REVERT: M 78 LYS cc_start: 0.9430 (tptp) cc_final: 0.9184 (tppt) REVERT: M 81 MET cc_start: 0.8958 (ppp) cc_final: 0.8202 (ppp) REVERT: N 86 GLU cc_start: 0.9433 (mp0) cc_final: 0.9218 (mp0) REVERT: N 89 MET cc_start: 0.9402 (mmp) cc_final: 0.8897 (mmt) REVERT: S 41 PHE cc_start: 0.8977 (OUTLIER) cc_final: 0.8663 (m-80) REVERT: S 66 MET cc_start: 0.9348 (mtp) cc_final: 0.8857 (mtp) outliers start: 33 outliers final: 19 residues processed: 165 average time/residue: 0.1192 time to fit residues: 30.5547 Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 133 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 41 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 136 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 32 GLN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.027139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.021270 restraints weight = 228557.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.021980 restraints weight = 100927.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.022406 restraints weight = 61417.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.022713 restraints weight = 45946.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022855 restraints weight = 38317.467| |-----------------------------------------------------------------------------| r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19802 Z= 0.233 Angle : 0.602 8.797 28949 Z= 0.349 Chirality : 0.039 0.303 3609 Planarity : 0.005 0.046 1995 Dihedral : 24.069 178.204 8374 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.91 % Allowed : 20.74 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.24), residues: 1092 helix: 0.12 (0.22), residues: 512 sheet: -0.85 (0.38), residues: 165 loop : -0.96 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 111 TYR 0.025 0.002 TYR C 168 PHE 0.015 0.002 PHE B 126 TRP 0.040 0.003 TRP G 103 HIS 0.010 0.002 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.23 (19801) covalent geometry : angle 0.60221 / 0.35 (28949) hydrogen bonds : bond 0.08473 / 8.51 ( 798) hydrogen bonds : angle 4.83300 / 6.18 ( 1823) metal coordination : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.386 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: B 122 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8561 (tm-30) REVERT: B 168 HIS cc_start: 0.9484 (t-90) cc_final: 0.9178 (t-170) REVERT: C 25 ASN cc_start: 0.9370 (m-40) cc_final: 0.9100 (m-40) REVERT: C 129 MET cc_start: 0.9267 (mmm) cc_final: 0.8826 (tpp) REVERT: C 134 MET cc_start: 0.9653 (ptp) cc_final: 0.9217 (ppp) REVERT: C 142 MET cc_start: 0.9401 (mmm) cc_final: 0.8932 (mmp) REVERT: C 183 ASP cc_start: 0.8564 (t0) cc_final: 0.8285 (t0) REVERT: C 211 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8232 (mmm) REVERT: G 29 ILE cc_start: 0.9601 (mm) cc_final: 0.9334 (tt) REVERT: G 31 MET cc_start: 0.8900 (ttp) cc_final: 0.8297 (ttp) REVERT: G 38 THR cc_start: 0.9469 (t) cc_final: 0.9247 (t) REVERT: G 103 TRP cc_start: 0.9679 (m-10) cc_final: 0.9310 (m100) REVERT: I 42 GLU cc_start: 0.9139 (pm20) cc_final: 0.8582 (pp20) REVERT: I 46 MET cc_start: 0.9225 (mmm) cc_final: 0.8629 (mmm) REVERT: I 57 MET cc_start: 0.9428 (tpp) cc_final: 0.9163 (tpp) REVERT: I 65 ILE cc_start: 0.9508 (pt) cc_final: 0.9078 (mm) REVERT: I 118 LEU cc_start: 0.9471 (mt) cc_final: 0.9230 (mt) REVERT: J 19 ASP cc_start: 0.9274 (m-30) cc_final: 0.9070 (m-30) REVERT: J 63 ASP cc_start: 0.9262 (t0) cc_final: 0.8796 (t0) REVERT: M 23 TYR cc_start: 0.8564 (t80) cc_final: 0.8180 (t80) REVERT: M 27 LYS cc_start: 0.9548 (tptt) cc_final: 0.8937 (tppt) REVERT: M 31 LYS cc_start: 0.9421 (pttp) cc_final: 0.9074 (pttp) REVERT: M 53 ILE cc_start: 0.9524 (OUTLIER) cc_final: 0.9317 (mp) REVERT: M 78 LYS cc_start: 0.9350 (tptp) cc_final: 0.8878 (tptp) REVERT: N 74 LEU cc_start: 0.9458 (mm) cc_final: 0.9224 (mm) REVERT: N 89 MET cc_start: 0.9439 (mmp) cc_final: 0.9037 (mmt) REVERT: S 66 MET cc_start: 0.9304 (mtp) cc_final: 0.8738 (mtp) outliers start: 36 outliers final: 24 residues processed: 160 average time/residue: 0.1128 time to fit residues: 28.3735 Evaluate side-chains 148 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 20.0000 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 178 ASN G 52 GLN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.027231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2588 r_free = 0.2588 target = 0.021471 restraints weight = 224677.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.022187 restraints weight = 99285.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022636 restraints weight = 60497.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.022923 restraints weight = 45190.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.023092 restraints weight = 37624.747| |-----------------------------------------------------------------------------| r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19802 Z= 0.177 Angle : 0.564 8.436 28949 Z= 0.328 Chirality : 0.038 0.290 3609 Planarity : 0.005 0.062 1995 Dihedral : 24.001 179.437 8374 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.34 % Allowed : 21.50 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.24), residues: 1092 helix: 0.25 (0.22), residues: 502 sheet: -0.72 (0.39), residues: 165 loop : -0.81 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 65 TYR 0.025 0.002 TYR C 168 PHE 0.015 0.002 PHE I 127 TRP 0.020 0.002 TRP G 103 HIS 0.006 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.18 (19801) covalent geometry : angle 0.56353 / 0.33 (28949) hydrogen bonds : bond 0.07455 / 7.47 ( 798) hydrogen bonds : angle 4.65078 / 5.94 ( 1823) metal coordination : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 134 time to evaluate : 0.307 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: C 25 ASN cc_start: 0.9372 (m-40) cc_final: 0.9119 (m-40) REVERT: C 129 MET cc_start: 0.9244 (mmm) cc_final: 0.8818 (tpp) REVERT: C 183 ASP cc_start: 0.8551 (t0) cc_final: 0.8261 (t0) REVERT: G 29 ILE cc_start: 0.9629 (mm) cc_final: 0.9341 (tt) REVERT: G 31 MET cc_start: 0.8966 (ttp) cc_final: 0.8252 (ttp) REVERT: G 38 THR cc_start: 0.9523 (t) cc_final: 0.9313 (t) REVERT: G 103 TRP cc_start: 0.9696 (m-10) cc_final: 0.9185 (m100) REVERT: I 42 GLU cc_start: 0.9188 (pm20) cc_final: 0.8597 (pp20) REVERT: I 46 MET cc_start: 0.9225 (mmm) cc_final: 0.8516 (mmm) REVERT: I 57 MET cc_start: 0.9445 (tpp) cc_final: 0.9197 (tpp) REVERT: I 65 ILE cc_start: 0.9534 (pt) cc_final: 0.9105 (mm) REVERT: J 63 ASP cc_start: 0.9249 (t0) cc_final: 0.8816 (t0) REVERT: M 23 TYR cc_start: 0.8669 (t80) cc_final: 0.8173 (t80) REVERT: M 78 LYS cc_start: 0.9402 (tptp) cc_final: 0.9142 (tptm) REVERT: N 6 MET cc_start: 0.8839 (mmt) cc_final: 0.8526 (mmp) REVERT: N 41 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8795 (ptp-110) REVERT: N 74 LEU cc_start: 0.9480 (mm) cc_final: 0.9274 (mm) REVERT: N 89 MET cc_start: 0.9426 (mmp) cc_final: 0.9072 (mmt) REVERT: S 66 MET cc_start: 0.9344 (mtp) cc_final: 0.8867 (mtp) outliers start: 40 outliers final: 27 residues processed: 159 average time/residue: 0.1162 time to fit residues: 29.1645 Evaluate side-chains 148 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 95 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 chunk 105 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 86 optimal weight: 9.9990 chunk 148 optimal weight: 0.0570 chunk 39 optimal weight: 10.0000 overall best weight: 6.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 ASN B 120 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.026100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.020458 restraints weight = 235911.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.021130 restraints weight = 105213.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2580 r_free = 0.2580 target = 0.021516 restraints weight = 65114.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.021821 restraints weight = 49366.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.021945 restraints weight = 41609.611| |-----------------------------------------------------------------------------| r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19802 Z= 0.344 Angle : 0.673 8.696 28949 Z= 0.388 Chirality : 0.042 0.312 3609 Planarity : 0.006 0.062 1995 Dihedral : 24.034 178.254 8374 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 29.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.21 % Allowed : 22.69 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.24), residues: 1092 helix: 0.22 (0.22), residues: 506 sheet: -0.98 (0.39), residues: 167 loop : -0.86 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 172 TYR 0.026 0.003 TYR C 168 PHE 0.019 0.002 PHE S 41 TRP 0.010 0.002 TRP S 34 HIS 0.012 0.002 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.34 (19801) covalent geometry : angle 0.67272 / 0.39 (28949) hydrogen bonds : bond 0.10188 / 10.29 ( 798) hydrogen bonds : angle 4.98275 / 6.38 ( 1823) metal coordination : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 0.455 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: B 27 MET cc_start: 0.5697 (OUTLIER) cc_final: 0.5477 (mtp) REVERT: B 49 MET cc_start: 0.9002 (mmp) cc_final: 0.8747 (mmp) REVERT: B 146 ASN cc_start: 0.9510 (OUTLIER) cc_final: 0.9066 (p0) REVERT: B 168 HIS cc_start: 0.9478 (t-90) cc_final: 0.9212 (t-170) REVERT: C 25 ASN cc_start: 0.9368 (m-40) cc_final: 0.9136 (m-40) REVERT: C 129 MET cc_start: 0.9304 (mmm) cc_final: 0.8828 (tpp) REVERT: C 134 MET cc_start: 0.9621 (ptp) cc_final: 0.9198 (ppp) REVERT: C 183 ASP cc_start: 0.8559 (t0) cc_final: 0.8241 (t0) REVERT: G 29 ILE cc_start: 0.9599 (mm) cc_final: 0.9274 (tt) REVERT: G 31 MET cc_start: 0.9011 (ttp) cc_final: 0.8360 (ttp) REVERT: G 103 TRP cc_start: 0.9638 (m-10) cc_final: 0.9300 (m100) REVERT: I 65 ILE cc_start: 0.9543 (pt) cc_final: 0.9207 (mm) REVERT: I 118 LEU cc_start: 0.9472 (mt) cc_final: 0.9248 (mt) REVERT: J 63 ASP cc_start: 0.9206 (t0) cc_final: 0.8804 (t0) REVERT: M 27 LYS cc_start: 0.9449 (tptt) cc_final: 0.9182 (tppt) REVERT: M 78 LYS cc_start: 0.9335 (tptp) cc_final: 0.9024 (tptp) REVERT: N 6 MET cc_start: 0.8854 (mmt) cc_final: 0.8579 (mmp) REVERT: N 38 ASP cc_start: 0.9039 (OUTLIER) cc_final: 0.8790 (p0) REVERT: N 41 ARG cc_start: 0.9177 (OUTLIER) cc_final: 0.8787 (ptp90) REVERT: N 74 LEU cc_start: 0.9507 (mm) cc_final: 0.9286 (mm) REVERT: N 89 MET cc_start: 0.9456 (mmp) cc_final: 0.9054 (mmt) REVERT: S 66 MET cc_start: 0.9370 (mtp) cc_final: 0.8971 (mtp) outliers start: 48 outliers final: 31 residues processed: 155 average time/residue: 0.1158 time to fit residues: 28.2273 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain G residue 122 ASN Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 45 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain N residue 41 ARG Chi-restraints excluded: chain N residue 62 ASN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 45 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 146 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.021143 restraints weight = 228313.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.021869 restraints weight = 100238.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.022303 restraints weight = 61265.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.022605 restraints weight = 46357.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.022742 restraints weight = 38914.993| |-----------------------------------------------------------------------------| r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 19802 Z= 0.156 Angle : 0.571 9.252 28949 Z= 0.330 Chirality : 0.038 0.284 3609 Planarity : 0.005 0.040 1995 Dihedral : 23.989 177.985 8374 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.69 % Allowed : 24.43 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.25), residues: 1092 helix: 0.36 (0.22), residues: 511 sheet: -0.73 (0.40), residues: 164 loop : -0.73 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 85 TYR 0.023 0.002 TYR C 168 PHE 0.017 0.002 PHE S 41 TRP 0.016 0.002 TRP G 103 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.16 (19801) covalent geometry : angle 0.57145 / 0.33 (28949) hydrogen bonds : bond 0.07249 / 7.28 ( 798) hydrogen bonds : angle 4.69170 / 5.96 ( 1823) metal coordination : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 132 time to evaluate : 0.410 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: B 27 MET cc_start: 0.5712 (OUTLIER) cc_final: 0.5437 (mtp) REVERT: B 49 MET cc_start: 0.8983 (mmp) cc_final: 0.8687 (mmp) REVERT: B 122 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8160 (pp30) REVERT: C 25 ASN cc_start: 0.9376 (m-40) cc_final: 0.9136 (m-40) REVERT: C 129 MET cc_start: 0.9260 (mmm) cc_final: 0.8837 (tpp) REVERT: C 134 MET cc_start: 0.9623 (ptp) cc_final: 0.9183 (ppp) REVERT: C 183 ASP cc_start: 0.8488 (t0) cc_final: 0.8116 (t0) REVERT: G 29 ILE cc_start: 0.9637 (mm) cc_final: 0.9329 (tt) REVERT: G 31 MET cc_start: 0.9001 (ttp) cc_final: 0.8305 (ttp) REVERT: G 103 TRP cc_start: 0.9653 (m-10) cc_final: 0.9350 (m100) REVERT: I 57 MET cc_start: 0.9453 (tpp) cc_final: 0.8992 (tpp) REVERT: I 65 ILE cc_start: 0.9531 (pt) cc_final: 0.9139 (mm) REVERT: I 98 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9166 (mm) REVERT: J 63 ASP cc_start: 0.9243 (t0) cc_final: 0.8822 (t0) REVERT: M 27 LYS cc_start: 0.9368 (tptt) cc_final: 0.9149 (tppt) REVERT: M 78 LYS cc_start: 0.9351 (tptp) cc_final: 0.9042 (tptp) REVERT: N 74 LEU cc_start: 0.9452 (mm) cc_final: 0.9242 (mm) REVERT: N 89 MET cc_start: 0.9449 (mmp) cc_final: 0.9088 (mmt) REVERT: S 66 MET cc_start: 0.9369 (mtp) cc_final: 0.8935 (mtp) outliers start: 34 outliers final: 25 residues processed: 152 average time/residue: 0.1190 time to fit residues: 28.1585 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 MET Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 139 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 111 ARG Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Chi-restraints excluded: chain S residue 65 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 149 optimal weight: 0.0770 chunk 89 optimal weight: 0.6980 chunk 61 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 76 optimal weight: 0.6980 chunk 79 optimal weight: 0.0050 chunk 69 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 overall best weight: 0.4952 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 GLN ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.027835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.022065 restraints weight = 222382.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.022802 restraints weight = 97103.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.023298 restraints weight = 59027.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.023553 restraints weight = 43182.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.023740 restraints weight = 36117.534| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 19802 Z= 0.128 Angle : 0.602 19.958 28949 Z= 0.336 Chirality : 0.037 0.316 3609 Planarity : 0.005 0.047 1995 Dihedral : 23.820 176.353 8374 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.93 % Allowed : 25.84 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.25), residues: 1092 helix: 0.38 (0.23), residues: 510 sheet: -0.42 (0.41), residues: 163 loop : -0.65 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 41 TYR 0.023 0.002 TYR C 168 PHE 0.015 0.002 PHE I 39 TRP 0.016 0.002 TRP G 103 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.13 (19801) covalent geometry : angle 0.60215 / 0.34 (28949) hydrogen bonds : bond 0.06210 / 6.14 ( 798) hydrogen bonds : angle 4.50825 / 5.68 ( 1823) metal coordination : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.343 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: B 36 ASN cc_start: 0.7641 (m-40) cc_final: 0.7328 (p0) REVERT: B 122 GLN cc_start: 0.8518 (tm-30) cc_final: 0.8148 (pp30) REVERT: C 25 ASN cc_start: 0.9347 (m-40) cc_final: 0.9090 (m-40) REVERT: C 129 MET cc_start: 0.9226 (mmm) cc_final: 0.8787 (tpp) REVERT: C 134 MET cc_start: 0.9597 (ptp) cc_final: 0.9185 (ppp) REVERT: C 183 ASP cc_start: 0.8539 (t0) cc_final: 0.8118 (t0) REVERT: C 211 MET cc_start: 0.8161 (mmm) cc_final: 0.7841 (mmm) REVERT: G 29 ILE cc_start: 0.9683 (mm) cc_final: 0.9373 (tt) REVERT: G 31 MET cc_start: 0.8984 (ttp) cc_final: 0.8246 (ttp) REVERT: G 103 TRP cc_start: 0.9671 (m-10) cc_final: 0.9343 (m100) REVERT: I 57 MET cc_start: 0.9413 (tpp) cc_final: 0.8949 (tpp) REVERT: I 65 ILE cc_start: 0.9517 (pt) cc_final: 0.9093 (mm) REVERT: I 98 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9236 (mm) REVERT: I 110 GLN cc_start: 0.8926 (mt0) cc_final: 0.8469 (mp10) REVERT: I 118 LEU cc_start: 0.9577 (mm) cc_final: 0.9242 (tp) REVERT: J 63 ASP cc_start: 0.9292 (t0) cc_final: 0.8865 (t0) REVERT: J 66 GLU cc_start: 0.8949 (tp30) cc_final: 0.7794 (tm-30) REVERT: M 23 TYR cc_start: 0.8737 (t80) cc_final: 0.8225 (t80) REVERT: M 27 LYS cc_start: 0.9439 (tptt) cc_final: 0.9097 (tptt) REVERT: M 78 LYS cc_start: 0.9389 (tptp) cc_final: 0.9165 (tptm) REVERT: N 6 MET cc_start: 0.8776 (mmt) cc_final: 0.8507 (mmp) REVERT: N 89 MET cc_start: 0.9475 (mmp) cc_final: 0.9002 (mmt) REVERT: S 66 MET cc_start: 0.9347 (mtp) cc_final: 0.8970 (mtp) outliers start: 27 outliers final: 17 residues processed: 153 average time/residue: 0.1171 time to fit residues: 27.8232 Evaluate side-chains 144 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 75 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 139 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.026878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.021165 restraints weight = 232100.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2596 r_free = 0.2596 target = 0.021873 restraints weight = 101195.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.022313 restraints weight = 62943.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.022589 restraints weight = 47161.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 63)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.022729 restraints weight = 39355.698| |-----------------------------------------------------------------------------| r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 19802 Z= 0.224 Angle : 0.619 16.585 28949 Z= 0.350 Chirality : 0.038 0.284 3609 Planarity : 0.005 0.039 1995 Dihedral : 23.795 179.411 8374 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.04 % Allowed : 26.06 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.25), residues: 1092 helix: 0.49 (0.23), residues: 508 sheet: -0.53 (0.40), residues: 168 loop : -0.58 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG G 111 TYR 0.024 0.002 TYR C 168 PHE 0.018 0.002 PHE I 127 TRP 0.011 0.002 TRP N 42 HIS 0.005 0.001 HIS M 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.22 (19801) covalent geometry : angle 0.61864 / 0.35 (28949) hydrogen bonds : bond 0.07622 / 7.65 ( 798) hydrogen bonds : angle 4.68396 / 5.98 ( 1823) metal coordination : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.317 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: B 30 PHE cc_start: 0.8390 (m-80) cc_final: 0.8012 (t80) REVERT: B 49 MET cc_start: 0.8979 (mmp) cc_final: 0.8767 (mmp) REVERT: B 122 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8222 (pp30) REVERT: B 146 ASN cc_start: 0.9585 (OUTLIER) cc_final: 0.9206 (p0) REVERT: C 25 ASN cc_start: 0.9318 (m-40) cc_final: 0.9064 (m-40) REVERT: C 129 MET cc_start: 0.9288 (mmm) cc_final: 0.8813 (tpp) REVERT: C 183 ASP cc_start: 0.8582 (t0) cc_final: 0.8191 (t0) REVERT: G 29 ILE cc_start: 0.9641 (mm) cc_final: 0.9295 (tt) REVERT: G 31 MET cc_start: 0.9008 (ttp) cc_final: 0.8286 (ttp) REVERT: G 103 TRP cc_start: 0.9646 (m-10) cc_final: 0.9366 (m100) REVERT: I 57 MET cc_start: 0.9430 (tpp) cc_final: 0.8972 (tpp) REVERT: I 65 ILE cc_start: 0.9537 (pt) cc_final: 0.9186 (mm) REVERT: I 98 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9258 (mm) REVERT: I 118 LEU cc_start: 0.9499 (mm) cc_final: 0.9104 (tp) REVERT: J 63 ASP cc_start: 0.9215 (t0) cc_final: 0.8749 (t0) REVERT: J 66 GLU cc_start: 0.8916 (tp30) cc_final: 0.8049 (tm-30) REVERT: M 27 LYS cc_start: 0.9431 (tptt) cc_final: 0.9051 (tptt) REVERT: M 34 LEU cc_start: 0.9294 (tp) cc_final: 0.8887 (tt) REVERT: M 78 LYS cc_start: 0.9380 (tptp) cc_final: 0.9104 (tptp) REVERT: N 6 MET cc_start: 0.8880 (mmt) cc_final: 0.8607 (mmp) REVERT: N 38 ASP cc_start: 0.8991 (OUTLIER) cc_final: 0.8768 (p0) REVERT: N 89 MET cc_start: 0.9523 (mmp) cc_final: 0.8985 (mmt) REVERT: S 66 MET cc_start: 0.9393 (mtp) cc_final: 0.8988 (mtp) outliers start: 28 outliers final: 21 residues processed: 144 average time/residue: 0.1129 time to fit residues: 25.7383 Evaluate side-chains 150 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 146 ASN Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 20 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 143 optimal weight: 0.9980 chunk 28 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 152 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.027921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.022011 restraints weight = 224046.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.022766 restraints weight = 97365.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.023208 restraints weight = 59558.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.023489 restraints weight = 45087.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 66)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.023649 restraints weight = 37889.272| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 19802 Z= 0.124 Angle : 0.606 14.856 28949 Z= 0.339 Chirality : 0.037 0.319 3609 Planarity : 0.005 0.045 1995 Dihedral : 23.734 176.341 8374 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.50 % Allowed : 27.04 % Favored : 70.47 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.25), residues: 1092 helix: 0.46 (0.23), residues: 510 sheet: -0.28 (0.41), residues: 163 loop : -0.61 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 111 TYR 0.022 0.002 TYR C 168 PHE 0.011 0.001 PHE C 23 TRP 0.016 0.002 TRP G 103 HIS 0.004 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (19801) covalent geometry : angle 0.60589 / 0.34 (28949) hydrogen bonds : bond 0.06049 / 6.05 ( 798) hydrogen bonds : angle 4.57478 / 5.76 ( 1823) metal coordination : bond 0.00011 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.441 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: B 30 PHE cc_start: 0.8440 (m-80) cc_final: 0.8067 (t80) REVERT: B 36 ASN cc_start: 0.7518 (m-40) cc_final: 0.7217 (p0) REVERT: B 49 MET cc_start: 0.8976 (mmp) cc_final: 0.8772 (mmp) REVERT: B 122 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8217 (pp30) REVERT: B 146 ASN cc_start: 0.9572 (m110) cc_final: 0.9219 (p0) REVERT: C 25 ASN cc_start: 0.9318 (m-40) cc_final: 0.9058 (m-40) REVERT: C 129 MET cc_start: 0.9242 (mmm) cc_final: 0.8787 (tpp) REVERT: C 134 MET cc_start: 0.9644 (ptp) cc_final: 0.9369 (ptt) REVERT: C 183 ASP cc_start: 0.8513 (t0) cc_final: 0.8129 (t0) REVERT: C 211 MET cc_start: 0.7901 (mmm) cc_final: 0.7525 (mmm) REVERT: G 29 ILE cc_start: 0.9647 (mm) cc_final: 0.9303 (tt) REVERT: G 31 MET cc_start: 0.8969 (ttp) cc_final: 0.8270 (ttp) REVERT: G 52 GLN cc_start: 0.9315 (mm110) cc_final: 0.8963 (pm20) REVERT: G 103 TRP cc_start: 0.9634 (m-10) cc_final: 0.9378 (m100) REVERT: I 57 MET cc_start: 0.9375 (tpp) cc_final: 0.8939 (tpp) REVERT: I 65 ILE cc_start: 0.9553 (pt) cc_final: 0.9137 (mm) REVERT: I 98 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9261 (mm) REVERT: I 118 LEU cc_start: 0.9548 (mm) cc_final: 0.9089 (tp) REVERT: J 63 ASP cc_start: 0.9298 (t0) cc_final: 0.8874 (t0) REVERT: J 66 GLU cc_start: 0.8862 (tp30) cc_final: 0.7975 (tm-30) REVERT: M 27 LYS cc_start: 0.9400 (tptt) cc_final: 0.9048 (tptt) REVERT: M 34 LEU cc_start: 0.9251 (tp) cc_final: 0.8914 (tt) REVERT: M 78 LYS cc_start: 0.9354 (tptp) cc_final: 0.9088 (tptp) REVERT: N 89 MET cc_start: 0.9474 (mmp) cc_final: 0.8963 (mmt) REVERT: S 66 MET cc_start: 0.9319 (mtp) cc_final: 0.8895 (mtp) outliers start: 23 outliers final: 21 residues processed: 148 average time/residue: 0.1202 time to fit residues: 27.9762 Evaluate side-chains 153 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 191 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 4 ILE Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 18 ASP Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 42 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 72 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.027134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2574 r_free = 0.2574 target = 0.021443 restraints weight = 230205.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.022162 restraints weight = 99980.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.022602 restraints weight = 60937.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2634 r_free = 0.2634 target = 0.022893 restraints weight = 45761.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.023052 restraints weight = 38187.945| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19802 Z= 0.197 Angle : 0.597 13.453 28949 Z= 0.339 Chirality : 0.037 0.272 3609 Planarity : 0.005 0.058 1995 Dihedral : 23.708 178.846 8374 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.82 % Allowed : 27.04 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 1092 helix: 0.53 (0.23), residues: 509 sheet: -0.42 (0.41), residues: 167 loop : -0.57 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 102 TYR 0.024 0.002 TYR C 168 PHE 0.019 0.002 PHE I 127 TRP 0.014 0.002 TRP G 103 HIS 0.009 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.20 (19801) covalent geometry : angle 0.59652 / 0.34 (28949) hydrogen bonds : bond 0.06958 / 7.01 ( 798) hydrogen bonds : angle 4.65384 / 5.87 ( 1823) metal coordination : bond 0.00041 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2641.13 seconds wall clock time: 46 minutes 54.49 seconds (2814.49 seconds total)