Starting phenix.real_space_refine on Mon Dec 30 01:25:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.map" model { file = "/net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h9m_34573/12_2024/8h9m_34573.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 7930 2.51 5 N 1932 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 12083 Number of models: 1 Model: "" Number of chains: 19 Chain: "3" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "4" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "5" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "6" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "7" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "8" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "1" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "2" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 534 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1485 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 5, 'TRANS': 185} Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 975 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 4, 'TRANS': 127} Chain: "I" Number of atoms: 354 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Chain: "K" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "M" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 311 Classifications: {'peptide': 36} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 30} Chain: "N" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1718 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "P" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 344 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 307 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 5, 'TRANS': 32} Chain: "R" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 621 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "S" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 605 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "T" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 346 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 39} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.00, per 1000 atoms: 0.83 Number of scatterers: 12083 At special positions: 0 Unit cell: (111.69, 103.66, 139.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 2158 8.00 N 1932 7.00 C 7930 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: 3.17 Conformation dependent library (CDL) restraints added in 1.6 seconds 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 5 sheets defined 76.3% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain '3' and resid 1 through 17 removed outlier: 3.970A pdb=" N LYS 3 7 " --> pdb=" O ASP 3 3 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE 3 8 " --> pdb=" O THR 3 4 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY 3 17 " --> pdb=" O ALA 3 13 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 39 Processing helix chain '3' and resid 42 through 73 Processing helix chain '4' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 4 17 " --> pdb=" O ALA 4 13 " (cutoff:3.500A) Processing helix chain '4' and resid 18 through 39 Processing helix chain '4' and resid 42 through 73 Processing helix chain '5' and resid 2 through 17 removed outlier: 3.911A pdb=" N GLY 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 18 through 39 Processing helix chain '5' and resid 42 through 73 Processing helix chain '6' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 6 17 " --> pdb=" O ALA 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 18 through 39 Processing helix chain '6' and resid 42 through 73 Processing helix chain '7' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 7 17 " --> pdb=" O ALA 7 13 " (cutoff:3.500A) Processing helix chain '7' and resid 18 through 39 Processing helix chain '7' and resid 42 through 73 Processing helix chain '8' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 8 17 " --> pdb=" O ALA 8 13 " (cutoff:3.500A) Processing helix chain '8' and resid 18 through 39 Processing helix chain '8' and resid 42 through 73 Processing helix chain '1' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 1 17 " --> pdb=" O ALA 1 13 " (cutoff:3.500A) Processing helix chain '1' and resid 18 through 39 Processing helix chain '1' and resid 42 through 73 Processing helix chain '2' and resid 2 through 17 removed outlier: 3.912A pdb=" N GLY 2 17 " --> pdb=" O ALA 2 13 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 39 Processing helix chain '2' and resid 42 through 73 Processing helix chain 'G' and resid 33 through 49 removed outlier: 4.230A pdb=" N LYS G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) Proline residue: G 40 - end of helix Processing helix chain 'G' and resid 49 through 55 Processing helix chain 'G' and resid 80 through 99 removed outlier: 3.682A pdb=" N ALA G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 118 removed outlier: 3.675A pdb=" N ARG G 113 " --> pdb=" O GLY G 109 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ARG G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 150 Processing helix chain 'G' and resid 180 through 186 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 197 through 221 removed outlier: 3.529A pdb=" N THR G 221 " --> pdb=" O LEU G 217 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 103 No H-bonds generated for 'chain 'H' and resid 101 through 103' Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.713A pdb=" N ALA H 108 " --> pdb=" O ASP H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 146 Processing helix chain 'I' and resid 3 through 9 Processing helix chain 'I' and resid 11 through 26 Processing helix chain 'I' and resid 28 through 39 removed outlier: 4.250A pdb=" N ALA I 33 " --> pdb=" O THR I 29 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASN I 34 " --> pdb=" O GLU I 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 30 Proline residue: K 27 - end of helix Processing helix chain 'K' and resid 31 through 48 removed outlier: 4.660A pdb=" N TYR K 35 " --> pdb=" O VAL K 31 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 96 removed outlier: 3.777A pdb=" N PHE K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Proline residue: K 76 - end of helix Processing helix chain 'M' and resid 131 through 139 Processing helix chain 'M' and resid 156 through 160 Processing helix chain 'N' and resid 19 through 26 Processing helix chain 'N' and resid 27 through 31 Processing helix chain 'N' and resid 40 through 59 removed outlier: 3.730A pdb=" N THR N 59 " --> pdb=" O LYS N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 68 through 86 Processing helix chain 'N' and resid 93 through 96 Processing helix chain 'N' and resid 97 through 119 Proline residue: N 107 - end of helix removed outlier: 4.010A pdb=" N SER N 119 " --> pdb=" O MET N 115 " (cutoff:3.500A) Processing helix chain 'N' and resid 120 through 127 Processing helix chain 'N' and resid 134 through 138 Processing helix chain 'N' and resid 139 through 181 removed outlier: 4.184A pdb=" N GLU N 145 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE N 147 " --> pdb=" O ILE N 143 " (cutoff:3.500A) Proline residue: N 153 - end of helix removed outlier: 3.794A pdb=" N ASN N 163 " --> pdb=" O ARG N 159 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA N 166 " --> pdb=" O ALA N 162 " (cutoff:3.500A) Processing helix chain 'N' and resid 185 through 224 Processing helix chain 'P' and resid 13 through 19 removed outlier: 3.722A pdb=" N LYS P 19 " --> pdb=" O PRO P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 41 removed outlier: 3.666A pdb=" N ALA P 41 " --> pdb=" O LYS P 37 " (cutoff:3.500A) Processing helix chain 'Q' and resid 1 through 5 Processing helix chain 'Q' and resid 8 through 21 Proline residue: Q 15 - end of helix Processing helix chain 'Q' and resid 22 through 29 Processing helix chain 'R' and resid 26 through 32 removed outlier: 3.777A pdb=" N LEU R 30 " --> pdb=" O PRO R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 Processing helix chain 'R' and resid 62 through 85 removed outlier: 4.261A pdb=" N VAL R 68 " --> pdb=" O GLY R 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LYS R 82 " --> pdb=" O SER R 78 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N HIS R 83 " --> pdb=" O PHE R 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 27 through 37 removed outlier: 4.300A pdb=" N VAL S 35 " --> pdb=" O TYR S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 62 Processing helix chain 'S' and resid 63 through 66 Processing helix chain 'S' and resid 68 through 94 Processing helix chain 'T' and resid 8 through 45 Proline residue: T 35 - end of helix removed outlier: 3.996A pdb=" N ALA T 45 " --> pdb=" O ARG T 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 171 through 179 removed outlier: 5.250A pdb=" N ASN G 163 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS G 66 " --> pdb=" O MET G 104 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL G 106 " --> pdb=" O HIS G 66 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU G 68 " --> pdb=" O VAL G 106 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N ILE G 108 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 70 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 9.778A pdb=" N VAL G 126 " --> pdb=" O VAL G 103 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU G 105 " --> pdb=" O VAL G 126 " (cutoff:3.500A) removed outlier: 8.533A pdb=" N PHE G 128 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY G 107 " --> pdb=" O PHE G 128 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 43 through 47 removed outlier: 6.225A pdb=" N SER H 17 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU H 92 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N THR H 19 " --> pdb=" O LEU H 92 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ALA H 94 " --> pdb=" O THR H 19 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ALA H 21 " --> pdb=" O ALA H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 43 through 47 removed outlier: 7.267A pdb=" N LEU H 62 " --> pdb=" O PRO H 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 12 through 13 Processing sheet with id=AA5, first strand: chain 'N' and resid 13 through 14 957 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.81 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3714 1.34 - 1.46: 2248 1.46 - 1.57: 6247 1.57 - 1.69: 0 1.69 - 1.81: 115 Bond restraints: 12324 Sorted by residual: bond pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 1.333 1.249 0.083 1.37e-02 5.33e+03 3.67e+01 bond pdb=" C ARG 7 38 " pdb=" N ASN 7 39 " ideal model delta sigma weight residual 1.332 1.413 -0.081 1.48e-02 4.57e+03 3.01e+01 bond pdb=" N ARG 1 38 " pdb=" CA ARG 1 38 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.27e-02 6.20e+03 7.32e+00 bond pdb=" N ARG 4 38 " pdb=" CA ARG 4 38 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.24e-02 6.50e+03 6.67e+00 bond pdb=" N ARG 7 38 " pdb=" CA ARG 7 38 " ideal model delta sigma weight residual 1.458 1.490 -0.033 1.27e-02 6.20e+03 6.61e+00 ... (remaining 12319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 15961 1.29 - 2.57: 600 2.57 - 3.86: 92 3.86 - 5.14: 26 5.14 - 6.43: 10 Bond angle restraints: 16689 Sorted by residual: angle pdb=" O ALA 7 37 " pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 122.39 115.96 6.43 1.30e+00 5.92e-01 2.45e+01 angle pdb=" C ARG 7 38 " pdb=" N ASN 7 39 " pdb=" CA ASN 7 39 " ideal model delta sigma weight residual 123.16 117.57 5.59 1.23e+00 6.61e-01 2.07e+01 angle pdb=" CA ALA 7 37 " pdb=" C ALA 7 37 " pdb=" N ARG 7 38 " ideal model delta sigma weight residual 118.08 123.68 -5.60 1.30e+00 5.92e-01 1.86e+01 angle pdb=" N ALA 3 5 " pdb=" CA ALA 3 5 " pdb=" C ALA 3 5 " ideal model delta sigma weight residual 112.68 108.62 4.06 1.33e+00 5.65e-01 9.30e+00 angle pdb=" N THR 3 4 " pdb=" CA THR 3 4 " pdb=" C THR 3 4 " ideal model delta sigma weight residual 113.38 109.91 3.47 1.23e+00 6.61e-01 7.94e+00 ... (remaining 16684 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 6536 17.76 - 35.52: 609 35.52 - 53.28: 76 53.28 - 71.04: 15 71.04 - 88.80: 13 Dihedral angle restraints: 7249 sinusoidal: 2711 harmonic: 4538 Sorted by residual: dihedral pdb=" CA TYR G 193 " pdb=" C TYR G 193 " pdb=" N ASP G 194 " pdb=" CA ASP G 194 " ideal model delta harmonic sigma weight residual -180.00 -158.33 -21.67 0 5.00e+00 4.00e-02 1.88e+01 dihedral pdb=" CA ARG N 118 " pdb=" C ARG N 118 " pdb=" N SER N 119 " pdb=" CA SER N 119 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CG ARG R 45 " pdb=" CD ARG R 45 " pdb=" NE ARG R 45 " pdb=" CZ ARG R 45 " ideal model delta sinusoidal sigma weight residual 180.00 135.12 44.88 2 1.50e+01 4.44e-03 1.06e+01 ... (remaining 7246 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1294 0.034 - 0.069: 495 0.069 - 0.103: 122 0.103 - 0.137: 57 0.137 - 0.172: 3 Chirality restraints: 1971 Sorted by residual: chirality pdb=" CA ILE 3 2 " pdb=" N ILE 3 2 " pdb=" C ILE 3 2 " pdb=" CB ILE 3 2 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.36e-01 chirality pdb=" CA ILE G 178 " pdb=" N ILE G 178 " pdb=" C ILE G 178 " pdb=" CB ILE G 178 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CB ILE N 144 " pdb=" CA ILE N 144 " pdb=" CG1 ILE N 144 " pdb=" CG2 ILE N 144 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 4.96e-01 ... (remaining 1968 not shown) Planarity restraints: 2066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG 6 38 " 0.281 9.50e-02 1.11e+02 1.26e-01 9.78e+00 pdb=" NE ARG 6 38 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG 6 38 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG 6 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 6 38 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 4 38 " -0.254 9.50e-02 1.11e+02 1.14e-01 7.92e+00 pdb=" NE ARG 4 38 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG 4 38 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG 4 38 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 4 38 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG 5 38 " 0.178 9.50e-02 1.11e+02 7.96e-02 3.89e+00 pdb=" NE ARG 5 38 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG 5 38 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG 5 38 " 0.006 2.00e-02 2.50e+03 ... (remaining 2063 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1886 2.75 - 3.29: 12877 3.29 - 3.83: 20518 3.83 - 4.36: 24258 4.36 - 4.90: 41412 Nonbonded interactions: 100951 Sorted by model distance: nonbonded pdb=" O ILE K 50 " pdb=" OH TYR R 77 " model vdw 2.218 3.040 nonbonded pdb=" OH TYR G 52 " pdb=" OE1 GLN G 205 " model vdw 2.220 3.040 nonbonded pdb=" O LYS N 55 " pdb=" OG1 THR N 59 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR G 214 " pdb=" O PRO H 23 " model vdw 2.250 3.040 nonbonded pdb=" ND2 ASN N 101 " pdb=" OG1 THR N 161 " model vdw 2.251 3.120 ... (remaining 100946 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.070 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:13.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 12324 Z= 0.266 Angle : 0.599 6.430 16689 Z= 0.365 Chirality : 0.041 0.172 1971 Planarity : 0.007 0.126 2066 Dihedral : 13.764 88.796 4353 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.19), residues: 1558 helix: -1.23 (0.14), residues: 1107 sheet: -1.80 (0.50), residues: 85 loop : -2.28 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 28 HIS 0.003 0.001 HIS G 120 PHE 0.021 0.001 PHE H 45 TYR 0.018 0.001 TYR G 193 ARG 0.006 0.000 ARG 3 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 75 ARG cc_start: 0.7454 (mtp85) cc_final: 0.6562 (tmt170) REVERT: H 118 GLU cc_start: 0.6937 (mt-10) cc_final: 0.6692 (mm-30) REVERT: K 14 TYR cc_start: 0.8452 (m-80) cc_final: 0.8180 (m-80) REVERT: N 140 MET cc_start: 0.5061 (tpt) cc_final: 0.4811 (ptm) REVERT: N 181 MET cc_start: 0.7860 (tpp) cc_final: 0.7573 (tpt) REVERT: P 5 ILE cc_start: 0.7536 (mp) cc_final: 0.7033 (mp) REVERT: P 31 MET cc_start: 0.8101 (tmm) cc_final: 0.7847 (tmm) REVERT: R 85 LYS cc_start: 0.8817 (ptmt) cc_final: 0.8486 (ptmm) REVERT: R 91 LYS cc_start: 0.7909 (tmmt) cc_final: 0.7662 (tptt) REVERT: T 36 ARG cc_start: 0.7203 (mpt-90) cc_final: 0.6393 (mpt90) outliers start: 0 outliers final: 0 residues processed: 263 average time/residue: 1.3376 time to fit residues: 379.9074 Evaluate side-chains 208 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 137 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 39 ASN 8 39 ASN G 120 HIS G 150 ASN G 163 ASN G 182 ASN H 85 ASN H 111 ASN M 159 ASN N 4 ASN N 46 GLN N 47 GLN N 61 HIS N 90 HIS N 172 HIS R 83 HIS S 75 ASN T 6 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12324 Z= 0.239 Angle : 0.588 9.868 16689 Z= 0.308 Chirality : 0.042 0.176 1971 Planarity : 0.004 0.037 2066 Dihedral : 4.260 20.136 1686 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 12.37 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.21), residues: 1558 helix: 0.74 (0.15), residues: 1098 sheet: -1.41 (0.52), residues: 85 loop : -1.82 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.003 0.001 HIS H 66 PHE 0.024 0.001 PHE 3 54 TYR 0.016 0.001 TYR G 44 ARG 0.006 0.001 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 1.282 Fit side-chains revert: symmetry clash REVERT: 5 75 MET cc_start: 0.5871 (OUTLIER) cc_final: 0.5120 (mtt) REVERT: 1 75 MET cc_start: 0.6348 (OUTLIER) cc_final: 0.5508 (mtm) REVERT: G 75 ARG cc_start: 0.7401 (mtp85) cc_final: 0.6498 (ppt170) REVERT: H 132 GLN cc_start: 0.7951 (mm-40) cc_final: 0.7604 (tm-30) REVERT: I 30 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.6887 (tm-30) REVERT: K 14 TYR cc_start: 0.8481 (m-80) cc_final: 0.8228 (m-80) REVERT: K 23 GLN cc_start: 0.7714 (mm-40) cc_final: 0.7489 (mm110) REVERT: N 181 MET cc_start: 0.7595 (tpp) cc_final: 0.7334 (tpt) REVERT: P 31 MET cc_start: 0.8129 (tmm) cc_final: 0.7793 (tmm) REVERT: Q 6 THR cc_start: 0.8888 (p) cc_final: 0.8609 (m) REVERT: R 85 LYS cc_start: 0.8775 (ptmt) cc_final: 0.8433 (ptmm) REVERT: R 91 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7744 (tptt) outliers start: 38 outliers final: 6 residues processed: 239 average time/residue: 1.2058 time to fit residues: 313.8358 Evaluate side-chains 219 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 66 MET Chi-restraints excluded: chain 5 residue 75 MET Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 30 GLU Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain Q residue 28 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 8 39 ASN G 150 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12324 Z= 0.228 Angle : 0.550 7.913 16689 Z= 0.288 Chirality : 0.041 0.188 1971 Planarity : 0.004 0.036 2066 Dihedral : 4.125 18.205 1686 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.31 % Allowed : 14.68 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.21), residues: 1558 helix: 1.23 (0.15), residues: 1117 sheet: -1.20 (0.54), residues: 83 loop : -1.18 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.020 0.001 PHE 3 69 TYR 0.014 0.001 TYR G 44 ARG 0.009 0.001 ARG G 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 216 time to evaluate : 1.364 Fit side-chains revert: symmetry clash REVERT: 3 4 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7852 (p) REVERT: 1 75 MET cc_start: 0.6433 (OUTLIER) cc_final: 0.5983 (mtm) REVERT: G 75 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6535 (ppt170) REVERT: H 118 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6754 (mm-30) REVERT: K 13 ARG cc_start: 0.7738 (ttm170) cc_final: 0.7398 (ttm110) REVERT: K 14 TYR cc_start: 0.8439 (m-80) cc_final: 0.7918 (m-80) REVERT: K 23 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7505 (mm110) REVERT: N 140 MET cc_start: 0.6870 (ptm) cc_final: 0.5560 (mmp) REVERT: N 181 MET cc_start: 0.7568 (tpp) cc_final: 0.7358 (tpt) REVERT: P 31 MET cc_start: 0.8156 (tmm) cc_final: 0.7956 (tmm) REVERT: R 19 GLU cc_start: 0.3278 (OUTLIER) cc_final: 0.2774 (tm-30) REVERT: R 85 LYS cc_start: 0.8755 (ptmt) cc_final: 0.8335 (ptmm) REVERT: R 91 LYS cc_start: 0.8008 (tmmt) cc_final: 0.7766 (tptt) REVERT: T 34 LYS cc_start: 0.8331 (mmmt) cc_final: 0.8071 (mmmm) outliers start: 54 outliers final: 17 residues processed: 243 average time/residue: 1.1395 time to fit residues: 302.4891 Evaluate side-chains 227 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 4 THR Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 3 residue 57 SER Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 34 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 63 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 63 SER Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 135 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 137 optimal weight: 0.0870 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12324 Z= 0.182 Angle : 0.524 7.217 16689 Z= 0.276 Chirality : 0.040 0.194 1971 Planarity : 0.004 0.038 2066 Dihedral : 4.029 17.557 1686 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.59 % Allowed : 17.88 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.22), residues: 1558 helix: 1.68 (0.16), residues: 1112 sheet: -1.15 (0.55), residues: 86 loop : -0.82 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.023 0.001 PHE 3 69 TYR 0.013 0.001 TYR G 44 ARG 0.005 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 221 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: 4 66 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6907 (mtt) REVERT: 6 70 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8178 (mp) REVERT: 1 75 MET cc_start: 0.6440 (mtt) cc_final: 0.6239 (mtm) REVERT: G 75 ARG cc_start: 0.7455 (mtp85) cc_final: 0.6569 (ppt170) REVERT: H 132 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7685 (mm-40) REVERT: K 14 TYR cc_start: 0.8409 (m-80) cc_final: 0.8190 (m-80) REVERT: K 23 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7599 (mm110) REVERT: N 140 MET cc_start: 0.6806 (ptm) cc_final: 0.5654 (mmp) REVERT: P 31 MET cc_start: 0.8157 (tmm) cc_final: 0.7933 (tmm) REVERT: Q 28 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7542 (mpp) REVERT: R 19 GLU cc_start: 0.3229 (OUTLIER) cc_final: 0.2650 (tm-30) REVERT: R 91 LYS cc_start: 0.8035 (tmmt) cc_final: 0.7767 (tptt) REVERT: S 45 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6975 (mp) outliers start: 45 outliers final: 11 residues processed: 240 average time/residue: 1.1821 time to fit residues: 309.9902 Evaluate side-chains 219 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 66 MET Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 28 MET Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain S residue 45 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 60 optimal weight: 0.0980 chunk 124 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 131 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN H 35 GLN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12324 Z= 0.169 Angle : 0.525 10.724 16689 Z= 0.273 Chirality : 0.040 0.191 1971 Planarity : 0.004 0.039 2066 Dihedral : 3.996 16.513 1686 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.03 % Allowed : 19.95 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1558 helix: 1.92 (0.16), residues: 1114 sheet: -1.12 (0.54), residues: 87 loop : -0.64 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.024 0.001 PHE 3 69 TYR 0.013 0.001 TYR R 77 ARG 0.007 0.000 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 1.337 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8162 (mp) REVERT: G 75 ARG cc_start: 0.7459 (mtp85) cc_final: 0.6567 (ppt170) REVERT: K 13 ARG cc_start: 0.7938 (ttp-170) cc_final: 0.7596 (ttp-110) REVERT: K 14 TYR cc_start: 0.8379 (m-80) cc_final: 0.7977 (m-10) REVERT: K 23 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7640 (mm110) REVERT: N 140 MET cc_start: 0.6785 (ptm) cc_final: 0.5687 (mmp) REVERT: P 31 MET cc_start: 0.8176 (tmm) cc_final: 0.7953 (tmm) REVERT: R 19 GLU cc_start: 0.3150 (OUTLIER) cc_final: 0.2584 (tm-30) REVERT: R 91 LYS cc_start: 0.8033 (tmmt) cc_final: 0.7761 (tptt) REVERT: S 45 ILE cc_start: 0.7291 (OUTLIER) cc_final: 0.6974 (mp) outliers start: 38 outliers final: 18 residues processed: 228 average time/residue: 1.1557 time to fit residues: 288.0529 Evaluate side-chains 220 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 199 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain S residue 45 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 49 optimal weight: 0.1980 chunk 131 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN G 182 ASN ** M 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12324 Z= 0.214 Angle : 0.544 9.418 16689 Z= 0.280 Chirality : 0.041 0.192 1971 Planarity : 0.004 0.036 2066 Dihedral : 3.992 17.717 1686 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.43 % Allowed : 20.67 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.22), residues: 1558 helix: 2.02 (0.15), residues: 1117 sheet: -1.02 (0.54), residues: 89 loop : -0.61 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.025 0.001 PHE 3 69 TYR 0.013 0.001 TYR R 77 ARG 0.006 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 209 time to evaluate : 1.357 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8286 (mp) REVERT: G 75 ARG cc_start: 0.7475 (mtp85) cc_final: 0.6522 (ppt170) REVERT: H 132 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7552 (mm-40) REVERT: K 13 ARG cc_start: 0.7947 (ttp-170) cc_final: 0.7554 (ttp-110) REVERT: K 14 TYR cc_start: 0.8398 (m-80) cc_final: 0.7891 (m-10) REVERT: K 23 GLN cc_start: 0.7875 (mm-40) cc_final: 0.7650 (mm110) REVERT: N 140 MET cc_start: 0.6855 (ptm) cc_final: 0.5766 (mmp) REVERT: R 19 GLU cc_start: 0.3088 (OUTLIER) cc_final: 0.2511 (tm-30) REVERT: R 91 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7781 (tptt) REVERT: S 45 ILE cc_start: 0.7269 (OUTLIER) cc_final: 0.6972 (mp) outliers start: 43 outliers final: 21 residues processed: 229 average time/residue: 1.1301 time to fit residues: 282.7898 Evaluate side-chains 224 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 2 residue 38 ARG Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain S residue 45 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 106 optimal weight: 0.4980 chunk 82 optimal weight: 0.6980 chunk 122 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 145 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12324 Z= 0.235 Angle : 0.560 9.383 16689 Z= 0.289 Chirality : 0.041 0.190 1971 Planarity : 0.004 0.038 2066 Dihedral : 4.021 20.829 1686 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 3.59 % Allowed : 21.31 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.22), residues: 1558 helix: 2.00 (0.15), residues: 1121 sheet: -1.12 (0.54), residues: 89 loop : -0.60 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.026 0.002 PHE 3 69 TYR 0.015 0.001 TYR R 77 ARG 0.007 0.000 ARG H 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 206 time to evaluate : 1.297 Fit side-chains revert: symmetry clash REVERT: 5 75 MET cc_start: 0.5875 (mpt) cc_final: 0.5602 (mpt) REVERT: 6 70 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8342 (mp) REVERT: 1 75 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.5528 (mpp) REVERT: G 75 ARG cc_start: 0.7545 (mtp85) cc_final: 0.6585 (tmt170) REVERT: H 132 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7578 (mm-40) REVERT: I 44 LYS cc_start: 0.8113 (OUTLIER) cc_final: 0.7674 (mttp) REVERT: K 13 ARG cc_start: 0.7974 (ttp-170) cc_final: 0.7558 (ttp-110) REVERT: K 14 TYR cc_start: 0.8392 (m-80) cc_final: 0.7822 (m-10) REVERT: K 23 GLN cc_start: 0.7882 (mm-40) cc_final: 0.7645 (mm110) REVERT: N 140 MET cc_start: 0.6877 (ptm) cc_final: 0.5817 (mmp) REVERT: R 19 GLU cc_start: 0.3005 (OUTLIER) cc_final: 0.2435 (tm-30) REVERT: R 91 LYS cc_start: 0.8071 (tmmt) cc_final: 0.7805 (tptt) REVERT: S 45 ILE cc_start: 0.7294 (OUTLIER) cc_final: 0.6982 (mp) outliers start: 45 outliers final: 23 residues processed: 229 average time/residue: 1.1704 time to fit residues: 292.8916 Evaluate side-chains 224 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 1 residue 75 MET Chi-restraints excluded: chain G residue 131 VAL Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 46 VAL Chi-restraints excluded: chain M residue 129 GLN Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 189 THR Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain S residue 45 ILE Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 90 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12324 Z= 0.188 Angle : 0.555 8.260 16689 Z= 0.285 Chirality : 0.040 0.190 1971 Planarity : 0.004 0.064 2066 Dihedral : 4.011 20.476 1686 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.79 % Allowed : 22.11 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.22), residues: 1558 helix: 2.05 (0.15), residues: 1132 sheet: -1.04 (0.54), residues: 89 loop : -0.39 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.027 0.001 PHE 3 69 TYR 0.014 0.001 TYR T 32 ARG 0.016 0.001 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 207 time to evaluate : 1.208 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8311 (mp) REVERT: G 75 ARG cc_start: 0.7557 (mtp85) cc_final: 0.6657 (ppt170) REVERT: H 132 GLN cc_start: 0.7824 (mm-40) cc_final: 0.7544 (mm-40) REVERT: H 136 GLU cc_start: 0.7032 (pt0) cc_final: 0.6819 (mt-10) REVERT: I 44 LYS cc_start: 0.8101 (OUTLIER) cc_final: 0.7605 (mttp) REVERT: K 13 ARG cc_start: 0.7939 (ttp-170) cc_final: 0.7538 (ttp-110) REVERT: K 14 TYR cc_start: 0.8367 (m-80) cc_final: 0.7785 (m-10) REVERT: K 23 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7617 (mm110) REVERT: N 140 MET cc_start: 0.6844 (ptm) cc_final: 0.5798 (mmp) REVERT: R 19 GLU cc_start: 0.2978 (OUTLIER) cc_final: 0.2375 (tm-30) REVERT: R 91 LYS cc_start: 0.8066 (tmmt) cc_final: 0.7813 (tptt) REVERT: S 45 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.6985 (mp) outliers start: 35 outliers final: 19 residues processed: 223 average time/residue: 1.1126 time to fit residues: 271.9005 Evaluate side-chains 222 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 199 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain S residue 45 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 139 optimal weight: 3.9990 chunk 127 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12324 Z= 0.211 Angle : 0.577 13.561 16689 Z= 0.293 Chirality : 0.041 0.188 1971 Planarity : 0.004 0.041 2066 Dihedral : 3.984 21.574 1686 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 3.03 % Allowed : 22.75 % Favored : 74.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1558 helix: 2.06 (0.15), residues: 1129 sheet: -0.88 (0.56), residues: 86 loop : -0.37 (0.34), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.028 0.001 PHE 6 69 TYR 0.017 0.001 TYR R 77 ARG 0.012 0.001 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8347 (mp) REVERT: G 75 ARG cc_start: 0.7563 (mtp85) cc_final: 0.6583 (ppt170) REVERT: H 132 GLN cc_start: 0.7811 (mm-40) cc_final: 0.7506 (tm-30) REVERT: I 44 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7572 (mttp) REVERT: K 13 ARG cc_start: 0.7946 (ttp-170) cc_final: 0.7523 (ttp-110) REVERT: K 14 TYR cc_start: 0.8374 (m-80) cc_final: 0.7775 (m-10) REVERT: K 23 GLN cc_start: 0.7900 (mm-40) cc_final: 0.7644 (mm110) REVERT: N 140 MET cc_start: 0.6907 (ptm) cc_final: 0.5846 (mmp) REVERT: R 19 GLU cc_start: 0.3046 (OUTLIER) cc_final: 0.2439 (tm-30) REVERT: R 91 LYS cc_start: 0.8089 (tmmt) cc_final: 0.7826 (tptt) outliers start: 38 outliers final: 24 residues processed: 224 average time/residue: 1.1151 time to fit residues: 273.2346 Evaluate side-chains 228 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 41 SER Chi-restraints excluded: chain 4 residue 41 SER Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 8 residue 21 SER Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain G residue 133 ARG Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 169 LEU Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain P residue 28 MET Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 87 GLU Chi-restraints excluded: chain T residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 87 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 138 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 92 optimal weight: 0.0020 chunk 73 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 0.2980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12324 Z= 0.178 Angle : 0.578 12.099 16689 Z= 0.292 Chirality : 0.040 0.193 1971 Planarity : 0.004 0.039 2066 Dihedral : 3.986 20.765 1686 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.31 % Allowed : 23.62 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.22), residues: 1558 helix: 2.09 (0.15), residues: 1136 sheet: -0.76 (0.57), residues: 86 loop : -0.28 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 10 HIS 0.004 0.001 HIS H 66 PHE 0.028 0.001 PHE 3 69 TYR 0.015 0.001 TYR R 77 ARG 0.008 0.000 ARG G 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3116 Ramachandran restraints generated. 1558 Oldfield, 0 Emsley, 1558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 212 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: 6 70 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8312 (mp) REVERT: G 75 ARG cc_start: 0.7584 (mtp85) cc_final: 0.6611 (ppt170) REVERT: H 132 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7445 (tm-30) REVERT: H 136 GLU cc_start: 0.7114 (pt0) cc_final: 0.6870 (mt-10) REVERT: I 44 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7499 (mttp) REVERT: K 13 ARG cc_start: 0.7905 (ttp-170) cc_final: 0.7565 (ttp-110) REVERT: K 14 TYR cc_start: 0.8361 (m-80) cc_final: 0.7757 (m-10) REVERT: N 140 MET cc_start: 0.6906 (ptm) cc_final: 0.5813 (mmp) REVERT: R 19 GLU cc_start: 0.2971 (OUTLIER) cc_final: 0.2392 (tm-30) REVERT: R 91 LYS cc_start: 0.8112 (tmmt) cc_final: 0.7840 (tptt) outliers start: 29 outliers final: 17 residues processed: 224 average time/residue: 1.1738 time to fit residues: 286.7042 Evaluate side-chains 226 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 63 PHE Chi-restraints excluded: chain 6 residue 42 LEU Chi-restraints excluded: chain 6 residue 70 LEU Chi-restraints excluded: chain 7 residue 57 SER Chi-restraints excluded: chain 1 residue 71 ILE Chi-restraints excluded: chain 2 residue 42 LEU Chi-restraints excluded: chain 2 residue 66 MET Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain N residue 74 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 115 MET Chi-restraints excluded: chain N residue 142 VAL Chi-restraints excluded: chain N residue 209 ILE Chi-restraints excluded: chain P residue 11 ILE Chi-restraints excluded: chain Q residue 6 THR Chi-restraints excluded: chain R residue 19 GLU Chi-restraints excluded: chain R residue 74 LEU Chi-restraints excluded: chain R residue 80 SER Chi-restraints excluded: chain R residue 87 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 150 ASN H 66 HIS K 23 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.160780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.120506 restraints weight = 16061.029| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.19 r_work: 0.3461 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12324 Z= 0.237 Angle : 0.611 14.352 16689 Z= 0.307 Chirality : 0.041 0.186 1971 Planarity : 0.004 0.041 2066 Dihedral : 4.002 22.848 1686 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.00 % Allowed : 24.02 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.22), residues: 1558 helix: 2.01 (0.15), residues: 1137 sheet: -0.66 (0.56), residues: 86 loop : -0.30 (0.35), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP P 10 HIS 0.004 0.001 HIS H 51 PHE 0.028 0.002 PHE 3 69 TYR 0.017 0.001 TYR R 77 ARG 0.007 0.001 ARG G 36 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5299.77 seconds wall clock time: 95 minutes 52.64 seconds (5752.64 seconds total)