Starting phenix.real_space_refine on Fri Aug 22 18:41:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.map" model { file = "/net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oj4_16904/08_2025/8oj4_16904.cif" } resolution = 4.35 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= 0.001 sd= 0.013 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 10 5.16 5 C 4442 2.51 5 N 1155 2.21 5 O 1376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6983 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1523 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 185, 1489 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 185, 1489 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 173} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1484 Chain: "A" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "B" Number of atoms: 899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 899 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "C" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 918 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain: "D" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 924 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "E" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Chain: "F" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 910 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 6, 'TRANS': 111} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ALEU H 65 " occ=0.45 ... (14 atoms not shown) pdb=" CD2BLEU H 65 " occ=0.55 residue: pdb=" N AARG H 153 " occ=0.48 ... (20 atoms not shown) pdb=" NH2BARG H 153 " occ=0.52 residue: pdb=" N AILE H 167 " occ=0.44 ... (14 atoms not shown) pdb=" CD1BILE H 167 " occ=0.56 residue: pdb=" N ATHR H 176 " occ=0.53 ... (12 atoms not shown) pdb=" CG2BTHR H 176 " occ=0.47 Time building chain proxies: 1.56, per 1000 atoms: 0.22 Number of scatterers: 6983 At special positions: 0 Unit cell: (112.18, 107.21, 92.3, 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 10 16.00 O 1376 8.00 N 1155 7.00 C 4442 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: 0.42 Conformation dependent library (CDL) restraints added in 395.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1642 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 9 sheets defined 16.8% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'H' and resid 26 through 44 removed outlier: 3.685A pdb=" N LEU H 30 " --> pdb=" O ASN H 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN H 44 " --> pdb=" O ASP H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 52 removed outlier: 4.110A pdb=" N ARG H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 63 removed outlier: 4.047A pdb=" N ASP H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 70 through 75 Processing helix chain 'H' and resid 79 through 85 Processing helix chain 'H' and resid 86 through 109 removed outlier: 4.610A pdb=" N GLU H 91 " --> pdb=" O PRO H 87 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ALA H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ARG H 98 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU H 99 " --> pdb=" O ALA H 95 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLN H 103 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA H 104 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 181 removed outlier: 4.024A pdb=" N ASN H 179 " --> pdb=" O THR H 175 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU H 180 " --> pdb=" O ATHR H 176 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TRP H 181 " --> pdb=" O LYS H 177 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 188 removed outlier: 3.664A pdb=" N ARG H 186 " --> pdb=" O GLY H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 197 removed outlier: 4.933A pdb=" N ALA H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN H 196 " --> pdb=" O GLY H 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 150 removed outlier: 4.291A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 151 removed outlier: 4.069A pdb=" N LEU B 146 " --> pdb=" O VAL B 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 150 removed outlier: 4.463A pdb=" N LEU C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 148 " --> pdb=" O GLU C 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 150 Processing helix chain 'E' and resid 144 through 150 Processing helix chain 'F' and resid 144 through 150 Processing sheet with id=AA1, first strand: chain 'H' and resid 130 through 135 removed outlier: 3.854A pdb=" N VAL H 135 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 148 " --> pdb=" O VAL H 135 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN H 162 " --> pdb=" O AARG H 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 45 removed outlier: 4.279A pdb=" N ALA A 44 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL A 82 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP A 70 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLU A 85 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 68 " --> pdb=" O GLU A 85 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N GLU A 87 " --> pdb=" O GLY A 66 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY A 66 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 98 through 103 removed outlier: 3.656A pdb=" N ARG A 102 " --> pdb=" O TYR A 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 40 through 45 removed outlier: 5.984A pdb=" N GLU B 85 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL B 68 " --> pdb=" O GLU B 85 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 58 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N LEU B 114 " --> pdb=" O PRO B 57 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N SER B 59 " --> pdb=" O LEU B 114 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL B 116 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 39 through 45 removed outlier: 6.703A pdb=" N GLU C 85 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL C 68 " --> pdb=" O GLU C 85 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N GLU C 87 " --> pdb=" O GLY C 66 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY C 66 " --> pdb=" O GLU C 87 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.969A pdb=" N SER C 59 " --> pdb=" O LEU C 114 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL C 116 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 111 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG C 102 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 98 through 103 removed outlier: 8.389A pdb=" N LEU D 114 " --> pdb=" O PRO D 57 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N SER D 59 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL D 58 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY D 66 " --> pdb=" O GLU D 87 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLU D 87 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL D 68 " --> pdb=" O GLU D 85 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLU D 85 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASP D 132 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 40 through 45 removed outlier: 6.176A pdb=" N GLU E 85 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N VAL E 68 " --> pdb=" O GLU E 85 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL E 58 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 112 " --> pdb=" O PRO E 57 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 114 " --> pdb=" O SER E 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 39 through 45 removed outlier: 6.262A pdb=" N GLU F 85 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N VAL F 68 " --> pdb=" O GLU F 85 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU F 87 " --> pdb=" O GLY F 66 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY F 66 " --> pdb=" O GLU F 87 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL F 58 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N LEU F 114 " --> pdb=" O PRO F 57 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER F 59 " --> pdb=" O LEU F 114 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N VAL F 116 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N TYR F 111 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 102 " --> pdb=" O TYR F 111 " (cutoff:3.500A) 177 hydrogen bonds defined for protein. 468 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: 0.59 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2306 1.34 - 1.46: 1216 1.46 - 1.57: 3568 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 7110 Sorted by residual: bond pdb=" CA ILE C 93 " pdb=" CB ILE C 93 " ideal model delta sigma weight residual 1.539 1.526 0.013 7.50e-03 1.78e+04 3.14e+00 bond pdb=" C LEU F 143 " pdb=" N GLU F 144 " ideal model delta sigma weight residual 1.332 1.311 0.021 1.40e-02 5.10e+03 2.32e+00 bond pdb=" N ILE C 93 " pdb=" CA ILE C 93 " ideal model delta sigma weight residual 1.454 1.466 -0.011 7.70e-03 1.69e+04 2.22e+00 bond pdb=" C ASP D 74 " pdb=" O ASP D 74 " ideal model delta sigma weight residual 1.249 1.236 0.013 8.50e-03 1.38e+04 2.18e+00 bond pdb=" N GLY D 108 " pdb=" CA GLY D 108 " ideal model delta sigma weight residual 1.453 1.441 0.012 8.60e-03 1.35e+04 1.85e+00 ... (remaining 7105 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.43: 8906 1.43 - 2.87: 664 2.87 - 4.30: 96 4.30 - 5.74: 14 5.74 - 7.17: 1 Bond angle restraints: 9681 Sorted by residual: angle pdb=" N TYR H 67 " pdb=" CA TYR H 67 " pdb=" C TYR H 67 " ideal model delta sigma weight residual 113.38 109.47 3.91 1.23e+00 6.61e-01 1.01e+01 angle pdb=" N THR C 36 " pdb=" CA THR C 36 " pdb=" C THR C 36 " ideal model delta sigma weight residual 108.38 112.56 -4.18 1.35e+00 5.49e-01 9.58e+00 angle pdb=" C LEU H 64 " pdb=" N BLEU H 65 " pdb=" CA BLEU H 65 " ideal model delta sigma weight residual 120.06 123.70 -3.64 1.19e+00 7.06e-01 9.34e+00 angle pdb=" N HIS D 92 " pdb=" CA HIS D 92 " pdb=" C HIS D 92 " ideal model delta sigma weight residual 107.23 112.15 -4.92 1.67e+00 3.59e-01 8.68e+00 angle pdb=" N SER F 139 " pdb=" CA SER F 139 " pdb=" C SER F 139 " ideal model delta sigma weight residual 108.38 112.17 -3.79 1.35e+00 5.49e-01 7.88e+00 ... (remaining 9676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.04: 3725 15.04 - 30.09: 419 30.09 - 45.13: 121 45.13 - 60.18: 13 60.18 - 75.22: 8 Dihedral angle restraints: 4286 sinusoidal: 1701 harmonic: 2585 Sorted by residual: dihedral pdb=" CA PRO E 38 " pdb=" C PRO E 38 " pdb=" N THR E 39 " pdb=" CA THR E 39 " ideal model delta harmonic sigma weight residual 180.00 -161.00 -19.00 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA GLU D 87 " pdb=" C GLU D 87 " pdb=" N GLN D 88 " pdb=" CA GLN D 88 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA GLU A 87 " pdb=" C GLU A 87 " pdb=" N GLN A 88 " pdb=" CA GLN A 88 " ideal model delta harmonic sigma weight residual 180.00 -161.47 -18.53 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 4283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 673 0.030 - 0.060: 293 0.060 - 0.090: 80 0.090 - 0.120: 76 0.120 - 0.151: 18 Chirality restraints: 1140 Sorted by residual: chirality pdb=" CG LEU E 107 " pdb=" CB LEU E 107 " pdb=" CD1 LEU E 107 " pdb=" CD2 LEU E 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.67e-01 chirality pdb=" CA ILE E 86 " pdb=" N ILE E 86 " pdb=" C ILE E 86 " pdb=" CB ILE E 86 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CA VAL F 58 " pdb=" N VAL F 58 " pdb=" C VAL F 58 " pdb=" CB VAL F 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.05e-01 ... (remaining 1137 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU C 37 " -0.043 5.00e-02 4.00e+02 6.63e-02 7.04e+00 pdb=" N PRO C 38 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 38 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 38 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C BLEU H 65 " -0.032 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO H 66 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO H 66 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 66 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALEU H 65 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO H 66 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO H 66 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 66 " -0.025 5.00e-02 4.00e+02 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 588 2.73 - 3.28: 7017 3.28 - 3.82: 9685 3.82 - 4.36: 10683 4.36 - 4.90: 18296 Nonbonded interactions: 46269 Sorted by model distance: nonbonded pdb=" OD1 ASP B 70 " pdb=" OG1 THR B 83 " model vdw 2.193 3.040 nonbonded pdb=" O THR E 133 " pdb=" NE2 GLN E 135 " model vdw 2.238 3.120 nonbonded pdb=" NZ LYS H 128 " pdb=" OG1 THR H 129 " model vdw 2.249 3.120 nonbonded pdb=" OG SER D 139 " pdb=" N ALA D 140 " model vdw 2.285 3.120 nonbonded pdb=" OG1 THR B 39 " pdb=" OE1 GLU B 85 " model vdw 2.296 3.040 ... (remaining 46264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 36 through 152) selection = (chain 'D' and resid 36 through 152) selection = (chain 'E' and resid 36 through 152) selection = (chain 'F' and resid 36 through 152) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 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: 2.870 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.550 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 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 0.046 7110 Z= 0.197 Angle : 0.817 7.169 9681 Z= 0.496 Chirality : 0.045 0.151 1140 Planarity : 0.005 0.066 1250 Dihedral : 13.746 75.219 2644 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 15.91 % Favored : 83.86 % Rotamer: Outliers : 0.26 % Allowed : 6.78 % Favored : 92.96 % 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 aren not related in a simple way. whole: -4.77 (0.22), residues: 892 helix: -3.04 (0.39), residues: 100 sheet: -2.61 (0.31), residues: 188 loop : -3.63 (0.20), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 143 TYR 0.013 0.001 TYR D 111 PHE 0.010 0.001 PHE F 46 TRP 0.004 0.001 TRP H 152 HIS 0.001 0.000 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 7110) covalent geometry : angle 0.81681 ( 9681) hydrogen bonds : bond 0.15463 ( 177) hydrogen bonds : angle 6.11495 ( 468) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 199 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 147 ARG cc_start: 0.8411 (mtt90) cc_final: 0.8109 (mtt-85) REVERT: A 79 LEU cc_start: 0.9083 (mm) cc_final: 0.8804 (mp) REVERT: A 109 GLU cc_start: 0.8059 (mp0) cc_final: 0.7806 (mp0) REVERT: B 115 ASN cc_start: 0.8965 (t0) cc_final: 0.8550 (t0) REVERT: C 76 LYS cc_start: 0.9233 (tppt) cc_final: 0.8925 (tppt) REVERT: D 67 ARG cc_start: 0.7901 (ptt180) cc_final: 0.7679 (ptt90) REVERT: D 115 ASN cc_start: 0.8279 (t0) cc_final: 0.8078 (t0) REVERT: D 150 PHE cc_start: 0.7352 (m-10) cc_final: 0.6976 (m-10) REVERT: E 67 ARG cc_start: 0.7627 (ptt90) cc_final: 0.7419 (ptt90) REVERT: E 130 ASP cc_start: 0.8325 (t0) cc_final: 0.7889 (t0) REVERT: E 132 ASP cc_start: 0.8208 (t0) cc_final: 0.7949 (t0) REVERT: E 150 PHE cc_start: 0.8351 (t80) cc_final: 0.8090 (t80) REVERT: F 129 LYS cc_start: 0.8801 (mppt) cc_final: 0.8312 (mtmm) REVERT: F 132 ASP cc_start: 0.8448 (m-30) cc_final: 0.8206 (m-30) REVERT: F 138 LYS cc_start: 0.8624 (mmmm) cc_final: 0.8242 (mmtt) REVERT: F 149 GLN cc_start: 0.7977 (mt0) cc_final: 0.7702 (mt0) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1020 time to fit residues: 24.9861 Evaluate side-chains 146 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0670 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 overall best weight: 0.8118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 GLN ** H 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN D 91 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.103019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.075045 restraints weight = 106657.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077880 restraints weight = 57057.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.081241 restraints weight = 24777.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.081691 restraints weight = 15235.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.082144 restraints weight = 13971.054| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3004 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7110 Z= 0.120 Angle : 0.676 8.262 9681 Z= 0.342 Chirality : 0.046 0.172 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.786 20.030 988 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 0.26 % Allowed : 5.87 % Favored : 93.87 % 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 aren not related in a simple way. whole: -3.95 (0.23), residues: 892 helix: -2.02 (0.41), residues: 106 sheet: -2.08 (0.33), residues: 187 loop : -3.13 (0.21), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 55 TYR 0.010 0.001 TYR D 40 PHE 0.005 0.001 PHE E 46 TRP 0.006 0.001 TRP H 181 HIS 0.003 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7110) covalent geometry : angle 0.67642 ( 9681) hydrogen bonds : bond 0.04531 ( 177) hydrogen bonds : angle 5.35674 ( 468) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7877 (tp30) REVERT: A 79 LEU cc_start: 0.9085 (mm) cc_final: 0.8790 (mp) REVERT: A 139 SER cc_start: 0.9388 (t) cc_final: 0.9069 (m) REVERT: B 119 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 127 ILE cc_start: 0.7696 (mm) cc_final: 0.7448 (mt) REVERT: C 67 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7821 (ttm170) REVERT: C 76 LYS cc_start: 0.9232 (tppt) cc_final: 0.8881 (tppt) REVERT: D 37 GLU cc_start: 0.7881 (mp0) cc_final: 0.7607 (mp0) REVERT: D 67 ARG cc_start: 0.8133 (ptt180) cc_final: 0.7927 (ptp90) REVERT: D 88 GLN cc_start: 0.6635 (tp40) cc_final: 0.6276 (tp-100) REVERT: D 144 GLU cc_start: 0.8992 (mp0) cc_final: 0.8169 (mp0) REVERT: D 150 PHE cc_start: 0.7399 (m-10) cc_final: 0.6948 (m-10) REVERT: E 130 ASP cc_start: 0.8475 (t0) cc_final: 0.7870 (t0) REVERT: E 132 ASP cc_start: 0.8467 (t0) cc_final: 0.8030 (t0) REVERT: E 135 GLN cc_start: 0.8069 (tp40) cc_final: 0.7835 (tp40) REVERT: E 150 PHE cc_start: 0.8308 (t80) cc_final: 0.8090 (t80) REVERT: F 129 LYS cc_start: 0.8719 (mppt) cc_final: 0.8438 (mtmm) REVERT: F 132 ASP cc_start: 0.8550 (m-30) cc_final: 0.8290 (m-30) REVERT: F 138 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8394 (mmtt) outliers start: 0 outliers final: 0 residues processed: 183 average time/residue: 0.1052 time to fit residues: 23.6679 Evaluate side-chains 147 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 155 ASN ** 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 = 0.3325 r_free = 0.3325 target = 0.099271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.069999 restraints weight = 93192.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.072755 restraints weight = 48404.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.075645 restraints weight = 24462.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.076516 restraints weight = 16102.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.076914 restraints weight = 15082.385| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7110 Z= 0.218 Angle : 0.731 8.120 9681 Z= 0.375 Chirality : 0.047 0.175 1140 Planarity : 0.005 0.064 1250 Dihedral : 5.228 19.137 988 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.50 % Favored : 87.39 % Rotamer: Outliers : 0.39 % Allowed : 6.00 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.61 (0.24), residues: 892 helix: -1.35 (0.45), residues: 106 sheet: -1.76 (0.36), residues: 174 loop : -3.00 (0.21), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 147 TYR 0.014 0.001 TYR D 40 PHE 0.013 0.002 PHE E 150 TRP 0.006 0.002 TRP H 161 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00519 ( 7110) covalent geometry : angle 0.73143 ( 9681) hydrogen bonds : bond 0.05466 ( 177) hydrogen bonds : angle 5.90940 ( 468) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7961 (tp30) REVERT: A 79 LEU cc_start: 0.9141 (mm) cc_final: 0.8796 (mp) REVERT: A 109 GLU cc_start: 0.7788 (mp0) cc_final: 0.7450 (mp0) REVERT: A 139 SER cc_start: 0.9419 (t) cc_final: 0.9002 (m) REVERT: B 119 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7426 (tm-30) REVERT: B 127 ILE cc_start: 0.7843 (mm) cc_final: 0.7633 (mt) REVERT: C 67 ARG cc_start: 0.8230 (ttm170) cc_final: 0.7847 (ttm170) REVERT: C 76 LYS cc_start: 0.9310 (tppt) cc_final: 0.8863 (tppt) REVERT: C 138 LYS cc_start: 0.8714 (tptt) cc_final: 0.8503 (tppp) REVERT: D 34 ILE cc_start: 0.8050 (mt) cc_final: 0.7833 (mt) REVERT: D 37 GLU cc_start: 0.7982 (mp0) cc_final: 0.7729 (mp0) REVERT: D 67 ARG cc_start: 0.8185 (ptt180) cc_final: 0.7954 (ptp90) REVERT: D 88 GLN cc_start: 0.7397 (tp40) cc_final: 0.6915 (tp-100) REVERT: D 141 MET cc_start: 0.8591 (tmm) cc_final: 0.8316 (tmm) REVERT: D 150 PHE cc_start: 0.7611 (m-10) cc_final: 0.7108 (m-10) REVERT: E 70 ASP cc_start: 0.8632 (t70) cc_final: 0.8422 (t0) REVERT: E 130 ASP cc_start: 0.8533 (t0) cc_final: 0.7960 (t0) REVERT: E 132 ASP cc_start: 0.8349 (t0) cc_final: 0.7950 (t0) REVERT: E 135 GLN cc_start: 0.8345 (tp40) cc_final: 0.7863 (tp40) REVERT: F 47 ASP cc_start: 0.8706 (p0) cc_final: 0.8187 (t0) REVERT: F 129 LYS cc_start: 0.8809 (mppt) cc_final: 0.8352 (mtmm) REVERT: F 132 ASP cc_start: 0.8703 (m-30) cc_final: 0.8349 (m-30) REVERT: F 138 LYS cc_start: 0.8685 (mmmm) cc_final: 0.8314 (mmtt) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1016 time to fit residues: 20.4640 Evaluate side-chains 146 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 overall best weight: 1.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.101472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.079915 restraints weight = 99993.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081448 restraints weight = 64328.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.085131 restraints weight = 23603.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.086527 restraints weight = 11576.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.086866 restraints weight = 8538.506| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7110 Z= 0.146 Angle : 0.696 7.469 9681 Z= 0.352 Chirality : 0.046 0.185 1140 Planarity : 0.005 0.063 1250 Dihedral : 4.875 20.745 988 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.75 % Favored : 91.02 % Rotamer: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % 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 aren not related in a simple way. whole: -3.25 (0.24), residues: 892 helix: -0.98 (0.45), residues: 112 sheet: -1.35 (0.39), residues: 167 loop : -2.83 (0.21), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.010 0.001 TYR D 40 PHE 0.009 0.001 PHE E 150 TRP 0.007 0.002 TRP H 181 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 7110) covalent geometry : angle 0.69565 ( 9681) hydrogen bonds : bond 0.04545 ( 177) hydrogen bonds : angle 5.62491 ( 468) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7793 (tp30) REVERT: A 79 LEU cc_start: 0.9106 (mm) cc_final: 0.8832 (mp) REVERT: A 109 GLU cc_start: 0.7632 (mp0) cc_final: 0.7248 (mp0) REVERT: C 67 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7565 (ttm170) REVERT: C 71 ILE cc_start: 0.8598 (pt) cc_final: 0.8371 (pt) REVERT: C 76 LYS cc_start: 0.9155 (tppt) cc_final: 0.8751 (tppt) REVERT: D 37 GLU cc_start: 0.7978 (mp0) cc_final: 0.7679 (mp0) REVERT: D 67 ARG cc_start: 0.8177 (ptt180) cc_final: 0.7951 (ptp90) REVERT: D 88 GLN cc_start: 0.7207 (tp40) cc_final: 0.6605 (tp-100) REVERT: D 141 MET cc_start: 0.8492 (tmm) cc_final: 0.8181 (tmm) REVERT: D 150 PHE cc_start: 0.7478 (m-10) cc_final: 0.6951 (m-10) REVERT: E 130 ASP cc_start: 0.8453 (t0) cc_final: 0.7825 (t0) REVERT: E 132 ASP cc_start: 0.8354 (t0) cc_final: 0.7943 (t0) REVERT: E 150 PHE cc_start: 0.8454 (t80) cc_final: 0.8063 (t80) REVERT: F 38 PRO cc_start: 0.8234 (Cg_exo) cc_final: 0.7996 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8684 (p0) cc_final: 0.8088 (t0) REVERT: F 129 LYS cc_start: 0.8782 (mppt) cc_final: 0.8413 (mtmm) REVERT: F 132 ASP cc_start: 0.8723 (m-30) cc_final: 0.8407 (m-30) REVERT: F 138 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8259 (mmtt) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1014 time to fit residues: 21.0445 Evaluate side-chains 144 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 63 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.079444 restraints weight = 60507.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082897 restraints weight = 47655.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.085133 restraints weight = 18779.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.086727 restraints weight = 12789.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087213 restraints weight = 9962.025| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3081 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7110 Z= 0.110 Angle : 0.678 9.814 9681 Z= 0.339 Chirality : 0.045 0.192 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.502 18.987 988 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.39 % Favored : 92.39 % Rotamer: Outliers : 0.26 % Allowed : 3.39 % Favored : 96.35 % 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 aren not related in a simple way. whole: -2.84 (0.25), residues: 892 helix: -0.40 (0.49), residues: 106 sheet: -1.16 (0.38), residues: 180 loop : -2.57 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.008 0.001 TYR H 112 PHE 0.010 0.001 PHE C 150 TRP 0.009 0.002 TRP H 181 HIS 0.001 0.000 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7110) covalent geometry : angle 0.67808 ( 9681) hydrogen bonds : bond 0.03645 ( 177) hydrogen bonds : angle 5.40521 ( 468) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 179 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9014 (mm) cc_final: 0.8750 (mp) REVERT: A 109 GLU cc_start: 0.7655 (mp0) cc_final: 0.7268 (mp0) REVERT: C 138 LYS cc_start: 0.8687 (tptt) cc_final: 0.8485 (tppp) REVERT: D 37 GLU cc_start: 0.8046 (mp0) cc_final: 0.7797 (mp0) REVERT: D 67 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7932 (ptp90) REVERT: D 88 GLN cc_start: 0.7094 (tp40) cc_final: 0.6443 (tp-100) REVERT: E 130 ASP cc_start: 0.8449 (t0) cc_final: 0.7787 (t0) REVERT: E 132 ASP cc_start: 0.8421 (t0) cc_final: 0.7966 (t0) REVERT: E 150 PHE cc_start: 0.8459 (t80) cc_final: 0.8024 (t80) REVERT: F 38 PRO cc_start: 0.8185 (Cg_exo) cc_final: 0.7970 (Cg_endo) REVERT: F 129 LYS cc_start: 0.8787 (mppt) cc_final: 0.8395 (mtmm) REVERT: F 132 ASP cc_start: 0.8672 (m-30) cc_final: 0.8366 (m-30) REVERT: F 138 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8305 (mmtt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1026 time to fit residues: 23.2074 Evaluate side-chains 146 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 72 optimal weight: 7.9990 chunk 13 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.099183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.070467 restraints weight = 109611.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.073562 restraints weight = 54125.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.076201 restraints weight = 24410.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.077140 restraints weight = 16573.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.077445 restraints weight = 14547.888| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2919 r_free = 0.2919 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7110 Z= 0.240 Angle : 0.759 6.993 9681 Z= 0.388 Chirality : 0.047 0.191 1140 Planarity : 0.005 0.060 1250 Dihedral : 5.254 18.632 988 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 12.27 % Favored : 87.61 % Rotamer: Outliers : 0.26 % Allowed : 3.78 % Favored : 95.96 % 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 aren not related in a simple way. whole: -2.89 (0.25), residues: 892 helix: -0.41 (0.48), residues: 103 sheet: -1.23 (0.38), residues: 181 loop : -2.60 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 147 TYR 0.014 0.001 TYR D 111 PHE 0.021 0.002 PHE D 46 TRP 0.009 0.002 TRP H 152 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 7110) covalent geometry : angle 0.75930 ( 9681) hydrogen bonds : bond 0.05457 ( 177) hydrogen bonds : angle 6.05460 ( 468) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7863 (mp0) cc_final: 0.7504 (mp0) REVERT: C 71 ILE cc_start: 0.8716 (pt) cc_final: 0.8454 (pt) REVERT: C 76 LYS cc_start: 0.9265 (tptp) cc_final: 0.9012 (tppt) REVERT: C 138 LYS cc_start: 0.8702 (tptt) cc_final: 0.8494 (tppp) REVERT: D 67 ARG cc_start: 0.8201 (ptt180) cc_final: 0.7751 (ptp90) REVERT: D 85 GLU cc_start: 0.8491 (pp20) cc_final: 0.7936 (pp20) REVERT: D 88 GLN cc_start: 0.7435 (tp40) cc_final: 0.6840 (tp-100) REVERT: D 150 PHE cc_start: 0.7531 (m-10) cc_final: 0.7070 (m-10) REVERT: E 130 ASP cc_start: 0.8591 (t0) cc_final: 0.7930 (t0) REVERT: E 132 ASP cc_start: 0.8464 (t0) cc_final: 0.8038 (t0) REVERT: F 38 PRO cc_start: 0.8415 (Cg_exo) cc_final: 0.8164 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8628 (p0) cc_final: 0.8231 (t0) REVERT: F 129 LYS cc_start: 0.8801 (mppt) cc_final: 0.8381 (mtmm) REVERT: F 132 ASP cc_start: 0.8784 (m-30) cc_final: 0.8418 (m-30) REVERT: F 138 LYS cc_start: 0.8657 (mmmm) cc_final: 0.8276 (mmtt) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.0991 time to fit residues: 20.2693 Evaluate side-chains 138 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 3 optimal weight: 0.0020 chunk 13 optimal weight: 6.9990 chunk 6 optimal weight: 0.0570 chunk 76 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.073779 restraints weight = 86478.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.076774 restraints weight = 44570.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.079515 restraints weight = 23210.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.079907 restraints weight = 15849.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.080300 restraints weight = 15047.940| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2959 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2959 r_free = 0.2959 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.2959 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7110 Z= 0.118 Angle : 0.692 8.244 9681 Z= 0.344 Chirality : 0.045 0.160 1140 Planarity : 0.005 0.058 1250 Dihedral : 4.687 18.404 988 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % Favored : 92.16 % Rotamer: Outliers : 0.26 % Allowed : 1.69 % Favored : 98.04 % 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 aren not related in a simple way. whole: -2.68 (0.26), residues: 892 helix: -0.33 (0.48), residues: 108 sheet: -1.13 (0.37), residues: 189 loop : -2.44 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 147 TYR 0.011 0.001 TYR B 152 PHE 0.009 0.001 PHE D 46 TRP 0.009 0.002 TRP H 181 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7110) covalent geometry : angle 0.69162 ( 9681) hydrogen bonds : bond 0.03781 ( 177) hydrogen bonds : angle 5.62309 ( 468) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LEU cc_start: 0.9012 (mm) cc_final: 0.8734 (mp) REVERT: A 109 GLU cc_start: 0.7828 (mp0) cc_final: 0.7472 (mp0) REVERT: A 110 GLN cc_start: 0.8600 (mt0) cc_final: 0.8309 (mt0) REVERT: C 76 LYS cc_start: 0.9256 (tptp) cc_final: 0.9008 (tppt) REVERT: D 37 GLU cc_start: 0.8203 (mp0) cc_final: 0.7949 (mp0) REVERT: D 67 ARG cc_start: 0.8181 (ptt180) cc_final: 0.7862 (ptp90) REVERT: E 130 ASP cc_start: 0.8485 (t0) cc_final: 0.7832 (t0) REVERT: E 132 ASP cc_start: 0.8475 (t0) cc_final: 0.8051 (t0) REVERT: E 135 GLN cc_start: 0.7927 (tp40) cc_final: 0.7696 (tp40) REVERT: F 38 PRO cc_start: 0.8308 (Cg_exo) cc_final: 0.8091 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8677 (p0) cc_final: 0.8042 (t0) REVERT: F 129 LYS cc_start: 0.8724 (mppt) cc_final: 0.8320 (mtmm) REVERT: F 132 ASP cc_start: 0.8723 (m-30) cc_final: 0.8379 (m-30) REVERT: F 138 LYS cc_start: 0.8654 (mmmm) cc_final: 0.8304 (mmtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.0954 time to fit residues: 21.0883 Evaluate side-chains 145 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 78 optimal weight: 0.0030 chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.104495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081109 restraints weight = 90183.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.083392 restraints weight = 57506.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087280 restraints weight = 21685.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089416 restraints weight = 11512.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089611 restraints weight = 8698.080| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 : 0.002 0.047 7110 Z= 0.109 Angle : 0.683 11.141 9681 Z= 0.335 Chirality : 0.044 0.178 1140 Planarity : 0.005 0.058 1250 Dihedral : 4.432 21.185 988 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.18 % Favored : 91.70 % Rotamer: Outliers : 0.26 % Allowed : 2.48 % Favored : 97.26 % 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 aren not related in a simple way. whole: -2.41 (0.26), residues: 892 helix: -0.17 (0.49), residues: 108 sheet: -0.81 (0.39), residues: 184 loop : -2.29 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 147 TYR 0.011 0.001 TYR E 152 PHE 0.005 0.001 PHE C 150 TRP 0.010 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7110) covalent geometry : angle 0.68267 ( 9681) hydrogen bonds : bond 0.03409 ( 177) hydrogen bonds : angle 5.39158 ( 468) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7702 (mp0) cc_final: 0.7309 (mp0) REVERT: A 110 GLN cc_start: 0.8635 (mt0) cc_final: 0.8263 (mt0) REVERT: C 55 ARG cc_start: 0.8198 (mmm-85) cc_final: 0.7997 (mmm-85) REVERT: C 67 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7860 (ttm170) REVERT: D 67 ARG cc_start: 0.8142 (ptt180) cc_final: 0.7870 (ptp90) REVERT: E 130 ASP cc_start: 0.8314 (t0) cc_final: 0.7658 (t0) REVERT: E 132 ASP cc_start: 0.8418 (t0) cc_final: 0.7983 (t0) REVERT: E 150 PHE cc_start: 0.8199 (t80) cc_final: 0.7934 (t80) REVERT: F 129 LYS cc_start: 0.8743 (mppt) cc_final: 0.8323 (mtmm) REVERT: F 132 ASP cc_start: 0.8688 (m-30) cc_final: 0.8431 (m-30) REVERT: F 138 LYS cc_start: 0.8584 (mmmm) cc_final: 0.8268 (mmtt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.0865 time to fit residues: 19.3873 Evaluate side-chains 138 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 59 optimal weight: 3.9990 chunk 78 optimal weight: 0.0060 chunk 83 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 0.0070 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.104775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080711 restraints weight = 74414.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.082938 restraints weight = 53663.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.085680 restraints weight = 21838.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.088089 restraints weight = 13769.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.089879 restraints weight = 9551.057| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7110 Z= 0.110 Angle : 0.690 9.274 9681 Z= 0.338 Chirality : 0.045 0.225 1140 Planarity : 0.005 0.059 1250 Dihedral : 4.343 22.883 988 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.84 % Favored : 91.93 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.24 (0.26), residues: 892 helix: -0.08 (0.49), residues: 108 sheet: -0.68 (0.39), residues: 184 loop : -2.17 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 147 TYR 0.009 0.001 TYR B 152 PHE 0.006 0.001 PHE D 46 TRP 0.010 0.001 TRP H 181 HIS 0.001 0.000 HIS D 92 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 7110) covalent geometry : angle 0.68980 ( 9681) hydrogen bonds : bond 0.03323 ( 177) hydrogen bonds : angle 5.30599 ( 468) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 THR cc_start: 0.8384 (t) cc_final: 0.7905 (t) REVERT: A 109 GLU cc_start: 0.7697 (mp0) cc_final: 0.7308 (mp0) REVERT: A 110 GLN cc_start: 0.8684 (mt0) cc_final: 0.8296 (mt0) REVERT: C 67 ARG cc_start: 0.8083 (ttm170) cc_final: 0.7820 (ttm170) REVERT: C 139 SER cc_start: 0.9079 (t) cc_final: 0.8347 (t) REVERT: D 67 ARG cc_start: 0.8098 (ptt180) cc_final: 0.7781 (ptp90) REVERT: E 130 ASP cc_start: 0.8395 (t0) cc_final: 0.7668 (t0) REVERT: E 132 ASP cc_start: 0.8465 (t0) cc_final: 0.7982 (t0) REVERT: E 150 PHE cc_start: 0.8158 (t80) cc_final: 0.7853 (t80) REVERT: F 129 LYS cc_start: 0.8743 (mppt) cc_final: 0.8308 (mtmm) REVERT: F 132 ASP cc_start: 0.8683 (m-30) cc_final: 0.8421 (m-30) REVERT: F 138 LYS cc_start: 0.8587 (mmmm) cc_final: 0.8321 (mmtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.1077 time to fit residues: 23.4238 Evaluate side-chains 142 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 55 optimal weight: 0.0470 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 45 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 overall best weight: 0.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080925 restraints weight = 76084.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.083937 restraints weight = 53088.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.086495 restraints weight = 20308.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.088862 restraints weight = 13153.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.089430 restraints weight = 9137.034| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7110 Z= 0.115 Angle : 0.702 8.954 9681 Z= 0.345 Chirality : 0.045 0.226 1140 Planarity : 0.005 0.059 1250 Dihedral : 4.322 22.888 988 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.05 % Rotamer: Outliers : 0.26 % Allowed : 0.65 % Favored : 99.09 % 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 aren not related in a simple way. whole: -2.14 (0.27), residues: 892 helix: -0.07 (0.49), residues: 109 sheet: -0.65 (0.38), residues: 192 loop : -2.09 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 147 TYR 0.011 0.001 TYR A 40 PHE 0.006 0.001 PHE D 46 TRP 0.010 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7110) covalent geometry : angle 0.70244 ( 9681) hydrogen bonds : bond 0.03340 ( 177) hydrogen bonds : angle 5.28000 ( 468) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1784 Ramachandran restraints generated. 892 Oldfield, 0 Emsley, 892 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7741 (mp0) cc_final: 0.7346 (mp0) REVERT: A 110 GLN cc_start: 0.8685 (mt0) cc_final: 0.8235 (mt0) REVERT: C 47 ASP cc_start: 0.8346 (p0) cc_final: 0.7904 (p0) REVERT: C 138 LYS cc_start: 0.8968 (tptt) cc_final: 0.8743 (tppp) REVERT: D 67 ARG cc_start: 0.8123 (ptt180) cc_final: 0.7786 (ptp90) REVERT: E 130 ASP cc_start: 0.8485 (t0) cc_final: 0.7624 (t0) REVERT: E 132 ASP cc_start: 0.8499 (t0) cc_final: 0.8008 (t0) REVERT: E 150 PHE cc_start: 0.8167 (t80) cc_final: 0.7890 (t80) REVERT: F 129 LYS cc_start: 0.8734 (mppt) cc_final: 0.8314 (mtmm) REVERT: F 132 ASP cc_start: 0.8697 (m-30) cc_final: 0.8443 (m-30) REVERT: F 138 LYS cc_start: 0.8629 (mmmm) cc_final: 0.8364 (mmtt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.1012 time to fit residues: 22.2918 Evaluate side-chains 139 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 0.0370 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 52 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.104628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.075360 restraints weight = 97383.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.079183 restraints weight = 45081.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.082225 restraints weight = 20628.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.082616 restraints weight = 14162.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.082939 restraints weight = 13244.083| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 19 | |-----------------------------------------------------------------------------| r_final: 0.3009 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.4021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7110 Z= 0.112 Angle : 0.680 8.633 9681 Z= 0.333 Chirality : 0.045 0.192 1140 Planarity : 0.005 0.059 1250 Dihedral : 4.295 22.968 988 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.50 % Favored : 92.27 % Rotamer: Outliers : 0.26 % Allowed : 1.04 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.27), residues: 892 helix: -0.00 (0.50), residues: 108 sheet: -0.63 (0.38), residues: 192 loop : -2.04 (0.24), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 147 TYR 0.008 0.001 TYR B 40 PHE 0.006 0.001 PHE D 46 TRP 0.009 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 7110) covalent geometry : angle 0.68047 ( 9681) hydrogen bonds : bond 0.03334 ( 177) hydrogen bonds : angle 5.21791 ( 468) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1371.28 seconds wall clock time: 24 minutes 14.01 seconds (1454.01 seconds total)