Starting phenix.real_space_refine on Wed Feb 12 00:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oj4_16904/02_2025/8oj4_16904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oj4_16904/02_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_16904/02_2025/8oj4_16904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oj4_16904/02_2025/8oj4_16904.map" model { file = "/net/cci-nas-00/data/ceres_data/8oj4_16904/02_2025/8oj4_16904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oj4_16904/02_2025/8oj4_16904.cif" } resolution = 4.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.013 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.01, per 1000 atoms: 0.86 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: 1.55 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.84 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: 1.81 Time building geometry restraints manager: 1.91 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: 3.420 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- 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= 0.237 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.004 0.001 TRP H 152 HIS 0.001 0.000 HIS B 92 PHE 0.010 0.001 PHE F 46 TYR 0.013 0.001 TYR D 111 ARG 0.002 0.000 ARG H 143 *********************** 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 : 0.838 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: 0.8549 (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: 0.7680 (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: 0.6977 (m-10) REVERT: E 67 ARG cc_start: 0.7627 (ptt90) cc_final: 0.7420 (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: 0.7703 (mt0) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.2644 time to fit residues: 64.5827 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 : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.100557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.071226 restraints weight = 91948.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.074578 restraints weight = 46837.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.077349 restraints weight = 22425.607| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2905 r_free = 0.2905 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7110 Z= 0.257 Angle : 0.706 8.293 9681 Z= 0.361 Chirality : 0.047 0.174 1140 Planarity : 0.005 0.063 1250 Dihedral : 5.070 20.701 988 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.57 % Favored : 89.43 % Rotamer: Outliers : 0.26 % Allowed : 7.69 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.23), residues: 892 helix: -2.08 (0.40), residues: 106 sheet: -2.11 (0.33), residues: 188 loop : -3.19 (0.20), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 181 HIS 0.003 0.001 HIS H 113 PHE 0.011 0.001 PHE F 46 TYR 0.013 0.001 TYR D 40 ARG 0.008 0.000 ARG H 57 *********************** 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 173 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7980 (tp30) REVERT: A 79 LEU cc_start: 0.9102 (mm) cc_final: 0.8725 (mp) REVERT: A 109 GLU cc_start: 0.7869 (mp0) cc_final: 0.7642 (mp0) REVERT: A 139 SER cc_start: 0.9439 (t) cc_final: 0.9109 (m) REVERT: B 119 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 127 ILE cc_start: 0.7727 (mm) cc_final: 0.7524 (mt) REVERT: C 67 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7794 (ttm170) REVERT: C 76 LYS cc_start: 0.9299 (tppt) cc_final: 0.8936 (tppt) REVERT: D 37 GLU cc_start: 0.7891 (mp0) cc_final: 0.7659 (mp0) REVERT: D 67 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7913 (ptp90) REVERT: D 88 GLN cc_start: 0.6882 (tp-100) cc_final: 0.6609 (tp-100) REVERT: D 150 PHE cc_start: 0.7482 (m-10) cc_final: 0.7060 (m-10) REVERT: E 130 ASP cc_start: 0.8560 (t0) cc_final: 0.7997 (t0) REVERT: E 132 ASP cc_start: 0.8481 (t0) cc_final: 0.8051 (t0) REVERT: E 135 GLN cc_start: 0.8188 (tp40) cc_final: 0.7909 (tp40) REVERT: E 150 PHE cc_start: 0.8439 (t80) cc_final: 0.8147 (t80) REVERT: F 47 ASP cc_start: 0.8704 (p0) cc_final: 0.8079 (t0) REVERT: F 129 LYS cc_start: 0.8722 (mppt) cc_final: 0.8425 (mtmm) REVERT: F 132 ASP cc_start: 0.8601 (m-30) cc_final: 0.8276 (m-30) REVERT: F 138 LYS cc_start: 0.8714 (mmmm) cc_final: 0.8362 (mmtt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2675 time to fit residues: 56.9215 Evaluate side-chains 143 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 5 optimal weight: 0.0040 chunk 13 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.3396 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.102544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.073097 restraints weight = 87061.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.076768 restraints weight = 44990.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.079108 restraints weight = 22298.089| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2668 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= 0.194 Angle : 0.666 8.601 9681 Z= 0.334 Chirality : 0.045 0.178 1140 Planarity : 0.005 0.063 1250 Dihedral : 4.766 18.454 988 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.34 % Favored : 89.43 % Rotamer: Outliers : 0.26 % Allowed : 4.56 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.24), residues: 892 helix: -1.40 (0.43), residues: 112 sheet: -1.83 (0.34), residues: 190 loop : -2.89 (0.22), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 181 HIS 0.002 0.001 HIS H 113 PHE 0.011 0.001 PHE E 150 TYR 0.015 0.001 TYR H 117 ARG 0.007 0.000 ARG H 147 *********************** 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 170 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8005 (tp30) REVERT: A 79 LEU cc_start: 0.9008 (mm) cc_final: 0.8727 (mp) REVERT: A 109 GLU cc_start: 0.7890 (mp0) cc_final: 0.7580 (mp0) REVERT: A 139 SER cc_start: 0.9427 (t) cc_final: 0.9054 (m) REVERT: B 119 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 127 ILE cc_start: 0.7823 (mm) cc_final: 0.7603 (mt) REVERT: C 67 ARG cc_start: 0.8190 (ttm170) cc_final: 0.7623 (ttm170) REVERT: C 76 LYS cc_start: 0.9268 (tppt) cc_final: 0.8923 (tppt) REVERT: D 36 THR cc_start: 0.8506 (p) cc_final: 0.8299 (p) REVERT: D 37 GLU cc_start: 0.7968 (mp0) cc_final: 0.7710 (mp0) REVERT: D 67 ARG cc_start: 0.8158 (ptt180) cc_final: 0.7937 (ptp90) REVERT: D 88 GLN cc_start: 0.6919 (tp-100) cc_final: 0.6588 (tp-100) REVERT: D 150 PHE cc_start: 0.7568 (m-10) cc_final: 0.7065 (m-10) REVERT: E 130 ASP cc_start: 0.8542 (t0) cc_final: 0.7945 (t0) REVERT: E 132 ASP cc_start: 0.8555 (t0) cc_final: 0.8024 (t0) REVERT: E 135 GLN cc_start: 0.8305 (tp40) cc_final: 0.7912 (tp40) REVERT: E 150 PHE cc_start: 0.8607 (t80) cc_final: 0.8364 (t80) REVERT: F 129 LYS cc_start: 0.8793 (mppt) cc_final: 0.8365 (mtmm) REVERT: F 132 ASP cc_start: 0.8659 (m-30) cc_final: 0.8323 (m-30) REVERT: F 138 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8424 (mmtt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2447 time to fit residues: 52.0526 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 : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 74 optimal weight: 6.9990 chunk 71 optimal weight: 0.6980 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.102164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.072499 restraints weight = 105768.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.075632 restraints weight = 56836.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.079214 restraints weight = 25113.469| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2940 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2940 r_free = 0.2940 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 = 0.2940 r_free = 0.2940 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3087 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= 0.202 Angle : 0.656 7.332 9681 Z= 0.330 Chirality : 0.045 0.188 1140 Planarity : 0.005 0.061 1250 Dihedral : 4.650 17.652 988 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.09 % Favored : 90.68 % Rotamer: Outliers : 0.26 % Allowed : 5.48 % Favored : 94.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.25), residues: 892 helix: -0.85 (0.46), residues: 112 sheet: -1.34 (0.37), residues: 180 loop : -2.71 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 152 HIS 0.003 0.001 HIS H 113 PHE 0.007 0.001 PHE F 46 TYR 0.013 0.001 TYR H 117 ARG 0.005 0.000 ARG H 147 *********************** 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 169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8024 (tp30) REVERT: A 79 LEU cc_start: 0.9033 (mm) cc_final: 0.8759 (mp) REVERT: A 109 GLU cc_start: 0.7967 (mp0) cc_final: 0.7547 (mp0) REVERT: A 139 SER cc_start: 0.9433 (t) cc_final: 0.9055 (m) REVERT: C 67 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7800 (ttp-170) REVERT: C 76 LYS cc_start: 0.9279 (tppt) cc_final: 0.8939 (tppt) REVERT: C 138 LYS cc_start: 0.9107 (tppp) cc_final: 0.8883 (tptt) REVERT: D 37 GLU cc_start: 0.8020 (mp0) cc_final: 0.7741 (mp0) REVERT: D 67 ARG cc_start: 0.8170 (ptt180) cc_final: 0.7943 (ptp90) REVERT: D 88 GLN cc_start: 0.6957 (tp-100) cc_final: 0.6583 (tp-100) REVERT: D 150 PHE cc_start: 0.7528 (m-10) cc_final: 0.7043 (m-10) REVERT: E 130 ASP cc_start: 0.8497 (t0) cc_final: 0.7902 (t0) REVERT: E 132 ASP cc_start: 0.8296 (t0) cc_final: 0.7844 (t0) REVERT: E 150 PHE cc_start: 0.8587 (t80) cc_final: 0.8217 (t80) REVERT: F 47 ASP cc_start: 0.8719 (p0) cc_final: 0.8092 (t0) REVERT: F 129 LYS cc_start: 0.8807 (mppt) cc_final: 0.8449 (mtmm) REVERT: F 132 ASP cc_start: 0.8731 (m-30) cc_final: 0.8371 (m-30) REVERT: F 138 LYS cc_start: 0.8717 (mmmm) cc_final: 0.8340 (mmtt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2396 time to fit residues: 50.6539 Evaluate side-chains 141 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 41 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 0.4980 chunk 29 optimal weight: 0.0470 overall best weight: 0.8882 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.103747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.074968 restraints weight = 85449.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.078343 restraints weight = 47394.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.081603 restraints weight = 22352.266| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 7110 Z= 0.169 Angle : 0.676 9.928 9681 Z= 0.335 Chirality : 0.045 0.200 1140 Planarity : 0.005 0.061 1250 Dihedral : 4.403 17.954 988 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.95 % Favored : 91.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.26), residues: 892 helix: -0.40 (0.49), residues: 106 sheet: -1.16 (0.38), residues: 182 loop : -2.46 (0.22), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 152 HIS 0.001 0.000 HIS H 113 PHE 0.008 0.001 PHE E 150 TYR 0.011 0.001 TYR H 117 ARG 0.006 0.000 ARG H 147 *********************** 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 : 0.752 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 109 GLU cc_start: 0.7856 (mp0) cc_final: 0.7465 (mp0) REVERT: A 139 SER cc_start: 0.9376 (t) cc_final: 0.8984 (m) REVERT: C 67 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7548 (ttm170) REVERT: C 76 LYS cc_start: 0.9248 (tppt) cc_final: 0.8923 (tppt) REVERT: D 67 ARG cc_start: 0.8120 (ptt180) cc_final: 0.7902 (ptp90) REVERT: D 150 PHE cc_start: 0.7393 (m-10) cc_final: 0.6932 (m-10) REVERT: E 130 ASP cc_start: 0.8429 (t0) cc_final: 0.7759 (t0) REVERT: E 132 ASP cc_start: 0.8289 (t0) cc_final: 0.7836 (t0) REVERT: E 150 PHE cc_start: 0.8520 (t80) cc_final: 0.8001 (t80) REVERT: F 38 PRO cc_start: 0.8284 (Cg_exo) cc_final: 0.8052 (Cg_endo) REVERT: F 129 LYS cc_start: 0.8823 (mppt) cc_final: 0.8465 (mtmm) REVERT: F 132 ASP cc_start: 0.8726 (m-30) cc_final: 0.8419 (m-30) REVERT: F 138 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8370 (mmtt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.2336 time to fit residues: 52.8369 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 : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 64 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 0.2980 chunk 73 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.103001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.080038 restraints weight = 92058.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.081917 restraints weight = 64155.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.085682 restraints weight = 22987.979| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3479 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= 0.188 Angle : 0.657 7.248 9681 Z= 0.326 Chirality : 0.044 0.196 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.408 18.195 988 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.41 % Favored : 91.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.26), residues: 892 helix: -0.21 (0.50), residues: 103 sheet: -1.01 (0.37), residues: 184 loop : -2.38 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 152 HIS 0.002 0.000 HIS B 92 PHE 0.006 0.001 PHE E 46 TYR 0.014 0.001 TYR B 152 ARG 0.005 0.000 ARG C 89 *********************** 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 169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7856 (mp0) cc_final: 0.7436 (mp0) REVERT: A 139 SER cc_start: 0.9425 (t) cc_final: 0.8993 (m) REVERT: C 76 LYS cc_start: 0.9217 (tppt) cc_final: 0.8942 (tppt) REVERT: D 67 ARG cc_start: 0.8116 (ptt180) cc_final: 0.7828 (ptp90) REVERT: D 88 GLN cc_start: 0.6855 (tp-100) cc_final: 0.6440 (tp-100) REVERT: D 150 PHE cc_start: 0.7338 (m-10) cc_final: 0.6909 (m-10) REVERT: E 53 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8717 (pttt) REVERT: E 130 ASP cc_start: 0.8416 (t0) cc_final: 0.7750 (t0) REVERT: E 132 ASP cc_start: 0.8364 (t0) cc_final: 0.7925 (t0) REVERT: E 150 PHE cc_start: 0.8503 (t80) cc_final: 0.8035 (t80) REVERT: F 38 PRO cc_start: 0.8248 (Cg_exo) cc_final: 0.8025 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8688 (p0) cc_final: 0.8155 (t0) REVERT: F 129 LYS cc_start: 0.8823 (mppt) cc_final: 0.8405 (mtmm) REVERT: F 132 ASP cc_start: 0.8739 (m-30) cc_final: 0.8423 (m-30) REVERT: F 138 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8331 (mmtt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2364 time to fit residues: 50.4136 Evaluate side-chains 140 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 18 optimal weight: 0.0020 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.103493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.079932 restraints weight = 84252.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.082246 restraints weight = 57744.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.086343 restraints weight = 22338.062| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 0.042 7110 Z= 0.171 Angle : 0.650 7.463 9681 Z= 0.323 Chirality : 0.044 0.199 1140 Planarity : 0.005 0.063 1250 Dihedral : 4.352 17.812 988 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.84 % Favored : 91.93 % Rotamer: Outliers : 0.26 % Allowed : 2.87 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.26), residues: 892 helix: -0.29 (0.49), residues: 109 sheet: -0.87 (0.38), residues: 178 loop : -2.25 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 152 HIS 0.001 0.000 HIS H 113 PHE 0.005 0.001 PHE E 46 TYR 0.014 0.001 TYR B 152 ARG 0.005 0.000 ARG C 89 *********************** 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 178 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7867 (mp0) cc_final: 0.7423 (mp0) REVERT: A 139 SER cc_start: 0.9388 (t) cc_final: 0.9004 (m) REVERT: C 67 ARG cc_start: 0.8078 (ttm170) cc_final: 0.7772 (ttp-170) REVERT: D 37 GLU cc_start: 0.8088 (mp0) cc_final: 0.7776 (mp0) REVERT: D 67 ARG cc_start: 0.8153 (ptt180) cc_final: 0.7812 (ptp90) REVERT: D 88 GLN cc_start: 0.6848 (tp-100) cc_final: 0.6417 (tp-100) REVERT: D 150 PHE cc_start: 0.7274 (m-10) cc_final: 0.6895 (m-10) REVERT: E 130 ASP cc_start: 0.8387 (t0) cc_final: 0.7714 (t0) REVERT: E 132 ASP cc_start: 0.8355 (t0) cc_final: 0.7909 (t0) REVERT: E 135 GLN cc_start: 0.8030 (tp40) cc_final: 0.7687 (tp40) REVERT: E 150 PHE cc_start: 0.8531 (t80) cc_final: 0.8041 (t80) REVERT: F 38 PRO cc_start: 0.8194 (Cg_exo) cc_final: 0.7960 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8667 (p0) cc_final: 0.8100 (t0) REVERT: F 129 LYS cc_start: 0.8820 (mppt) cc_final: 0.8405 (mtmm) REVERT: F 132 ASP cc_start: 0.8761 (m-30) cc_final: 0.8476 (m-30) REVERT: F 138 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8321 (mmtt) outliers start: 0 outliers final: 0 residues processed: 178 average time/residue: 0.2423 time to fit residues: 54.3282 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 : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 53 optimal weight: 0.0980 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 ASN D 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.079763 restraints weight = 87173.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.082194 restraints weight = 57069.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.085902 restraints weight = 21381.585| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3056 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3056 r_free = 0.3056 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3056 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3740 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= 0.183 Angle : 0.661 8.090 9681 Z= 0.326 Chirality : 0.044 0.182 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.309 17.828 988 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.41 % Favored : 91.48 % Rotamer: Outliers : 0.26 % Allowed : 1.43 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.26), residues: 892 helix: -0.18 (0.49), residues: 109 sheet: -0.76 (0.38), residues: 178 loop : -2.20 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 152 HIS 0.001 0.000 HIS H 113 PHE 0.005 0.001 PHE F 46 TYR 0.012 0.001 TYR B 152 ARG 0.006 0.000 ARG C 89 *********************** 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 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7863 (mp0) cc_final: 0.7421 (mp0) REVERT: A 139 SER cc_start: 0.9384 (t) cc_final: 0.8889 (m) REVERT: C 76 LYS cc_start: 0.9169 (tptp) cc_final: 0.8962 (tppt) REVERT: D 37 GLU cc_start: 0.8130 (mp0) cc_final: 0.7799 (mp0) REVERT: D 67 ARG cc_start: 0.8176 (ptt180) cc_final: 0.7836 (ptp90) REVERT: D 88 GLN cc_start: 0.6808 (tp-100) cc_final: 0.6365 (tp-100) REVERT: D 150 PHE cc_start: 0.7232 (m-10) cc_final: 0.6861 (m-10) REVERT: E 130 ASP cc_start: 0.8349 (t0) cc_final: 0.7713 (t0) REVERT: E 132 ASP cc_start: 0.8332 (t0) cc_final: 0.7876 (t0) REVERT: E 135 GLN cc_start: 0.7878 (tp40) cc_final: 0.7677 (tp40) REVERT: E 150 PHE cc_start: 0.8505 (t80) cc_final: 0.8046 (t80) REVERT: F 38 PRO cc_start: 0.8142 (Cg_exo) cc_final: 0.7936 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8672 (p0) cc_final: 0.8154 (t0) REVERT: F 129 LYS cc_start: 0.8822 (mppt) cc_final: 0.8390 (mtmm) REVERT: F 132 ASP cc_start: 0.8726 (m-30) cc_final: 0.8447 (m-30) REVERT: F 138 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8234 (mmtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2471 time to fit residues: 54.8698 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 : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 50 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.100293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.076960 restraints weight = 94672.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.079228 restraints weight = 64282.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.082835 restraints weight = 23288.115| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 7110 Z= 0.308 Angle : 0.729 10.756 9681 Z= 0.369 Chirality : 0.045 0.161 1140 Planarity : 0.005 0.063 1250 Dihedral : 4.866 18.262 988 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.68 % Favored : 89.20 % Rotamer: Outliers : 0.26 % Allowed : 2.09 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.26), residues: 892 helix: -0.12 (0.49), residues: 103 sheet: -0.85 (0.38), residues: 181 loop : -2.34 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP H 181 HIS 0.002 0.001 HIS H 113 PHE 0.011 0.001 PHE F 46 TYR 0.012 0.001 TYR B 40 ARG 0.007 0.001 ARG C 89 *********************** 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 170 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7972 (mp0) cc_final: 0.7547 (mp0) REVERT: C 55 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8286 (mmm160) REVERT: C 76 LYS cc_start: 0.9234 (tptp) cc_final: 0.9024 (tppt) REVERT: D 37 GLU cc_start: 0.8156 (mp0) cc_final: 0.7832 (mp0) REVERT: D 67 ARG cc_start: 0.8197 (ptt180) cc_final: 0.7809 (ptp90) REVERT: D 150 PHE cc_start: 0.7400 (m-10) cc_final: 0.7015 (m-10) REVERT: E 130 ASP cc_start: 0.8414 (t0) cc_final: 0.7721 (t0) REVERT: E 132 ASP cc_start: 0.8388 (t0) cc_final: 0.7923 (t0) REVERT: E 135 GLN cc_start: 0.7955 (tp40) cc_final: 0.7746 (tp40) REVERT: E 150 PHE cc_start: 0.8553 (t80) cc_final: 0.8064 (t80) REVERT: F 38 PRO cc_start: 0.8236 (Cg_exo) cc_final: 0.8020 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8706 (p0) cc_final: 0.8176 (t0) REVERT: F 129 LYS cc_start: 0.8828 (mppt) cc_final: 0.8377 (mtmm) REVERT: F 132 ASP cc_start: 0.8795 (m-30) cc_final: 0.8483 (m-30) REVERT: F 138 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8320 (mmtt) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2452 time to fit residues: 53.0955 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 : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 1 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 0.7980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.080689 restraints weight = 92917.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.082609 restraints weight = 61037.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.085049 restraints weight = 21839.079| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3687 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= 0.197 Angle : 0.719 10.390 9681 Z= 0.354 Chirality : 0.045 0.273 1140 Planarity : 0.005 0.063 1250 Dihedral : 4.576 17.979 988 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.95 % Favored : 91.93 % Rotamer: Outliers : 0.26 % Allowed : 1.30 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.26), residues: 892 helix: -0.10 (0.49), residues: 109 sheet: -0.85 (0.38), residues: 187 loop : -2.23 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 181 HIS 0.001 0.001 HIS H 113 PHE 0.009 0.001 PHE D 46 TYR 0.009 0.001 TYR B 152 ARG 0.007 0.000 ARG C 89 ********************** 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 166 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7877 (mp0) cc_final: 0.7544 (mp0) REVERT: A 110 GLN cc_start: 0.8769 (mt0) cc_final: 0.8268 (mt0) REVERT: B 67 ARG cc_start: 0.8566 (mmm-85) cc_final: 0.8120 (mmm-85) REVERT: C 138 LYS cc_start: 0.9164 (tppp) cc_final: 0.8928 (tptt) REVERT: D 37 GLU cc_start: 0.8173 (mp0) cc_final: 0.7917 (mp0) REVERT: D 67 ARG cc_start: 0.8201 (ptt180) cc_final: 0.7849 (ptp90) REVERT: E 130 ASP cc_start: 0.8434 (t0) cc_final: 0.7775 (t0) REVERT: E 132 ASP cc_start: 0.8430 (t0) cc_final: 0.8003 (t0) REVERT: E 150 PHE cc_start: 0.8465 (t80) cc_final: 0.8130 (t80) REVERT: F 47 ASP cc_start: 0.8748 (p0) cc_final: 0.8147 (t0) REVERT: F 129 LYS cc_start: 0.8800 (mppt) cc_final: 0.8371 (mtmm) REVERT: F 132 ASP cc_start: 0.8793 (m-30) cc_final: 0.8475 (m-30) REVERT: F 138 LYS cc_start: 0.8687 (mmmm) cc_final: 0.8320 (mmtt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2396 time to fit residues: 50.3547 Evaluate side-chains 141 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 54 optimal weight: 0.0050 chunk 70 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 51 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.0670 chunk 2 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 GLN ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.105401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.076416 restraints weight = 87877.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079697 restraints weight = 42953.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.082757 restraints weight = 21608.885| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7110 Z= 0.168 Angle : 0.718 9.612 9681 Z= 0.353 Chirality : 0.046 0.261 1140 Planarity : 0.005 0.061 1250 Dihedral : 4.317 20.288 988 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.61 % Favored : 92.16 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.27), residues: 892 helix: -0.21 (0.49), residues: 115 sheet: -0.51 (0.39), residues: 186 loop : -2.09 (0.24), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 181 HIS 0.001 0.000 HIS D 92 PHE 0.008 0.001 PHE D 46 TYR 0.011 0.001 TYR E 40 ARG 0.006 0.000 ARG C 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2797.20 seconds wall clock time: 50 minutes 58.87 seconds (3058.87 seconds total)