Starting phenix.real_space_refine on Wed Mar 12 00:39:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8oj4_16904/03_2025/8oj4_16904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8oj4_16904/03_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_16904/03_2025/8oj4_16904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8oj4_16904/03_2025/8oj4_16904.map" model { file = "/net/cci-nas-00/data/ceres_data/8oj4_16904/03_2025/8oj4_16904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8oj4_16904/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.76, per 1000 atoms: 0.82 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: 1.70 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: 0.68 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: 1.54 Time building geometry restraints manager: 1.94 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: 2.480 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.530 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.470 ------------------------------------------------------------------------------- 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 : 0.756 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: 0.2576 time to fit residues: 63.2477 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 : 0.850 ------------------------------------------------------------------------------- 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 = 91948.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.074575 restraints weight = 46835.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.077353 restraints weight = 22432.307| |-----------------------------------------------------------------------------| 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 : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7981 (tp30) REVERT: A 79 LEU cc_start: 0.9103 (mm) cc_final: 0.8725 (mp) REVERT: A 109 GLU cc_start: 0.7868 (mp0) cc_final: 0.7642 (mp0) REVERT: A 139 SER cc_start: 0.9438 (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: 0.7523 (mt) REVERT: C 67 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7793 (ttm170) REVERT: C 76 LYS cc_start: 0.9298 (tppt) cc_final: 0.8936 (tppt) REVERT: D 37 GLU cc_start: 0.7892 (mp0) cc_final: 0.7660 (mp0) REVERT: D 67 ARG cc_start: 0.8150 (ptt180) cc_final: 0.7914 (ptp90) REVERT: D 88 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6609 (tp-100) REVERT: D 150 PHE cc_start: 0.7482 (m-10) cc_final: 0.7059 (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: 0.8599 (m-30) cc_final: 0.8274 (m-30) REVERT: F 138 LYS cc_start: 0.8713 (mmmm) cc_final: 0.8362 (mmtt) outliers start: 0 outliers final: 0 residues processed: 173 average time/residue: 0.2687 time to fit residues: 56.9886 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 : 0.752 ------------------------------------------------------------------------------- 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: 0.0870 chunk 13 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 16 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7498 ------------------------------------------------------------------------------- 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** H 202 GLN 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 = 0.3400 r_free = 0.3400 target = 0.104343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.075149 restraints weight = 86195.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.078745 restraints weight = 44818.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.081232 restraints weight = 22527.727| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2810 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= 0.156 Angle : 0.649 8.014 9681 Z= 0.323 Chirality : 0.045 0.168 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.584 17.917 988 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.75 % Favored : 91.02 % Rotamer: Outliers : 0.26 % Allowed : 4.82 % Favored : 94.92 % 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: -3.41 (0.24), residues: 892 helix: -1.31 (0.43), residues: 112 sheet: -1.62 (0.36), residues: 185 loop : -2.86 (0.21), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 181 HIS 0.002 0.000 HIS H 113 PHE 0.013 0.001 PHE E 150 TYR 0.015 0.001 TYR H 117 ARG 0.006 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 185 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7980 (tp30) REVERT: A 109 GLU cc_start: 0.7818 (mp0) cc_final: 0.7517 (mp0) REVERT: A 139 SER cc_start: 0.9391 (t) cc_final: 0.9010 (m) REVERT: B 119 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 127 ILE cc_start: 0.7790 (mm) cc_final: 0.7485 (mt) REVERT: C 76 LYS cc_start: 0.9226 (tppt) cc_final: 0.8888 (tppt) REVERT: D 34 ILE cc_start: 0.8119 (mt) cc_final: 0.7824 (mt) REVERT: D 36 THR cc_start: 0.8466 (p) cc_final: 0.8241 (p) REVERT: D 37 GLU cc_start: 0.7977 (mp0) cc_final: 0.7703 (mp0) REVERT: D 88 GLN cc_start: 0.6820 (tp40) cc_final: 0.6364 (tp-100) REVERT: D 150 PHE cc_start: 0.7528 (m-10) cc_final: 0.7018 (m-10) REVERT: E 130 ASP cc_start: 0.8497 (t0) cc_final: 0.7862 (t0) REVERT: E 132 ASP cc_start: 0.8504 (t0) cc_final: 0.8046 (t0) REVERT: E 135 GLN cc_start: 0.8238 (tp40) cc_final: 0.7880 (tp40) REVERT: E 150 PHE cc_start: 0.8543 (t80) cc_final: 0.8218 (t80) REVERT: F 129 LYS cc_start: 0.8815 (mppt) cc_final: 0.8414 (mtmm) REVERT: F 132 ASP cc_start: 0.8640 (m-30) cc_final: 0.8354 (m-30) REVERT: F 138 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8429 (mmtt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2316 time to fit residues: 53.9214 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 : 0.848 ------------------------------------------------------------------------------- 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: 1.9990 chunk 71 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.105055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.075889 restraints weight = 103894.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.079199 restraints weight = 53164.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.082476 restraints weight = 22682.229| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- 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 = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3004 r_free = 0.3004 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3004 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3348 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= 0.153 Angle : 0.639 7.657 9681 Z= 0.318 Chirality : 0.044 0.185 1140 Planarity : 0.005 0.062 1250 Dihedral : 4.358 16.900 988 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.50 % Favored : 92.27 % Rotamer: Outliers : 0.26 % Allowed : 4.95 % Favored : 94.78 % 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: -2.91 (0.26), residues: 892 helix: -0.74 (0.47), residues: 112 sheet: -1.19 (0.38), residues: 184 loop : -2.59 (0.22), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 181 HIS 0.002 0.000 HIS H 113 PHE 0.011 0.001 PHE E 150 TYR 0.014 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 180 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 99 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7984 (tp30) REVERT: A 109 GLU cc_start: 0.7782 (mp0) cc_final: 0.7445 (mp0) REVERT: A 139 SER cc_start: 0.9377 (t) cc_final: 0.9017 (m) REVERT: C 67 ARG cc_start: 0.7981 (ttm170) cc_final: 0.7683 (ttm170) REVERT: C 76 LYS cc_start: 0.9220 (tppt) cc_final: 0.8936 (tppt) REVERT: C 138 LYS cc_start: 0.9099 (tppp) cc_final: 0.8879 (tptt) REVERT: D 34 ILE cc_start: 0.8125 (mt) cc_final: 0.7909 (mt) REVERT: D 37 GLU cc_start: 0.8067 (mp0) cc_final: 0.7781 (mp0) REVERT: D 88 GLN cc_start: 0.6684 (tp40) cc_final: 0.6226 (tp-100) REVERT: E 130 ASP cc_start: 0.8456 (t0) cc_final: 0.7844 (t0) REVERT: E 132 ASP cc_start: 0.8180 (t0) cc_final: 0.7778 (t0) REVERT: E 150 PHE cc_start: 0.8531 (t80) cc_final: 0.8143 (t80) REVERT: F 129 LYS cc_start: 0.8828 (mppt) cc_final: 0.8476 (mtmm) REVERT: F 132 ASP cc_start: 0.8654 (m-30) cc_final: 0.8353 (m-30) REVERT: F 138 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8448 (mmtt) outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.2369 time to fit residues: 53.2849 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 : 0.820 ------------------------------------------------------------------------------- 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: 1.9990 chunk 82 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 10 optimal weight: 0.0070 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 overall best weight: 0.8602 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.104656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.075504 restraints weight = 84518.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.078577 restraints weight = 45652.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.081454 restraints weight = 22297.881| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 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 = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3490 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= 0.163 Angle : 0.646 9.712 9681 Z= 0.320 Chirality : 0.044 0.188 1140 Planarity : 0.004 0.061 1250 Dihedral : 4.259 17.414 988 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.07 % Favored : 91.70 % Rotamer: Outliers : 0.26 % Allowed : 2.74 % Favored : 97.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.26), residues: 892 helix: -0.32 (0.49), residues: 106 sheet: -0.94 (0.39), residues: 181 loop : -2.41 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 181 HIS 0.001 0.000 HIS H 113 PHE 0.006 0.001 PHE E 150 TYR 0.013 0.001 TYR H 117 ARG 0.005 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 177 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 0.764 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: A 109 GLU cc_start: 0.7880 (mp0) cc_final: 0.7516 (mp0) REVERT: A 139 SER cc_start: 0.9350 (t) cc_final: 0.9011 (m) REVERT: C 76 LYS cc_start: 0.9227 (tppt) cc_final: 0.8958 (tppt) REVERT: C 141 MET cc_start: 0.7996 (tmm) cc_final: 0.7792 (tmm) REVERT: D 141 MET cc_start: 0.8434 (tmm) cc_final: 0.8136 (tmm) REVERT: D 150 PHE cc_start: 0.7392 (m-10) cc_final: 0.6970 (m-10) REVERT: E 53 LYS cc_start: 0.8976 (ptmt) cc_final: 0.8766 (pttt) REVERT: E 130 ASP cc_start: 0.8454 (t0) cc_final: 0.7813 (t0) REVERT: E 132 ASP cc_start: 0.8310 (t0) cc_final: 0.7836 (t0) REVERT: E 150 PHE cc_start: 0.8512 (t80) cc_final: 0.8015 (t80) REVERT: F 129 LYS cc_start: 0.8819 (mppt) cc_final: 0.8472 (mtmm) REVERT: F 132 ASP cc_start: 0.8685 (m-30) cc_final: 0.8381 (m-30) REVERT: F 138 LYS cc_start: 0.8660 (mmmm) cc_final: 0.8375 (mmtt) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.2466 time to fit residues: 54.8572 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 : 0.755 ------------------------------------------------------------------------------- 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: 1.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 0.0170 overall best weight: 0.9622 ------------------------------------------------------------------------------- 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 = 0.104346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.075426 restraints weight = 92847.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.078558 restraints weight = 49006.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.081752 restraints weight = 23621.127| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2981 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2981 r_free = 0.2981 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 = 0.2981 r_free = 0.2981 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2981 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3607 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 : 0.626 8.630 9681 Z= 0.311 Chirality : 0.043 0.144 1140 Planarity : 0.005 0.060 1250 Dihedral : 4.207 17.526 988 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.30 % Favored : 91.70 % 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: -2.48 (0.26), residues: 892 helix: -0.39 (0.48), residues: 112 sheet: -0.86 (0.38), residues: 183 loop : -2.31 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 152 HIS 0.001 0.000 HIS H 113 PHE 0.005 0.001 PHE F 46 TYR 0.009 0.001 TYR H 117 ARG 0.004 0.000 ARG H 147 *********************** 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 174 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 GLU cc_start: 0.7908 (mp0) cc_final: 0.7504 (mp0) REVERT: A 139 SER cc_start: 0.9386 (t) cc_final: 0.8981 (m) REVERT: C 76 LYS cc_start: 0.9228 (tppt) cc_final: 0.8971 (tppt) REVERT: D 141 MET cc_start: 0.8385 (tmm) cc_final: 0.8120 (tmm) REVERT: E 130 ASP cc_start: 0.8468 (t0) cc_final: 0.7730 (t0) REVERT: E 132 ASP cc_start: 0.8352 (t0) cc_final: 0.7860 (t0) REVERT: E 150 PHE cc_start: 0.8489 (t80) cc_final: 0.8043 (t80) REVERT: F 47 ASP cc_start: 0.8670 (p0) cc_final: 0.8171 (t0) REVERT: F 129 LYS cc_start: 0.8813 (mppt) cc_final: 0.8405 (mtmm) REVERT: F 132 ASP cc_start: 0.8699 (m-30) cc_final: 0.8374 (m-30) REVERT: F 138 LYS cc_start: 0.8622 (mmmm) cc_final: 0.8324 (mmtt) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2498 time to fit residues: 54.5711 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 : 0.875 ------------------------------------------------------------------------------- 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: 4.9990 chunk 64 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.4980 chunk 31 optimal weight: 0.2980 chunk 11 optimal weight: 20.0000 chunk 66 optimal weight: 0.0370 chunk 67 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3429 r_free = 0.3429 target = 0.106202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.083531 restraints weight = 83413.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.085729 restraints weight = 61253.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.088379 restraints weight = 22060.769| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3786 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= 0.153 Angle : 0.625 7.020 9681 Z= 0.308 Chirality : 0.043 0.147 1140 Planarity : 0.004 0.059 1250 Dihedral : 4.091 17.218 988 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.05 % 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: -2.23 (0.26), residues: 892 helix: -0.15 (0.49), residues: 110 sheet: -0.74 (0.39), residues: 180 loop : -2.11 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP H 181 HIS 0.001 0.000 HIS D 92 PHE 0.004 0.001 PHE E 46 TYR 0.009 0.001 TYR B 152 ARG 0.005 0.000 ARG H 147 *********************** 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 181 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 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: 0.7811 (mp0) cc_final: 0.7412 (mp0) REVERT: A 139 SER cc_start: 0.9394 (t) cc_final: 0.8976 (m) REVERT: C 76 LYS cc_start: 0.9181 (tppt) cc_final: 0.8974 (tppt) REVERT: D 141 MET cc_start: 0.8412 (tmm) cc_final: 0.8152 (tmm) REVERT: E 130 ASP cc_start: 0.8326 (t0) cc_final: 0.7679 (t0) REVERT: E 132 ASP cc_start: 0.8309 (t0) cc_final: 0.7795 (t0) REVERT: E 150 PHE cc_start: 0.8489 (t80) cc_final: 0.8049 (t80) REVERT: F 38 PRO cc_start: 0.8222 (Cg_exo) cc_final: 0.8002 (Cg_endo) REVERT: F 129 LYS cc_start: 0.8790 (mppt) cc_final: 0.8384 (mtmm) REVERT: F 132 ASP cc_start: 0.8711 (m-30) cc_final: 0.8429 (m-30) REVERT: F 138 LYS cc_start: 0.8523 (mmmm) cc_final: 0.8214 (mmtt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2399 time to fit residues: 54.4203 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 : 0.796 ------------------------------------------------------------------------------- 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: 0.0570 chunk 39 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 23 optimal weight: 0.0980 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 46 GLN H 52 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.106366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.084004 restraints weight = 87176.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085918 restraints weight = 62155.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.088419 restraints weight = 22577.885| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3963 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= 0.155 Angle : 0.637 8.032 9681 Z= 0.315 Chirality : 0.044 0.220 1140 Planarity : 0.004 0.056 1250 Dihedral : 3.996 17.047 988 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.61 % Favored : 92.16 % Rotamer: Outliers : 0.26 % Allowed : 0.91 % Favored : 98.83 % 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: -2.04 (0.27), residues: 892 helix: 0.18 (0.51), residues: 104 sheet: -0.64 (0.39), residues: 187 loop : -2.01 (0.23), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 PHE 0.013 0.001 PHE C 150 TYR 0.007 0.001 TYR F 40 ARG 0.004 0.000 ARG H 147 *********************** 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 181 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 0.836 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: 0.7835 (mp0) cc_final: 0.7439 (mp0) REVERT: A 139 SER cc_start: 0.9395 (t) cc_final: 0.8977 (m) REVERT: B 109 GLU cc_start: 0.7231 (tp30) cc_final: 0.6730 (mm-30) REVERT: C 122 GLU cc_start: 0.7890 (pt0) cc_final: 0.7653 (pt0) REVERT: C 135 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7959 (mm-40) REVERT: D 37 GLU cc_start: 0.7983 (mp0) cc_final: 0.7659 (mp0) REVERT: D 141 MET cc_start: 0.8396 (tmm) cc_final: 0.8163 (tmm) REVERT: E 130 ASP cc_start: 0.8374 (t0) cc_final: 0.7674 (t0) REVERT: E 132 ASP cc_start: 0.8307 (t0) cc_final: 0.7791 (t0) REVERT: E 150 PHE cc_start: 0.8458 (t80) cc_final: 0.8043 (t80) REVERT: F 38 PRO cc_start: 0.8245 (Cg_exo) cc_final: 0.8044 (Cg_endo) REVERT: F 129 LYS cc_start: 0.8794 (mppt) cc_final: 0.8375 (mtmm) REVERT: F 132 ASP cc_start: 0.8727 (m-30) cc_final: 0.8414 (m-30) REVERT: F 138 LYS cc_start: 0.8590 (mmmm) cc_final: 0.8324 (mmtt) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.2290 time to fit residues: 52.1788 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 : 0.887 ------------------------------------------------------------------------------- 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: 6.9990 chunk 31 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 24 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 57 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.102060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.080608 restraints weight = 94322.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.081992 restraints weight = 64804.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.085568 restraints weight = 23519.987| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 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 = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7110 Z= 0.245 Angle : 0.664 6.819 9681 Z= 0.335 Chirality : 0.044 0.212 1140 Planarity : 0.005 0.057 1250 Dihedral : 4.388 16.860 988 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.11 % Allowed : 10.57 % Favored : 89.32 % 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: -2.07 (0.27), residues: 892 helix: 0.30 (0.51), residues: 104 sheet: -0.71 (0.38), residues: 187 loop : -2.04 (0.24), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 152 HIS 0.002 0.001 HIS B 92 PHE 0.010 0.001 PHE D 46 TYR 0.013 0.001 TYR A 40 ARG 0.004 0.000 ARG H 147 *********************** 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 169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 GLU cc_start: 0.7806 (tm-30) cc_final: 0.7499 (tm-30) REVERT: A 109 GLU cc_start: 0.7873 (mp0) cc_final: 0.7441 (mp0) REVERT: A 139 SER cc_start: 0.9385 (t) cc_final: 0.8909 (m) REVERT: D 37 GLU cc_start: 0.8003 (mp0) cc_final: 0.7698 (mp0) REVERT: D 141 MET cc_start: 0.8306 (tmm) cc_final: 0.8081 (tmm) REVERT: D 150 PHE cc_start: 0.7366 (m-10) cc_final: 0.6918 (m-10) REVERT: E 130 ASP cc_start: 0.8329 (t0) cc_final: 0.7692 (t0) REVERT: E 132 ASP cc_start: 0.8380 (t0) cc_final: 0.7892 (t0) REVERT: E 150 PHE cc_start: 0.8475 (t80) cc_final: 0.8101 (t80) REVERT: F 38 PRO cc_start: 0.8214 (Cg_exo) cc_final: 0.8010 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8732 (p0) cc_final: 0.8367 (t0) REVERT: F 129 LYS cc_start: 0.8826 (mppt) cc_final: 0.8385 (mtmm) REVERT: F 132 ASP cc_start: 0.8822 (m-30) cc_final: 0.8508 (m-30) REVERT: F 138 LYS cc_start: 0.8626 (mmmm) cc_final: 0.8267 (mmtt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2246 time to fit residues: 47.7803 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 : 0.770 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 0.4980 chunk 4 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 60 optimal weight: 0.1980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3388 r_free = 0.3388 target = 0.103375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.074107 restraints weight = 93016.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.077318 restraints weight = 46692.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.080479 restraints weight = 22983.902| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 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 = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3922 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= 0.189 Angle : 0.667 6.891 9681 Z= 0.330 Chirality : 0.044 0.204 1140 Planarity : 0.004 0.057 1250 Dihedral : 4.279 16.573 988 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.73 % 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: -2.05 (0.27), residues: 892 helix: 0.08 (0.49), residues: 110 sheet: -0.53 (0.40), residues: 176 loop : -2.03 (0.24), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 PHE 0.005 0.001 PHE D 46 TYR 0.010 0.001 TYR B 40 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 169 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.835 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 37 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7530 (tm-30) REVERT: A 109 GLU cc_start: 0.7923 (mp0) cc_final: 0.7516 (mp0) REVERT: C 76 LYS cc_start: 0.9259 (tptp) cc_final: 0.9011 (tppt) REVERT: D 34 ILE cc_start: 0.7932 (mt) cc_final: 0.7730 (mt) REVERT: D 37 GLU cc_start: 0.8010 (mp0) cc_final: 0.7713 (mp0) REVERT: D 141 MET cc_start: 0.8426 (tmm) cc_final: 0.8139 (tmm) REVERT: D 150 PHE cc_start: 0.7374 (m-10) cc_final: 0.6915 (m-10) REVERT: E 130 ASP cc_start: 0.8346 (t0) cc_final: 0.7733 (t0) REVERT: E 132 ASP cc_start: 0.8411 (t0) cc_final: 0.7913 (t0) REVERT: E 135 GLN cc_start: 0.7978 (tp40) cc_final: 0.7596 (tp40) REVERT: E 150 PHE cc_start: 0.8543 (t80) cc_final: 0.8103 (t80) REVERT: F 38 PRO cc_start: 0.8277 (Cg_exo) cc_final: 0.8059 (Cg_endo) REVERT: F 47 ASP cc_start: 0.8713 (p0) cc_final: 0.8275 (t0) REVERT: F 129 LYS cc_start: 0.8738 (mppt) cc_final: 0.8293 (mtmm) REVERT: F 132 ASP cc_start: 0.8776 (m-30) cc_final: 0.8421 (m-30) REVERT: F 138 LYS cc_start: 0.8668 (mmmm) cc_final: 0.8397 (mmtt) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2316 time to fit residues: 49.2400 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 : 0.744 ------------------------------------------------------------------------------- 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: 5.9990 chunk 70 optimal weight: 0.0570 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 2 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.5716 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.104963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.082181 restraints weight = 88623.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.084134 restraints weight = 63759.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087894 restraints weight = 23178.092| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4047 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= 0.163 Angle : 0.664 9.506 9681 Z= 0.328 Chirality : 0.045 0.243 1140 Planarity : 0.004 0.056 1250 Dihedral : 4.151 16.721 988 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.27), residues: 892 helix: 0.29 (0.50), residues: 110 sheet: -0.22 (0.41), residues: 173 loop : -2.03 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 181 HIS 0.001 0.000 HIS H 113 PHE 0.005 0.001 PHE E 46 TYR 0.008 0.001 TYR A 90 ARG 0.004 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2775.87 seconds wall clock time: 48 minutes 43.47 seconds (2923.47 seconds total)