Starting phenix.real_space_refine on Sat Dec 9 17:55:50 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z0o_14428/12_2023/7z0o_14428.pdb" } resolution = 2.8 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= 0.019 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: 5 Type Number sf(0) Gaussians P 78 5.49 5 S 29 5.16 5 C 7291 2.51 5 N 2111 2.21 5 O 2355 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 51": "OE1" <-> "OE2" Residue "A GLU 74": "OE1" <-> "OE2" Residue "A GLU 95": "OE1" <-> "OE2" Residue "A GLU 98": "OE1" <-> "OE2" Residue "A GLU 106": "OE1" <-> "OE2" Residue "B GLU 53": "OE1" <-> "OE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B GLU 75": "OE1" <-> "OE2" Residue "C GLU 51": "OE1" <-> "OE2" Residue "C GLU 60": "OE1" <-> "OE2" Residue "C GLU 74": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "D GLU 11": "OE1" <-> "OE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "E GLU 74": "OE1" <-> "OE2" Residue "E GLU 112": "OE1" <-> "OE2" Residue "E GLU 296": "OE1" <-> "OE2" Residue "E GLU 302": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "F PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 59": "OE1" <-> "OE2" Residue "F GLU 130": "OE1" <-> "OE2" Residue "G GLU 69": "OE1" <-> "OE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H GLU 186": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 11864 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 774 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "C" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "D" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2436 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 9, 'TRANS': 286} Chain breaks: 5 Chain: "E" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2518 Classifications: {'peptide': 301} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "F" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1067 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain breaks: 2 Chain: "G" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 681 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "H" Number of atoms: 1380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1380 Classifications: {'peptide': 175} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 166} Chain: "N" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 820 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "T" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 779 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Time building chain proxies: 6.53, per 1000 atoms: 0.55 Number of scatterers: 11864 At special positions: 0 Unit cell: (74.175, 126.42, 132.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 78 15.00 O 2355 8.00 N 2111 7.00 C 7291 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 - 3.50 Amino acid : False - 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: 4.91 Conformation dependent library (CDL) restraints added in 2.0 seconds 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2430 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 9 sheets defined 64.8% alpha, 6.0% beta 36 base pairs and 74 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 64 through 79 Processing helix chain 'A' and resid 86 through 115 removed outlier: 3.695A pdb=" N ALA A 99 " --> pdb=" O GLU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 133 removed outlier: 3.526A pdb=" N ILE A 125 " --> pdb=" O GLN A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 removed outlier: 3.508A pdb=" N ILE B 30 " --> pdb=" O ILE B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 42 removed outlier: 3.662A pdb=" N ILE B 35 " --> pdb=" O THR B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 77 removed outlier: 3.562A pdb=" N SER B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.603A pdb=" N ILE C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE C 55 " --> pdb=" O GLU C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 79 removed outlier: 3.621A pdb=" N ASP C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 79 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 115 Processing helix chain 'C' and resid 121 through 132 removed outlier: 3.581A pdb=" N ILE C 125 " --> pdb=" O GLN C 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 22 Processing helix chain 'D' and resid 63 through 77 Processing helix chain 'D' and resid 78 through 80 No H-bonds generated for 'chain 'D' and resid 78 through 80' Processing helix chain 'D' and resid 81 through 86 removed outlier: 3.501A pdb=" N TRP D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 93 through 110 Processing helix chain 'D' and resid 128 through 147 Processing helix chain 'D' and resid 148 through 150 No H-bonds generated for 'chain 'D' and resid 148 through 150' Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.893A pdb=" N TRP D 168 " --> pdb=" O ASP D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 179 Processing helix chain 'D' and resid 181 through 185 Processing helix chain 'D' and resid 195 through 218 Processing helix chain 'D' and resid 219 through 224 removed outlier: 4.521A pdb=" N ALA D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 256 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 264 through 276 removed outlier: 3.679A pdb=" N VAL D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 302 Processing helix chain 'D' and resid 340 through 363 Processing helix chain 'E' and resid 36 through 54 removed outlier: 3.566A pdb=" N ASP E 54 " --> pdb=" O SER E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 129 through 160 Processing helix chain 'E' and resid 171 through 208 Processing helix chain 'E' and resid 229 through 240 Processing helix chain 'E' and resid 244 through 256 Processing helix chain 'E' and resid 258 through 262 Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.700A pdb=" N ARG E 268 " --> pdb=" O ARG E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 286 through 294 Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.529A pdb=" N LYS E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 340 Processing helix chain 'E' and resid 352 through 356 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 22 through 31 Processing helix chain 'F' and resid 41 through 48 Processing helix chain 'F' and resid 49 through 55 Processing helix chain 'F' and resid 67 through 83 Processing helix chain 'F' and resid 84 through 87 removed outlier: 3.937A pdb=" N ILE F 87 " --> pdb=" O PRO F 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 84 through 87' Processing helix chain 'F' and resid 91 through 109 removed outlier: 3.772A pdb=" N TYR F 109 " --> pdb=" O TRP F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 132 removed outlier: 4.460A pdb=" N CYS F 129 " --> pdb=" O GLY F 125 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 132 " --> pdb=" O PRO F 128 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 16 removed outlier: 3.608A pdb=" N MET G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.569A pdb=" N LYS G 33 " --> pdb=" O ARG G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 58 removed outlier: 3.878A pdb=" N LEU G 57 " --> pdb=" O LYS G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 86 removed outlier: 3.581A pdb=" N GLU G 85 " --> pdb=" O GLU G 81 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 89 Processing helix chain 'H' and resid 128 through 146 Processing helix chain 'H' and resid 173 through 179 removed outlier: 3.945A pdb=" N PHE H 177 " --> pdb=" O GLU H 173 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS H 179 " --> pdb=" O LEU H 175 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 236 Proline residue: H 232 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.665A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA4, first strand: chain 'C' and resid 40 through 41 removed outlier: 4.121A pdb=" N LEU D 187 " --> pdb=" O ARG C 41 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 83 through 85 Processing sheet with id=AA6, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'D' and resid 226 through 228 Processing sheet with id=AA8, first strand: chain 'F' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'H' and resid 102 through 106 removed outlier: 3.627A pdb=" N MET H 104 " --> pdb=" O ALA H 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR H 111 " --> pdb=" O ILE H 106 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU H 67 " --> pdb=" O GLY H 162 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY H 162 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASN H 69 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ILE H 160 " --> pdb=" O ASN H 69 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL H 71 " --> pdb=" O GLN H 158 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N THR H 75 " --> pdb=" O ASP H 154 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ASP H 154 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE H 160 " --> pdb=" O GLY H 216 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY H 216 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE H 202 " --> pdb=" O MET H 197 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET H 197 " --> pdb=" O ILE H 202 " (cutoff:3.500A) 598 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 74 stacking parallelities Total time for adding SS restraints: 3.65 Time building geometry restraints manager: 5.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3656 1.34 - 1.46: 3057 1.46 - 1.58: 5318 1.58 - 1.70: 154 1.70 - 1.82: 46 Bond restraints: 12231 Sorted by residual: bond pdb=" CG PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 1.503 1.557 -0.054 3.40e-02 8.65e+02 2.50e+00 bond pdb=" CB PRO G 62 " pdb=" CG PRO G 62 " ideal model delta sigma weight residual 1.492 1.563 -0.071 5.00e-02 4.00e+02 2.03e+00 bond pdb=" CB GLU G 81 " pdb=" CG GLU G 81 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.71e+00 bond pdb=" C1' DT T 76 " pdb=" N1 DT T 76 " ideal model delta sigma weight residual 1.490 1.454 0.036 3.00e-02 1.11e+03 1.45e+00 bond pdb=" C1' DT T 56 " pdb=" N1 DT T 56 " ideal model delta sigma weight residual 1.490 1.454 0.036 3.00e-02 1.11e+03 1.44e+00 ... (remaining 12226 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.73: 426 104.73 - 112.05: 6385 112.05 - 119.38: 4012 119.38 - 126.70: 5655 126.70 - 134.03: 330 Bond angle restraints: 16808 Sorted by residual: angle pdb=" CA GLN G 43 " pdb=" CB GLN G 43 " pdb=" CG GLN G 43 " ideal model delta sigma weight residual 114.10 121.86 -7.76 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA GLU G 81 " pdb=" CB GLU G 81 " pdb=" CG GLU G 81 " ideal model delta sigma weight residual 114.10 121.04 -6.94 2.00e+00 2.50e-01 1.20e+01 angle pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " ideal model delta sigma weight residual 112.00 119.54 -7.54 2.20e+00 2.07e-01 1.17e+01 angle pdb=" CA PRO G 62 " pdb=" N PRO G 62 " pdb=" CD PRO G 62 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 angle pdb=" N GLU E 112 " pdb=" CA GLU E 112 " pdb=" C GLU E 112 " ideal model delta sigma weight residual 114.56 110.32 4.24 1.27e+00 6.20e-01 1.12e+01 ... (remaining 16803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 6040 18.08 - 36.15: 825 36.15 - 54.22: 364 54.22 - 72.30: 87 72.30 - 90.37: 14 Dihedral angle restraints: 7330 sinusoidal: 3614 harmonic: 3716 Sorted by residual: dihedral pdb=" CA SER D 41 " pdb=" C SER D 41 " pdb=" N ILE D 42 " pdb=" CA ILE D 42 " ideal model delta harmonic sigma weight residual 180.00 -161.44 -18.56 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LYS F 126 " pdb=" C LYS F 126 " pdb=" N GLY F 127 " pdb=" CA GLY F 127 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CG ARG H 98 " pdb=" CD ARG H 98 " pdb=" NE ARG H 98 " pdb=" CZ ARG H 98 " ideal model delta sinusoidal sigma weight residual 90.00 41.51 48.49 2 1.50e+01 4.44e-03 1.20e+01 ... (remaining 7327 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1303 0.032 - 0.064: 407 0.064 - 0.097: 131 0.097 - 0.129: 52 0.129 - 0.161: 4 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CB ILE D 42 " pdb=" CA ILE D 42 " pdb=" CG1 ILE D 42 " pdb=" CG2 ILE D 42 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.47e-01 chirality pdb=" CA GLN G 43 " pdb=" N GLN G 43 " pdb=" C GLN G 43 " pdb=" CB GLN G 43 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" C1' DC T 55 " pdb=" O4' DC T 55 " pdb=" C2' DC T 55 " pdb=" N1 DC T 55 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1894 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 168 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO H 169 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO H 169 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 169 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 61 " 0.031 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO G 62 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 62 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO G 62 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 28 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" CD GLN B 28 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLN B 28 " 0.011 2.00e-02 2.50e+03 pdb=" NE2 GLN B 28 " 0.010 2.00e-02 2.50e+03 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 687 2.73 - 3.27: 11598 3.27 - 3.82: 20751 3.82 - 4.36: 25016 4.36 - 4.90: 40566 Nonbonded interactions: 98618 Sorted by model distance: nonbonded pdb=" OG SER G 42 " pdb=" OE1 GLN G 43 " model vdw 2.189 2.440 nonbonded pdb=" O THR H 111 " pdb=" OH TYR H 139 " model vdw 2.231 2.440 nonbonded pdb=" OD1 ASP C 107 " pdb=" NZ LYS D 275 " model vdw 2.254 2.520 nonbonded pdb=" OG SER E 95 " pdb=" OD1 ASN F 88 " model vdw 2.255 2.440 nonbonded pdb=" O ASN G 5 " pdb=" OG SER G 8 " model vdw 2.276 2.440 ... (remaining 98613 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'C' and resid 40 through 133) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.100 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: 17.970 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 36.120 Find NCS groups from input model: 0.340 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:10.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 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 0.071 12231 Z= 0.226 Angle : 0.663 9.596 16808 Z= 0.400 Chirality : 0.038 0.161 1897 Planarity : 0.004 0.053 1854 Dihedral : 19.644 90.375 4900 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.42 % Allowed : 19.54 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.08 (0.23), residues: 1222 helix: 1.45 (0.19), residues: 740 sheet: 0.07 (0.76), residues: 47 loop : -0.40 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 85 HIS 0.003 0.001 HIS E 58 PHE 0.010 0.001 PHE H 177 TYR 0.008 0.001 TYR E 230 ARG 0.014 0.000 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 279 time to evaluate : 1.340 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 290 average time/residue: 1.6087 time to fit residues: 495.9764 Evaluate side-chains 266 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 259 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 0.6064 time to fit residues: 3.9471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN A 121 GLN D 248 GLN D 356 GLN F 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12231 Z= 0.301 Angle : 0.611 10.252 16808 Z= 0.342 Chirality : 0.043 0.193 1897 Planarity : 0.004 0.041 1854 Dihedral : 20.311 65.477 2271 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.24 % Allowed : 20.96 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.56 (0.23), residues: 1222 helix: 1.90 (0.18), residues: 750 sheet: -0.43 (0.63), residues: 68 loop : -0.29 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 85 HIS 0.006 0.001 HIS D 38 PHE 0.016 0.002 PHE D 70 TYR 0.015 0.002 TYR E 230 ARG 0.006 0.001 ARG E 265 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 240 time to evaluate : 1.292 Fit side-chains outliers start: 59 outliers final: 24 residues processed: 276 average time/residue: 1.5029 time to fit residues: 445.1537 Evaluate side-chains 253 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 229 time to evaluate : 1.539 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.7394 time to fit residues: 11.9358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 96 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN D 248 GLN D 294 HIS D 356 GLN E 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12231 Z= 0.331 Angle : 0.592 9.682 16808 Z= 0.332 Chirality : 0.043 0.197 1897 Planarity : 0.004 0.045 1854 Dihedral : 20.358 62.703 2271 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.35 % Allowed : 22.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.50 (0.23), residues: 1222 helix: 1.94 (0.18), residues: 743 sheet: -0.63 (0.61), residues: 68 loop : -0.44 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP D 85 HIS 0.006 0.001 HIS G 54 PHE 0.018 0.002 PHE F 90 TYR 0.013 0.002 TYR E 230 ARG 0.008 0.001 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 252 time to evaluate : 1.291 Fit side-chains outliers start: 49 outliers final: 31 residues processed: 281 average time/residue: 1.4117 time to fit residues: 425.1377 Evaluate side-chains 269 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 238 time to evaluate : 1.226 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 17 residues processed: 14 average time/residue: 0.6270 time to fit residues: 11.7137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 0.0670 chunk 60 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 116 optimal weight: 9.9990 chunk 123 optimal weight: 1.9990 chunk 61 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.5722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN D 356 GLN E 337 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12231 Z= 0.237 Angle : 0.540 9.411 16808 Z= 0.305 Chirality : 0.040 0.225 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.367 60.144 2271 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.26 % Allowed : 23.00 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.68 (0.23), residues: 1222 helix: 2.14 (0.18), residues: 743 sheet: -0.62 (0.62), residues: 68 loop : -0.47 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 85 HIS 0.005 0.001 HIS D 353 PHE 0.014 0.002 PHE D 70 TYR 0.012 0.001 TYR E 230 ARG 0.008 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 233 time to evaluate : 1.330 Fit side-chains outliers start: 48 outliers final: 28 residues processed: 265 average time/residue: 1.5090 time to fit residues: 427.8758 Evaluate side-chains 259 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 231 time to evaluate : 1.233 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.4450 time to fit residues: 7.1066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 111 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 337 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12231 Z= 0.268 Angle : 0.547 9.293 16808 Z= 0.307 Chirality : 0.041 0.174 1897 Planarity : 0.004 0.054 1854 Dihedral : 20.410 60.227 2271 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.88 % Allowed : 22.82 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.66 (0.23), residues: 1222 helix: 2.12 (0.18), residues: 742 sheet: -0.57 (0.66), residues: 63 loop : -0.48 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 85 HIS 0.006 0.001 HIS E 135 PHE 0.017 0.002 PHE D 70 TYR 0.013 0.001 TYR E 230 ARG 0.010 0.000 ARG E 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 236 time to evaluate : 1.264 Fit side-chains outliers start: 55 outliers final: 38 residues processed: 265 average time/residue: 1.5060 time to fit residues: 426.8554 Evaluate side-chains 273 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 1.249 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 22 residues processed: 16 average time/residue: 0.6648 time to fit residues: 13.9897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12231 Z= 0.310 Angle : 0.569 9.480 16808 Z= 0.318 Chirality : 0.042 0.164 1897 Planarity : 0.004 0.054 1854 Dihedral : 20.428 60.439 2271 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.35 % Allowed : 23.36 % Favored : 72.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.53 (0.23), residues: 1222 helix: 2.03 (0.18), residues: 742 sheet: -0.48 (0.67), residues: 63 loop : -0.58 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 85 HIS 0.005 0.001 HIS D 353 PHE 0.019 0.002 PHE D 70 TYR 0.013 0.002 TYR F 74 ARG 0.009 0.000 ARG E 309 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.241 Fit side-chains outliers start: 49 outliers final: 37 residues processed: 264 average time/residue: 1.4769 time to fit residues: 416.7390 Evaluate side-chains 268 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 231 time to evaluate : 1.216 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 26 residues processed: 11 average time/residue: 0.5649 time to fit residues: 8.9410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0970 chunk 13 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 88 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 12231 Z= 0.263 Angle : 0.551 9.166 16808 Z= 0.309 Chirality : 0.040 0.158 1897 Planarity : 0.004 0.046 1854 Dihedral : 20.433 60.857 2271 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.35 % Allowed : 23.53 % Favored : 72.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.61 (0.23), residues: 1222 helix: 2.11 (0.18), residues: 742 sheet: -0.49 (0.66), residues: 63 loop : -0.58 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 85 HIS 0.006 0.001 HIS E 135 PHE 0.016 0.002 PHE D 70 TYR 0.014 0.001 TYR F 74 ARG 0.006 0.000 ARG E 309 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 234 time to evaluate : 1.231 Fit side-chains outliers start: 49 outliers final: 33 residues processed: 267 average time/residue: 1.5215 time to fit residues: 434.5780 Evaluate side-chains 265 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 232 time to evaluate : 1.304 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 27 residues processed: 6 average time/residue: 0.5951 time to fit residues: 5.9812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 0.0770 chunk 73 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 24 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 0.4676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 88 GLN F 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 12231 Z= 0.219 Angle : 0.544 8.778 16808 Z= 0.301 Chirality : 0.039 0.172 1897 Planarity : 0.004 0.043 1854 Dihedral : 20.433 62.730 2271 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.44 % Allowed : 23.71 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.72 (0.24), residues: 1222 helix: 2.21 (0.19), residues: 742 sheet: -0.55 (0.65), residues: 63 loop : -0.54 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 148 HIS 0.004 0.001 HIS D 353 PHE 0.015 0.001 PHE D 70 TYR 0.011 0.001 TYR E 230 ARG 0.005 0.000 ARG C 64 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 229 time to evaluate : 1.246 Fit side-chains outliers start: 50 outliers final: 37 residues processed: 264 average time/residue: 1.4385 time to fit residues: 406.8805 Evaluate side-chains 264 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 30 residues processed: 8 average time/residue: 0.7166 time to fit residues: 8.2461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 0.0570 chunk 75 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12231 Z= 0.277 Angle : 0.567 9.190 16808 Z= 0.314 Chirality : 0.041 0.171 1897 Planarity : 0.004 0.046 1854 Dihedral : 20.425 62.770 2271 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.64 % Allowed : 24.69 % Favored : 71.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.60 (0.23), residues: 1222 helix: 2.10 (0.18), residues: 742 sheet: -0.61 (0.65), residues: 63 loop : -0.57 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 85 HIS 0.005 0.001 HIS E 135 PHE 0.017 0.002 PHE D 70 TYR 0.013 0.002 TYR E 230 ARG 0.013 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 234 time to evaluate : 1.226 Fit side-chains outliers start: 41 outliers final: 36 residues processed: 261 average time/residue: 1.4412 time to fit residues: 403.9196 Evaluate side-chains 269 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 9 average time/residue: 0.7037 time to fit residues: 8.9699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 10 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 62 optimal weight: 0.0980 chunk 80 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12231 Z= 0.212 Angle : 0.551 8.847 16808 Z= 0.305 Chirality : 0.039 0.167 1897 Planarity : 0.004 0.062 1854 Dihedral : 20.416 64.564 2271 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.11 % Allowed : 25.31 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.70 (0.24), residues: 1222 helix: 2.20 (0.19), residues: 742 sheet: -0.66 (0.64), residues: 63 loop : -0.54 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.004 0.001 HIS D 353 PHE 0.011 0.001 PHE D 70 TYR 0.012 0.001 TYR E 230 ARG 0.013 0.000 ARG D 274 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2444 Ramachandran restraints generated. 1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 227 time to evaluate : 1.252 Fit side-chains outliers start: 35 outliers final: 32 residues processed: 254 average time/residue: 1.4673 time to fit residues: 399.4215 Evaluate side-chains 259 residues out of total 1126 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.109 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 5 average time/residue: 0.4857 time to fit residues: 4.6037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 1.9990 chunk 93 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 356 GLN E 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.134923 restraints weight = 13898.243| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 1.43 r_work: 0.3496 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 12231 Z= 0.239 Angle : 0.559 8.955 16808 Z= 0.308 Chirality : 0.040 0.166 1897 Planarity : 0.004 0.057 1854 Dihedral : 20.431 64.686 2271 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.11 % Allowed : 25.40 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.67 (0.24), residues: 1222 helix: 2.16 (0.19), residues: 742 sheet: -0.72 (0.65), residues: 63 loop : -0.53 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 168 HIS 0.005 0.001 HIS D 353 PHE 0.015 0.001 PHE D 70 TYR 0.012 0.001 TYR E 230 ARG 0.013 0.000 ARG D 274 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6430.29 seconds wall clock time: 114 minutes 24.64 seconds (6864.64 seconds total)