Starting phenix.real_space_refine on Wed Feb 14 09:27:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6mhu_9118/02_2024/6mhu_9118_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 42 5.16 5 C 5658 2.51 5 N 1482 2.21 5 O 1624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 33": "NH1" <-> "NH2" Residue "G ARG 99": "NH1" <-> "NH2" Residue "G ARG 133": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 184": "NH1" <-> "NH2" Residue "G ARG 270": "NH1" <-> "NH2" Residue "G ARG 301": "NH1" <-> "NH2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 144": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8810 Number of models: 1 Model: "" Number of chains: 5 Chain: "F" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2393 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2643 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 2 Chain: "A" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "B" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1787 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 8, 'TRANS': 221} Chain: "G" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 200 Unusual residues: {'JSG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.61 Number of scatterers: 8810 At special positions: 0 Unit cell: (92.25, 95.94, 145.14, 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 42 16.00 P 4 15.00 O 1624 8.00 N 1482 7.00 C 5658 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: 3.91 Conformation dependent library (CDL) restraints added in 1.7 seconds 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 10 sheets defined 45.7% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'F' and resid 7 through 39 removed outlier: 3.742A pdb=" N LEU F 12 " --> pdb=" O ARG F 9 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS F 13 " --> pdb=" O GLU F 10 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE F 18 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU F 23 " --> pdb=" O PHE F 20 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N LEU F 24 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE F 26 " --> pdb=" O LEU F 23 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N LEU F 31 " --> pdb=" O CYS F 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU F 35 " --> pdb=" O VAL F 32 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL F 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 53 removed outlier: 3.715A pdb=" N GLY F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.762A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE F 63 " --> pdb=" O MET F 59 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) Proline residue: F 65 - end of helix removed outlier: 3.978A pdb=" N THR F 75 " --> pdb=" O GLY F 71 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS F 78 " --> pdb=" O MET F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 88 No H-bonds generated for 'chain 'F' and resid 85 through 88' Processing helix chain 'F' and resid 95 through 119 removed outlier: 3.778A pdb=" N VAL F 117 " --> pdb=" O ALA F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 128 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 265 through 283 removed outlier: 4.379A pdb=" N ILE F 270 " --> pdb=" O LEU F 266 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL F 273 " --> pdb=" O ARG F 269 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ALA F 280 " --> pdb=" O VAL F 276 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LEU F 281 " --> pdb=" O PHE F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 317 removed outlier: 3.683A pdb=" N LEU F 308 " --> pdb=" O LEU F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 346 Processing helix chain 'G' and resid 8 through 40 removed outlier: 3.683A pdb=" N SER G 30 " --> pdb=" O LEU G 26 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS G 40 " --> pdb=" O VAL G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 65 removed outlier: 4.650A pdb=" N LEU G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) Proline residue: G 61 - end of helix removed outlier: 3.665A pdb=" N GLN G 65 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 85 removed outlier: 4.098A pdb=" N LEU G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N LEU G 83 " --> pdb=" O GLY G 79 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA G 84 " --> pdb=" O LEU G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 95 Processing helix chain 'G' and resid 99 through 123 removed outlier: 4.120A pdb=" N THR G 109 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE G 111 " --> pdb=" O MET G 107 " (cutoff:3.500A) Proline residue: G 112 - end of helix removed outlier: 4.009A pdb=" N GLU G 122 " --> pdb=" O MET G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 137 removed outlier: 4.382A pdb=" N ALA G 137 " --> pdb=" O ARG G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 202 No H-bonds generated for 'chain 'G' and resid 200 through 202' Processing helix chain 'G' and resid 251 through 254 No H-bonds generated for 'chain 'G' and resid 251 through 254' Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.667A pdb=" N ILE G 279 " --> pdb=" O MET G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 305 through 326 Processing helix chain 'G' and resid 337 through 342 Processing helix chain 'G' and resid 346 through 356 removed outlier: 4.242A pdb=" N ILE G 351 " --> pdb=" O SER G 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 72 through 78 Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.646A pdb=" N GLU A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 154 removed outlier: 3.763A pdb=" N ALA A 154 " --> pdb=" O ARG A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 Processing helix chain 'A' and resid 197 through 200 No H-bonds generated for 'chain 'A' and resid 197 through 200' Processing helix chain 'A' and resid 221 through 226 Processing helix chain 'B' and resid 42 through 50 removed outlier: 3.853A pdb=" N PHE B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 69 No H-bonds generated for 'chain 'B' and resid 67 through 69' Processing helix chain 'B' and resid 72 through 77 Processing helix chain 'B' and resid 95 through 105 removed outlier: 5.026A pdb=" N ILE B 105 " --> pdb=" O ALA B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 140 through 154 removed outlier: 3.552A pdb=" N ALA B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 185 removed outlier: 3.758A pdb=" N ILE B 174 " --> pdb=" O PRO B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 200 No H-bonds generated for 'chain 'B' and resid 197 through 200' Processing helix chain 'B' and resid 221 through 226 Processing sheet with id= A, first strand: chain 'F' and resid 187 through 189 Processing sheet with id= B, first strand: chain 'G' and resid 160 through 162 removed outlier: 3.577A pdb=" N PHE G 160 " --> pdb=" O TYR G 178 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR G 162 " --> pdb=" O SER G 176 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'G' and resid 210 through 212 Processing sheet with id= D, first strand: chain 'A' and resid 25 through 27 Processing sheet with id= E, first strand: chain 'A' and resid 214 through 219 removed outlier: 7.231A pdb=" N ILE A 209 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N HIS A 218 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA A 207 " --> pdb=" O HIS A 218 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ARG A 206 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL A 190 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N LEU A 34 " --> pdb=" O VAL A 190 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ILE A 192 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 193 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 83 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 9 through 11 removed outlier: 7.920A pdb=" N LYS A 11 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N GLU A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 25 through 27 Processing sheet with id= H, first strand: chain 'B' and resid 31 through 34 removed outlier: 5.956A pdb=" N VAL B 190 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU B 34 " --> pdb=" O VAL B 190 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE B 192 " --> pdb=" O LEU B 34 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR B 193 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 9 through 11 removed outlier: 7.899A pdb=" N LYS B 11 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU B 20 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.587A pdb=" N ALA B 217 " --> pdb=" O ILE B 209 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 927 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: 2.12 Time building geometry restraints manager: 4.15 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: 2785 1.34 - 1.46: 1431 1.46 - 1.57: 4662 1.57 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 8963 Sorted by residual: bond pdb=" C7 JSG G 401 " pdb=" N2 JSG G 401 " ideal model delta sigma weight residual 1.621 1.344 0.277 2.00e-02 2.50e+03 1.92e+02 bond pdb=" CDO JSG G 401 " pdb=" NAO JSG G 401 " ideal model delta sigma weight residual 1.505 1.343 0.162 2.00e-02 2.50e+03 6.58e+01 bond pdb=" CEE JSG G 401 " pdb=" OAQ JSG G 401 " ideal model delta sigma weight residual 1.469 1.356 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" CAN JSG G 401 " pdb=" NAO JSG G 401 " ideal model delta sigma weight residual 1.577 1.471 0.106 2.00e-02 2.50e+03 2.83e+01 bond pdb=" CBV JSG G 401 " pdb=" OBW JSG G 401 " ideal model delta sigma weight residual 1.526 1.423 0.103 2.00e-02 2.50e+03 2.66e+01 ... (remaining 8958 not shown) Histogram of bond angle deviations from ideal: 96.27 - 104.01: 144 104.01 - 111.76: 4109 111.76 - 119.50: 3605 119.50 - 127.25: 4196 127.25 - 135.00: 87 Bond angle restraints: 12141 Sorted by residual: angle pdb=" CA ASP G 198 " pdb=" C ASP G 198 " pdb=" N PRO G 199 " ideal model delta sigma weight residual 117.68 121.17 -3.49 7.10e-01 1.98e+00 2.42e+01 angle pdb=" N GLY G 173 " pdb=" CA GLY G 173 " pdb=" C GLY G 173 " ideal model delta sigma weight residual 113.18 102.23 10.95 2.37e+00 1.78e-01 2.13e+01 angle pdb=" C GLU B 228 " pdb=" N HIS B 229 " pdb=" CA HIS B 229 " ideal model delta sigma weight residual 121.56 128.22 -6.66 1.56e+00 4.11e-01 1.82e+01 angle pdb=" C PHE F 173 " pdb=" N LEU F 174 " pdb=" CA LEU F 174 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C MET G 140 " pdb=" N TYR G 141 " pdb=" CA TYR G 141 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 ... (remaining 12136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.14: 5169 23.14 - 46.29: 191 46.29 - 69.43: 22 69.43 - 92.57: 9 92.57 - 115.71: 6 Dihedral angle restraints: 5397 sinusoidal: 2214 harmonic: 3183 Sorted by residual: dihedral pdb=" CA GLU B 228 " pdb=" C GLU B 228 " pdb=" N HIS B 229 " pdb=" CA HIS B 229 " ideal model delta harmonic sigma weight residual -180.00 -145.60 -34.40 0 5.00e+00 4.00e-02 4.73e+01 dihedral pdb=" CA GLY G 173 " pdb=" C GLY G 173 " pdb=" N GLY G 174 " pdb=" CA GLY G 174 " ideal model delta harmonic sigma weight residual -180.00 -146.76 -33.24 0 5.00e+00 4.00e-02 4.42e+01 dihedral pdb=" CA VAL F 288 " pdb=" C VAL F 288 " pdb=" N VAL F 289 " pdb=" CA VAL F 289 " ideal model delta harmonic sigma weight residual -180.00 -146.88 -33.12 0 5.00e+00 4.00e-02 4.39e+01 ... (remaining 5394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.930: 1445 0.930 - 1.860: 0 1.860 - 2.790: 0 2.790 - 3.720: 0 3.720 - 4.650: 1 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CCB JSG G 401 " pdb=" CCC JSG G 401 " pdb=" OBF JSG G 401 " pdb=" OCL JSG G 401 " both_signs ideal model delta sigma weight residual False 2.42 -2.23 4.65 2.00e-01 2.50e+01 5.40e+02 chirality pdb=" CB ILE F 234 " pdb=" CA ILE F 234 " pdb=" CG1 ILE F 234 " pdb=" CG2 ILE F 234 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.03e+00 chirality pdb=" CBP JSG G 401 " pdb=" CBM JSG G 401 " pdb=" CBQ JSG G 401 " pdb=" OBW JSG G 401 " both_signs ideal model delta sigma weight residual False -2.50 -2.82 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 1443 not shown) Planarity restraints: 1513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE G 68 " 0.044 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO G 69 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 69 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 69 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 245 " -0.040 5.00e-02 4.00e+02 6.12e-02 6.00e+00 pdb=" N PRO G 246 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO G 246 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 246 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 268 " 0.017 2.00e-02 2.50e+03 1.54e-02 5.89e+00 pdb=" CG TRP F 268 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP F 268 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP F 268 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 268 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP F 268 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 268 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 268 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 268 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 268 " 0.000 2.00e-02 2.50e+03 ... (remaining 1510 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2084 2.79 - 3.32: 8277 3.32 - 3.85: 14446 3.85 - 4.37: 16343 4.37 - 4.90: 27247 Nonbonded interactions: 68397 Sorted by model distance: nonbonded pdb=" OD2 ASP G 37 " pdb=" OAS JSG G 401 " model vdw 2.267 2.440 nonbonded pdb=" O ALA B 2 " pdb=" OG SER B 28 " model vdw 2.282 2.440 nonbonded pdb=" O LEU F 272 " pdb=" OG1 THR F 275 " model vdw 2.293 2.440 nonbonded pdb=" O THR B 25 " pdb=" OH TYR B 208 " model vdw 2.307 2.440 nonbonded pdb=" OH TYR A 47 " pdb=" OD2 ASP A 162 " model vdw 2.330 2.440 ... (remaining 68392 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 'B' } 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 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: 0.630 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: 2.000 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 28.260 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 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 : 0.010 0.277 8963 Z= 0.657 Angle : 1.241 11.842 12141 Z= 0.616 Chirality : 0.138 4.650 1446 Planarity : 0.008 0.065 1513 Dihedral : 13.394 115.714 3345 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.76 % Allowed : 6.59 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.38 % 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: -4.84 (0.19), residues: 1094 helix: -2.92 (0.16), residues: 523 sheet: -2.77 (0.41), residues: 99 loop : -3.59 (0.23), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP F 268 HIS 0.009 0.002 HIS F 89 PHE 0.035 0.004 PHE G 348 TYR 0.027 0.003 TYR F 338 ARG 0.007 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 382 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7212 (mt-10) REVERT: G 15 ILE cc_start: 0.9371 (mm) cc_final: 0.9046 (tp) REVERT: G 58 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7726 (tm) REVERT: G 91 VAL cc_start: 0.8876 (t) cc_final: 0.8283 (t) REVERT: G 100 MET cc_start: 0.7890 (tpp) cc_final: 0.7501 (tpp) REVERT: G 155 LYS cc_start: 0.3750 (ttpp) cc_final: 0.3103 (mmtt) REVERT: G 177 ILE cc_start: 0.6824 (mt) cc_final: 0.6535 (mm) REVERT: G 205 ARG cc_start: 0.5604 (tmt170) cc_final: 0.5086 (tpm170) REVERT: G 289 MET cc_start: 0.8847 (mtt) cc_final: 0.8647 (mtt) REVERT: G 291 MET cc_start: 0.8600 (tmt) cc_final: 0.7508 (tpp) REVERT: G 293 LEU cc_start: 0.9385 (mp) cc_final: 0.9166 (mm) REVERT: G 305 MET cc_start: 0.7315 (tpp) cc_final: 0.7075 (tpp) REVERT: G 357 MET cc_start: 0.6335 (ptp) cc_final: 0.5511 (tmm) REVERT: A 8 ASN cc_start: 0.7410 (t160) cc_final: 0.7062 (t0) REVERT: A 11 LYS cc_start: 0.6759 (tptp) cc_final: 0.6119 (tptm) REVERT: A 31 ILE cc_start: 0.9007 (mt) cc_final: 0.8795 (mp) REVERT: A 62 ILE cc_start: 0.8237 (mt) cc_final: 0.7770 (pt) REVERT: A 96 TYR cc_start: 0.7815 (t80) cc_final: 0.7410 (t80) REVERT: A 100 MET cc_start: 0.7961 (mpt) cc_final: 0.7581 (mpp) REVERT: A 133 SER cc_start: 0.8580 (m) cc_final: 0.8305 (t) REVERT: A 186 SER cc_start: 0.8290 (m) cc_final: 0.7953 (t) REVERT: A 198 ARG cc_start: 0.7175 (ptm160) cc_final: 0.4805 (mpt180) REVERT: B 48 MET cc_start: 0.7572 (mtm) cc_final: 0.7317 (mtm) REVERT: B 75 ARG cc_start: 0.8683 (mtt180) cc_final: 0.8351 (ttm110) REVERT: B 124 GLU cc_start: 0.8273 (tt0) cc_final: 0.7773 (tp30) REVERT: B 195 HIS cc_start: 0.5255 (p-80) cc_final: 0.5021 (p-80) REVERT: B 220 THR cc_start: 0.8505 (p) cc_final: 0.6703 (p) outliers start: 7 outliers final: 4 residues processed: 385 average time/residue: 0.2348 time to fit residues: 118.9474 Evaluate side-chains 244 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 239 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 343 ILE Chi-restraints excluded: chain F residue 345 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 290 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 8.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.0570 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 0.0570 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 46 ASN F 138 ASN F 148 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 138 GLN G 216 ASN A 8 ASN A 38 ASN A 104 GLN A 119 ASN B 113 GLN B 212 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8963 Z= 0.189 Angle : 0.717 10.490 12141 Z= 0.354 Chirality : 0.044 0.212 1446 Planarity : 0.006 0.051 1513 Dihedral : 12.136 99.992 1336 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 4.21 % Allowed : 15.98 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.51 (0.22), residues: 1094 helix: -1.62 (0.20), residues: 540 sheet: -2.58 (0.43), residues: 102 loop : -3.08 (0.25), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 204 HIS 0.005 0.001 HIS B 195 PHE 0.023 0.002 PHE G 349 TYR 0.019 0.002 TYR B 82 ARG 0.007 0.001 ARG A 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 268 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7260 (mt-10) REVERT: F 103 MET cc_start: 0.8527 (mmp) cc_final: 0.8187 (mmt) REVERT: F 329 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6963 (tt) REVERT: G 100 MET cc_start: 0.7788 (tpp) cc_final: 0.7514 (tpp) REVERT: G 291 MET cc_start: 0.8609 (tmt) cc_final: 0.7892 (tmt) REVERT: A 14 LYS cc_start: 0.7119 (mttt) cc_final: 0.6037 (mptt) REVERT: A 198 ARG cc_start: 0.6797 (ptm160) cc_final: 0.5067 (mpt180) REVERT: B 48 MET cc_start: 0.7554 (mtm) cc_final: 0.7194 (mtm) REVERT: B 75 ARG cc_start: 0.8531 (mtt180) cc_final: 0.8254 (ttm110) REVERT: B 124 GLU cc_start: 0.8004 (tt0) cc_final: 0.7592 (tp30) REVERT: B 181 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7831 (mm-30) REVERT: B 224 ILE cc_start: 0.7847 (mm) cc_final: 0.6951 (mm) outliers start: 39 outliers final: 26 residues processed: 296 average time/residue: 0.2087 time to fit residues: 84.7981 Evaluate side-chains 249 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 222 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 329 LEU Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 351 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 127 ILE Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 223 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 83 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 81 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 228 GLN A 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8963 Z= 0.160 Angle : 0.665 9.604 12141 Z= 0.326 Chirality : 0.043 0.255 1446 Planarity : 0.005 0.060 1513 Dihedral : 11.399 95.993 1330 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.21 % Allowed : 18.25 % Favored : 77.54 % 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: -2.70 (0.23), residues: 1094 helix: -0.75 (0.22), residues: 523 sheet: -2.31 (0.44), residues: 99 loop : -2.90 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 204 HIS 0.004 0.001 HIS B 195 PHE 0.023 0.001 PHE G 349 TYR 0.012 0.001 TYR B 82 ARG 0.003 0.000 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 254 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7182 (mt-10) REVERT: F 103 MET cc_start: 0.8291 (mmp) cc_final: 0.7967 (mmp) REVERT: G 24 PHE cc_start: 0.8015 (t80) cc_final: 0.7755 (t80) REVERT: G 100 MET cc_start: 0.7851 (tpp) cc_final: 0.7551 (tpp) REVERT: G 237 ASP cc_start: 0.6194 (p0) cc_final: 0.5986 (p0) REVERT: G 291 MET cc_start: 0.8568 (tmt) cc_final: 0.7787 (tmt) REVERT: A 4 LEU cc_start: 0.8787 (tp) cc_final: 0.8314 (tt) REVERT: A 14 LYS cc_start: 0.7102 (mttt) cc_final: 0.6102 (mptt) REVERT: A 130 LEU cc_start: 0.8050 (mt) cc_final: 0.7365 (pp) REVERT: A 157 LYS cc_start: 0.8860 (mptt) cc_final: 0.8188 (mmmt) REVERT: A 162 ASP cc_start: 0.8183 (t0) cc_final: 0.7841 (t0) REVERT: A 169 ASP cc_start: 0.7661 (OUTLIER) cc_final: 0.6892 (p0) REVERT: A 198 ARG cc_start: 0.6527 (ptm160) cc_final: 0.5148 (mtt90) REVERT: B 124 GLU cc_start: 0.8098 (tt0) cc_final: 0.7636 (tp30) outliers start: 39 outliers final: 24 residues processed: 273 average time/residue: 0.1976 time to fit residues: 75.1948 Evaluate side-chains 253 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 chunk 89 optimal weight: 0.0870 chunk 60 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN F 150 GLN F 228 GLN G 216 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8963 Z= 0.155 Angle : 0.665 9.572 12141 Z= 0.319 Chirality : 0.043 0.184 1446 Planarity : 0.005 0.047 1513 Dihedral : 10.954 93.247 1330 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.32 % Allowed : 19.98 % Favored : 75.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.33 (0.24), residues: 1094 helix: -0.39 (0.23), residues: 527 sheet: -1.98 (0.45), residues: 99 loop : -2.83 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 204 HIS 0.002 0.001 HIS A 195 PHE 0.027 0.001 PHE G 349 TYR 0.008 0.001 TYR A 96 ARG 0.009 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 254 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7859 (mm-30) cc_final: 0.7282 (mt-10) REVERT: G 24 PHE cc_start: 0.8120 (t80) cc_final: 0.7917 (t80) REVERT: G 291 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8256 (tmm) REVERT: A 4 LEU cc_start: 0.8644 (tp) cc_final: 0.8314 (tt) REVERT: A 14 LYS cc_start: 0.7077 (mttt) cc_final: 0.6070 (mptt) REVERT: A 100 MET cc_start: 0.8059 (mmt) cc_final: 0.7857 (mmt) REVERT: A 130 LEU cc_start: 0.7960 (mt) cc_final: 0.7320 (pp) REVERT: A 157 LYS cc_start: 0.8757 (mptt) cc_final: 0.8130 (mmmt) REVERT: A 169 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7516 (p0) REVERT: A 198 ARG cc_start: 0.6673 (ptm160) cc_final: 0.4672 (mmt90) REVERT: B 124 GLU cc_start: 0.8056 (tt0) cc_final: 0.7753 (tp30) REVERT: B 136 GLN cc_start: 0.7185 (tm-30) cc_final: 0.6801 (tm-30) REVERT: B 178 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7412 (mtm110) outliers start: 40 outliers final: 26 residues processed: 274 average time/residue: 0.2119 time to fit residues: 79.1780 Evaluate side-chains 256 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 169 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 64 ASP Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 195 HIS Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0370 chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 0.0070 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 0.0070 chunk 96 optimal weight: 7.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 0.0870 chunk 21 optimal weight: 20.0000 overall best weight: 0.0370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN F 150 GLN G 93 GLN A 38 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 ASN B 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8963 Z= 0.147 Angle : 0.641 10.724 12141 Z= 0.310 Chirality : 0.043 0.254 1446 Planarity : 0.004 0.041 1513 Dihedral : 10.502 90.204 1329 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 4.00 % Allowed : 20.41 % Favored : 75.59 % 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: -2.03 (0.24), residues: 1094 helix: -0.14 (0.23), residues: 520 sheet: -1.77 (0.49), residues: 90 loop : -2.65 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 204 HIS 0.002 0.000 HIS B 195 PHE 0.029 0.002 PHE B 46 TYR 0.009 0.001 TYR G 191 ARG 0.005 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 253 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7208 (mt-10) REVERT: F 18 ILE cc_start: 0.8938 (mm) cc_final: 0.8666 (tp) REVERT: F 82 GLU cc_start: 0.7065 (tt0) cc_final: 0.6588 (tt0) REVERT: F 103 MET cc_start: 0.7664 (mmt) cc_final: 0.5658 (ttt) REVERT: F 281 LEU cc_start: 0.8494 (tt) cc_final: 0.8289 (mm) REVERT: F 337 ILE cc_start: 0.9158 (tt) cc_final: 0.8622 (mt) REVERT: F 343 ILE cc_start: 0.9161 (mm) cc_final: 0.8955 (tp) REVERT: G 24 PHE cc_start: 0.8176 (t80) cc_final: 0.7911 (t80) REVERT: G 40 LYS cc_start: 0.7235 (pttm) cc_final: 0.6553 (ptpt) REVERT: G 291 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.8238 (tmm) REVERT: A 14 LYS cc_start: 0.7086 (mttt) cc_final: 0.6023 (mptt) REVERT: A 157 LYS cc_start: 0.8740 (mptt) cc_final: 0.8093 (mmmt) REVERT: A 196 ASN cc_start: 0.6342 (p0) cc_final: 0.6026 (p0) REVERT: A 198 ARG cc_start: 0.6660 (ptm160) cc_final: 0.4324 (mmt90) REVERT: B 96 TYR cc_start: 0.8055 (t80) cc_final: 0.7834 (t80) REVERT: B 124 GLU cc_start: 0.8001 (tt0) cc_final: 0.7660 (tp30) REVERT: B 178 ARG cc_start: 0.7858 (mtp85) cc_final: 0.7407 (mtm110) outliers start: 37 outliers final: 28 residues processed: 273 average time/residue: 0.1969 time to fit residues: 73.8640 Evaluate side-chains 263 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 234 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 228 GLN Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 8 optimal weight: 0.0270 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 138 ASN F 148 GLN F 150 GLN A 196 ASN B 27 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8963 Z= 0.153 Angle : 0.640 9.782 12141 Z= 0.309 Chirality : 0.043 0.211 1446 Planarity : 0.004 0.038 1513 Dihedral : 10.311 90.516 1329 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 4.75 % Allowed : 21.60 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.25), residues: 1094 helix: 0.08 (0.23), residues: 520 sheet: -1.68 (0.48), residues: 99 loop : -2.51 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 204 HIS 0.003 0.000 HIS B 195 PHE 0.021 0.001 PHE G 349 TYR 0.008 0.001 TYR G 191 ARG 0.004 0.000 ARG A 150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 242 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7229 (mt-10) REVERT: G 40 LYS cc_start: 0.7267 (pttm) cc_final: 0.6582 (ptpt) REVERT: G 291 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8132 (tmm) REVERT: G 348 PHE cc_start: 0.7872 (t80) cc_final: 0.7569 (t80) REVERT: A 14 LYS cc_start: 0.7105 (mttt) cc_final: 0.6145 (mppt) REVERT: A 100 MET cc_start: 0.7928 (mmt) cc_final: 0.7574 (mmt) REVERT: A 130 LEU cc_start: 0.8009 (mt) cc_final: 0.7350 (pp) REVERT: A 157 LYS cc_start: 0.8669 (mptt) cc_final: 0.8110 (mmmt) REVERT: A 196 ASN cc_start: 0.6474 (OUTLIER) cc_final: 0.6028 (p0) REVERT: B 115 GLU cc_start: 0.7562 (mp0) cc_final: 0.7282 (mp0) REVERT: B 124 GLU cc_start: 0.8092 (tt0) cc_final: 0.7487 (tp30) REVERT: B 178 ARG cc_start: 0.7843 (mtp85) cc_final: 0.7490 (mtm110) outliers start: 44 outliers final: 32 residues processed: 267 average time/residue: 0.1949 time to fit residues: 71.9897 Evaluate side-chains 259 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 59 SER Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 148 GLN F 154 ASN A 38 ASN A 196 ASN B 119 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8963 Z= 0.166 Angle : 0.645 8.654 12141 Z= 0.315 Chirality : 0.043 0.202 1446 Planarity : 0.004 0.038 1513 Dihedral : 10.274 90.394 1329 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.75 % Allowed : 21.92 % Favored : 73.33 % 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: -1.66 (0.25), residues: 1094 helix: 0.15 (0.23), residues: 526 sheet: -1.61 (0.48), residues: 99 loop : -2.47 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 204 HIS 0.003 0.001 HIS B 195 PHE 0.020 0.001 PHE B 46 TYR 0.006 0.001 TYR B 82 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 240 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7257 (mt-10) REVERT: F 281 LEU cc_start: 0.8634 (tt) cc_final: 0.8362 (tt) REVERT: G 88 GLU cc_start: 0.7233 (mp0) cc_final: 0.6925 (mp0) REVERT: G 291 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8090 (tmm) REVERT: G 348 PHE cc_start: 0.7879 (t80) cc_final: 0.7581 (t80) REVERT: A 14 LYS cc_start: 0.7110 (mttt) cc_final: 0.6156 (mppt) REVERT: A 130 LEU cc_start: 0.8100 (mt) cc_final: 0.7476 (pp) REVERT: A 157 LYS cc_start: 0.8643 (mptt) cc_final: 0.8129 (mmmt) REVERT: A 196 ASN cc_start: 0.6286 (OUTLIER) cc_final: 0.5927 (p0) REVERT: B 124 GLU cc_start: 0.8157 (tt0) cc_final: 0.7480 (tp30) REVERT: B 178 ARG cc_start: 0.7870 (mtp85) cc_final: 0.7485 (mtm110) outliers start: 44 outliers final: 35 residues processed: 264 average time/residue: 0.1923 time to fit residues: 70.9398 Evaluate side-chains 265 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 228 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 295 PHE Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 196 ASN Chi-restraints excluded: chain A residue 200 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 0.0670 chunk 68 optimal weight: 0.0980 chunk 72 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 84 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 chunk 102 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.4940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8963 Z= 0.155 Angle : 0.654 9.136 12141 Z= 0.317 Chirality : 0.043 0.189 1446 Planarity : 0.004 0.036 1513 Dihedral : 10.137 89.813 1329 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.43 % Allowed : 23.11 % Favored : 72.46 % 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: -1.52 (0.25), residues: 1094 helix: 0.24 (0.23), residues: 520 sheet: -1.55 (0.49), residues: 99 loop : -2.34 (0.27), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 204 HIS 0.003 0.001 HIS B 195 PHE 0.025 0.001 PHE G 349 TYR 0.020 0.001 TYR F 306 ARG 0.006 0.000 ARG A 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 232 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7142 (mt-10) REVERT: F 13 LYS cc_start: 0.8132 (mtpt) cc_final: 0.7621 (ttmt) REVERT: F 84 GLU cc_start: 0.7154 (tp30) cc_final: 0.6660 (mm-30) REVERT: F 281 LEU cc_start: 0.8617 (tt) cc_final: 0.8316 (tt) REVERT: G 40 LYS cc_start: 0.7367 (pttm) cc_final: 0.6746 (ptpt) REVERT: G 88 GLU cc_start: 0.7217 (mp0) cc_final: 0.6866 (mp0) REVERT: G 291 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8027 (tmm) REVERT: G 348 PHE cc_start: 0.7776 (t80) cc_final: 0.7494 (t80) REVERT: G 349 PHE cc_start: 0.8402 (t80) cc_final: 0.8005 (t80) REVERT: A 100 MET cc_start: 0.8200 (mmt) cc_final: 0.7896 (mmp) REVERT: A 130 LEU cc_start: 0.8042 (mt) cc_final: 0.7389 (pp) REVERT: A 157 LYS cc_start: 0.8545 (mptt) cc_final: 0.8059 (mmmt) REVERT: A 198 ARG cc_start: 0.6527 (ptm160) cc_final: 0.4534 (mmt180) REVERT: B 124 GLU cc_start: 0.8118 (tt0) cc_final: 0.7446 (tp30) REVERT: B 178 ARG cc_start: 0.7859 (mtp85) cc_final: 0.7455 (mtm110) outliers start: 41 outliers final: 33 residues processed: 251 average time/residue: 0.1919 time to fit residues: 66.9508 Evaluate side-chains 259 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 127 HIS Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 267 ASN ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8963 Z= 0.173 Angle : 0.667 8.389 12141 Z= 0.324 Chirality : 0.044 0.208 1446 Planarity : 0.004 0.044 1513 Dihedral : 10.143 90.340 1329 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.32 % Allowed : 24.30 % Favored : 71.38 % 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: -1.49 (0.25), residues: 1094 helix: 0.24 (0.23), residues: 529 sheet: -1.51 (0.49), residues: 99 loop : -2.34 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 268 HIS 0.003 0.001 HIS B 195 PHE 0.022 0.001 PHE G 349 TYR 0.027 0.001 TYR B 82 ARG 0.011 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7247 (mt-10) REVERT: F 13 LYS cc_start: 0.8119 (mtpt) cc_final: 0.7671 (ttmt) REVERT: F 27 PHE cc_start: 0.8055 (m-10) cc_final: 0.7771 (m-10) REVERT: F 82 GLU cc_start: 0.6811 (tt0) cc_final: 0.6603 (tt0) REVERT: F 281 LEU cc_start: 0.8658 (tt) cc_final: 0.8341 (tt) REVERT: G 88 GLU cc_start: 0.7379 (mp0) cc_final: 0.7075 (mp0) REVERT: G 291 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8126 (tmm) REVERT: G 348 PHE cc_start: 0.7725 (t80) cc_final: 0.7183 (t80) REVERT: G 349 PHE cc_start: 0.8412 (t80) cc_final: 0.8015 (t80) REVERT: A 14 LYS cc_start: 0.7229 (mttt) cc_final: 0.6260 (mppt) REVERT: A 157 LYS cc_start: 0.8535 (mptt) cc_final: 0.8062 (mmmt) REVERT: A 198 ARG cc_start: 0.6681 (ptm160) cc_final: 0.4337 (mmt180) REVERT: B 124 GLU cc_start: 0.8128 (tt0) cc_final: 0.7458 (tp30) REVERT: B 136 GLN cc_start: 0.7118 (tm-30) cc_final: 0.6659 (tm-30) REVERT: B 178 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7444 (mtm110) outliers start: 40 outliers final: 33 residues processed: 254 average time/residue: 0.1954 time to fit residues: 68.7841 Evaluate side-chains 257 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 223 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 196 ASN Chi-restraints excluded: chain B residue 206 ARG Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 9.9990 chunk 88 optimal weight: 9.9990 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.3980 chunk 53 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8963 Z= 0.175 Angle : 0.692 11.515 12141 Z= 0.332 Chirality : 0.044 0.189 1446 Planarity : 0.004 0.041 1513 Dihedral : 10.068 90.283 1329 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.78 % Allowed : 25.27 % Favored : 70.95 % 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: -1.45 (0.25), residues: 1094 helix: 0.24 (0.23), residues: 524 sheet: -1.49 (0.50), residues: 90 loop : -2.25 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 268 HIS 0.003 0.001 HIS F 89 PHE 0.022 0.001 PHE G 349 TYR 0.017 0.001 TYR F 306 ARG 0.011 0.001 ARG A 55 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2188 Ramachandran restraints generated. 1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 230 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 10 GLU cc_start: 0.7918 (mm-30) cc_final: 0.7229 (mt-10) REVERT: F 13 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7799 (ttmt) REVERT: F 27 PHE cc_start: 0.8146 (m-10) cc_final: 0.7836 (m-10) REVERT: F 281 LEU cc_start: 0.8743 (tt) cc_final: 0.8403 (tt) REVERT: G 88 GLU cc_start: 0.7397 (mp0) cc_final: 0.7110 (mp0) REVERT: G 291 MET cc_start: 0.8644 (OUTLIER) cc_final: 0.8144 (tmm) REVERT: G 348 PHE cc_start: 0.7660 (t80) cc_final: 0.7143 (t80) REVERT: A 14 LYS cc_start: 0.7129 (mttt) cc_final: 0.6199 (mppt) REVERT: A 157 LYS cc_start: 0.8489 (mptt) cc_final: 0.8024 (mmmt) REVERT: B 124 GLU cc_start: 0.8140 (tt0) cc_final: 0.7464 (tp30) REVERT: B 136 GLN cc_start: 0.7144 (tm-30) cc_final: 0.6652 (tm-30) REVERT: B 178 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7438 (mtm110) outliers start: 35 outliers final: 29 residues processed: 246 average time/residue: 0.1901 time to fit residues: 65.4697 Evaluate side-chains 252 residues out of total 927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 222 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 21 ILE Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 268 TRP Chi-restraints excluded: chain F residue 289 VAL Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 330 TRP Chi-restraints excluded: chain F residue 332 TRP Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 291 MET Chi-restraints excluded: chain G residue 322 LEU Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain B residue 8 ASN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 169 ASP Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 11 optimal weight: 6.9990 chunk 16 optimal weight: 20.0000 chunk 77 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 226 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.163136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135939 restraints weight = 17386.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138241 restraints weight = 10526.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.139768 restraints weight = 7344.273| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.5163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8963 Z= 0.180 Angle : 0.691 12.515 12141 Z= 0.330 Chirality : 0.044 0.189 1446 Planarity : 0.004 0.060 1513 Dihedral : 10.014 90.299 1329 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 25.59 % Favored : 70.73 % 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: -1.51 (0.25), residues: 1094 helix: 0.12 (0.23), residues: 540 sheet: -1.41 (0.50), residues: 88 loop : -2.28 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 268 HIS 0.003 0.001 HIS F 89 PHE 0.022 0.001 PHE G 349 TYR 0.016 0.001 TYR F 306 ARG 0.008 0.000 ARG A 16 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2185.22 seconds wall clock time: 40 minutes 21.61 seconds (2421.61 seconds total)