Starting phenix.real_space_refine on Wed Feb 14 01:59:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i7v_35234/02_2024/8i7v_35234_updated.pdb" } resolution = 2.77 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= -0.002 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5345 2.51 5 N 1434 2.21 5 O 1533 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 73": "OD1" <-> "OD2" Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 33": "OE1" <-> "OE2" Residue "B PHE 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 234": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8374 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2369 Classifications: {'peptide': 291} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 280} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1152 Classifications: {'peptide': 145} Modifications used: {'COO': 1} Link IDs: {'TRANS': 144} Chain breaks: 3 Chain: "C" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "D" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "E" Number of atoms: 1791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1791 Classifications: {'peptide': 233} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Chain: "A" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'OJX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.15, per 1000 atoms: 0.61 Number of scatterers: 8374 At special positions: 0 Unit cell: (89.64, 118.275, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1533 8.00 N 1434 7.00 C 5345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 18 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 266 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 177 " distance=2.03 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 149 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 seconds 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1988 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 13 sheets defined 32.4% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 30 through 53 Processing helix chain 'A' and resid 62 through 89 Proline residue: A 81 - end of helix removed outlier: 3.904A pdb=" N ARG A 89 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 129 Processing helix chain 'A' and resid 135 through 138 Processing helix chain 'A' and resid 141 through 162 removed outlier: 5.048A pdb=" N HIS A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LEU A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 217 Proline residue: A 200 - end of helix Processing helix chain 'A' and resid 224 through 260 Proline residue: A 246 - end of helix Processing helix chain 'A' and resid 266 through 294 removed outlier: 3.531A pdb=" N ARG A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 271 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU A 280 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP A 290 " --> pdb=" O SER A 287 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.854A pdb=" N TYR A 294 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 32 removed outlier: 4.145A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 52 Processing helix chain 'B' and resid 208 through 211 removed outlier: 3.954A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 328 through 351 Processing helix chain 'C' and resid 4 through 24 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'D' and resid 7 through 22 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 74 through 76 No H-bonds generated for 'chain 'E' and resid 74 through 76' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'B' and resid 319 through 323 removed outlier: 6.912A pdb=" N ILE B 264 " --> pdb=" O TYR B 320 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N HIS B 322 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 266 " --> pdb=" O HIS B 322 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N CYS B 224 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N HIS B 195 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU B 36 " --> pdb=" O HIS B 195 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS B 197 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU B 38 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N PHE B 199 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.782A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.799A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS C 121 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.630A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 198 through 202 removed outlier: 3.561A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.694A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.562A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 46 through 51 removed outlier: 3.745A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 6.032A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.558A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.672A pdb=" N ALA E 211 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 225 through 231 removed outlier: 3.560A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1011 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: 2.34 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1344 1.31 - 1.45: 2417 1.45 - 1.58: 4702 1.58 - 1.71: 1 1.71 - 1.84: 90 Bond restraints: 8554 Sorted by residual: bond pdb=" C THR B 340 " pdb=" O THR B 340 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.15e-02 7.56e+03 2.40e+01 bond pdb=" C PRO A 99 " pdb=" O PRO A 99 " ideal model delta sigma weight residual 1.237 1.192 0.046 1.16e-02 7.43e+03 1.54e+01 bond pdb=" N ILE B 343 " pdb=" CA ILE B 343 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.21e-02 6.83e+03 8.94e+00 bond pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 7.00e+00 bond pdb=" N CYS B 351 " pdb=" CA CYS B 351 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.20e-02 6.94e+03 6.66e+00 ... (remaining 8549 not shown) Histogram of bond angle deviations from ideal: 96.21 - 103.80: 84 103.80 - 111.39: 3731 111.39 - 118.97: 3149 118.97 - 126.56: 4477 126.56 - 134.15: 135 Bond angle restraints: 11576 Sorted by residual: angle pdb=" CA PRO E 75 " pdb=" N PRO E 75 " pdb=" CD PRO E 75 " ideal model delta sigma weight residual 112.00 103.92 8.08 1.40e+00 5.10e-01 3.33e+01 angle pdb=" N ILE C 270 " pdb=" CA ILE C 270 " pdb=" C ILE C 270 " ideal model delta sigma weight residual 113.71 108.66 5.05 9.50e-01 1.11e+00 2.83e+01 angle pdb=" CA PHE B 354 " pdb=" CB PHE B 354 " pdb=" CG PHE B 354 " ideal model delta sigma weight residual 113.80 118.66 -4.86 1.00e+00 1.00e+00 2.36e+01 angle pdb=" CA THR B 340 " pdb=" C THR B 340 " pdb=" O THR B 340 " ideal model delta sigma weight residual 120.82 115.75 5.07 1.05e+00 9.07e-01 2.33e+01 angle pdb=" CA MET B 53 " pdb=" CB MET B 53 " pdb=" CG MET B 53 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 ... (remaining 11571 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 4393 17.20 - 34.40: 488 34.40 - 51.60: 141 51.60 - 68.80: 21 68.80 - 85.99: 10 Dihedral angle restraints: 5053 sinusoidal: 1978 harmonic: 3075 Sorted by residual: dihedral pdb=" CA MET A 167 " pdb=" C MET A 167 " pdb=" N PRO A 168 " pdb=" CA PRO A 168 " ideal model delta harmonic sigma weight residual 180.00 157.37 22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA PHE A 197 " pdb=" C PHE A 197 " pdb=" N PHE A 198 " pdb=" CA PHE A 198 " ideal model delta harmonic sigma weight residual 180.00 -160.85 -19.15 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CB CYS A 19 " pdb=" SG CYS A 19 " pdb=" SG CYS A 266 " pdb=" CB CYS A 266 " ideal model delta sinusoidal sigma weight residual -86.00 -54.87 -31.13 1 1.00e+01 1.00e-02 1.38e+01 ... (remaining 5050 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1115 0.060 - 0.120: 177 0.120 - 0.180: 13 0.180 - 0.240: 2 0.240 - 0.299: 1 Chirality restraints: 1308 Sorted by residual: chirality pdb=" CA ILE B 344 " pdb=" N ILE B 344 " pdb=" C ILE B 344 " pdb=" CB ILE B 344 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA MET B 53 " pdb=" N MET B 53 " pdb=" C MET B 53 " pdb=" CB MET B 53 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA LEU B 353 " pdb=" N LEU B 353 " pdb=" C LEU B 353 " pdb=" CB LEU B 353 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 1305 not shown) Planarity restraints: 1460 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.080 5.00e-02 4.00e+02 1.17e-01 2.17e+01 pdb=" N PRO E 75 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 30 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.76e+00 pdb=" N PRO A 31 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 31 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 31 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.030 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO C 236 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.026 5.00e-02 4.00e+02 ... (remaining 1457 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 2 2.06 - 2.77: 1432 2.77 - 3.48: 11352 3.48 - 4.19: 20275 4.19 - 4.90: 36837 Nonbonded interactions: 69898 Sorted by model distance: nonbonded pdb=" O PRO A 299 " pdb=" O PHE B 354 " model vdw 1.346 3.040 nonbonded pdb=" O LYS A 57 " pdb=" OD2 ASP C 312 " model vdw 1.899 3.040 nonbonded pdb=" O PRO A 299 " pdb=" C PHE B 354 " model vdw 2.143 3.270 nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.185 2.440 nonbonded pdb=" O HIS B 213 " pdb=" OH TYR C 59 " model vdw 2.191 2.440 ... (remaining 69893 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.390 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: 2.210 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.530 Find NCS groups from input model: 0.270 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:13.530 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 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 0.110 8554 Z= 0.237 Angle : 0.625 8.178 11576 Z= 0.364 Chirality : 0.044 0.299 1308 Planarity : 0.005 0.117 1460 Dihedral : 16.063 85.994 3047 Min Nonbonded Distance : 1.346 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 1.76 % Allowed : 18.33 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.74 (0.26), residues: 1048 helix: 1.65 (0.28), residues: 331 sheet: 0.64 (0.30), residues: 291 loop : -0.48 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 256 HIS 0.004 0.001 HIS E 35 PHE 0.020 0.001 PHE B 354 TYR 0.012 0.001 TYR E 103 ARG 0.004 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 LEU cc_start: 0.6729 (OUTLIER) cc_final: 0.5965 (tm) REVERT: A 222 ARG cc_start: 0.7640 (ptp-170) cc_final: 0.7233 (ppt170) REVERT: A 285 MET cc_start: 0.6129 (ttp) cc_final: 0.5163 (tpt) REVERT: C 175 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: C 314 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7380 (ttp-110) outliers start: 16 outliers final: 8 residues processed: 132 average time/residue: 1.0369 time to fit residues: 146.9988 Evaluate side-chains 112 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain B residue 351 CYS Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 177 THR Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.0070 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN B 195 HIS C 259 GLN C 295 ASN E 3 GLN E 39 GLN E 179 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8554 Z= 0.292 Angle : 0.627 9.774 11576 Z= 0.330 Chirality : 0.044 0.152 1308 Planarity : 0.005 0.070 1460 Dihedral : 6.244 63.176 1171 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.06 % Allowed : 18.00 % Favored : 77.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.87 (0.26), residues: 1048 helix: 1.95 (0.27), residues: 327 sheet: 0.54 (0.29), residues: 293 loop : -0.43 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 63 HIS 0.006 0.001 HIS C 142 PHE 0.018 0.002 PHE A 10 TYR 0.017 0.002 TYR E 103 ARG 0.006 0.000 ARG C 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 112 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LEU cc_start: 0.6930 (OUTLIER) cc_final: 0.6469 (tp) REVERT: A 80 LEU cc_start: 0.6135 (OUTLIER) cc_final: 0.5914 (mt) REVERT: A 167 MET cc_start: 0.3379 (tpp) cc_final: 0.3179 (tpp) REVERT: A 222 ARG cc_start: 0.7739 (ptp-170) cc_final: 0.6586 (mmt90) REVERT: A 285 MET cc_start: 0.6207 (ttp) cc_final: 0.5244 (tpt) REVERT: B 198 MET cc_start: 0.7696 (mmm) cc_final: 0.7279 (mmm) REVERT: B 345 LYS cc_start: 0.7347 (OUTLIER) cc_final: 0.6522 (mptt) REVERT: C 61 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8772 (ppp) REVERT: C 295 ASN cc_start: 0.8539 (OUTLIER) cc_final: 0.8302 (p0) REVERT: D 38 MET cc_start: 0.8536 (ttp) cc_final: 0.8315 (ttp) REVERT: E 43 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6829 (ttpm) outliers start: 37 outliers final: 12 residues processed: 134 average time/residue: 1.0781 time to fit residues: 155.1143 Evaluate side-chains 120 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 208 SER Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 271 SER Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS C 156 GLN C 259 GLN C 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8554 Z= 0.215 Angle : 0.589 9.185 11576 Z= 0.306 Chirality : 0.042 0.143 1308 Planarity : 0.005 0.058 1460 Dihedral : 5.094 57.272 1154 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.95 % Allowed : 19.98 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.98 (0.26), residues: 1048 helix: 2.06 (0.28), residues: 326 sheet: 0.58 (0.30), residues: 274 loop : -0.31 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.002 PHE A 197 TYR 0.014 0.002 TYR E 103 ARG 0.005 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 MET cc_start: 0.5476 (OUTLIER) cc_final: 0.5270 (pp-130) REVERT: A 150 LEU cc_start: 0.7008 (tp) cc_final: 0.6775 (tt) REVERT: A 167 MET cc_start: 0.3432 (tpp) cc_final: 0.3053 (tpp) REVERT: A 222 ARG cc_start: 0.7732 (ptp-170) cc_final: 0.6545 (mmt90) REVERT: A 228 ARG cc_start: 0.6355 (ttm-80) cc_final: 0.6044 (ptt180) REVERT: A 285 MET cc_start: 0.6254 (ttp) cc_final: 0.5281 (tpt) REVERT: B 198 MET cc_start: 0.7660 (mmm) cc_final: 0.7187 (mmm) REVERT: B 345 LYS cc_start: 0.7547 (OUTLIER) cc_final: 0.6993 (mptt) REVERT: C 43 ILE cc_start: 0.7523 (OUTLIER) cc_final: 0.6996 (mt) REVERT: D 38 MET cc_start: 0.8514 (ttp) cc_final: 0.8300 (ttp) REVERT: E 39 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8223 (tt0) outliers start: 36 outliers final: 15 residues processed: 129 average time/residue: 1.0859 time to fit residues: 150.4742 Evaluate side-chains 116 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 345 LYS Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS C 156 GLN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8554 Z= 0.271 Angle : 0.608 9.676 11576 Z= 0.317 Chirality : 0.043 0.146 1308 Planarity : 0.005 0.055 1460 Dihedral : 5.112 54.671 1154 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.39 % Allowed : 21.95 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.91 (0.26), residues: 1048 helix: 2.01 (0.28), residues: 324 sheet: 0.63 (0.31), residues: 268 loop : -0.41 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.006 0.001 HIS E 35 PHE 0.028 0.002 PHE A 74 TYR 0.016 0.002 TYR E 103 ARG 0.004 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 101 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 LEU cc_start: 0.6376 (OUTLIER) cc_final: 0.5966 (pp) REVERT: A 75 LEU cc_start: 0.7124 (mp) cc_final: 0.6902 (mp) REVERT: A 76 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.6632 (tp) REVERT: A 106 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4140 (ttp) REVERT: A 109 MET cc_start: 0.5526 (OUTLIER) cc_final: 0.5153 (pp-130) REVERT: A 150 LEU cc_start: 0.6964 (tp) cc_final: 0.6713 (tt) REVERT: A 222 ARG cc_start: 0.7803 (ptp-170) cc_final: 0.6614 (mmt90) REVERT: A 228 ARG cc_start: 0.6316 (ttm-80) cc_final: 0.5887 (ptt90) REVERT: B 198 MET cc_start: 0.7673 (mmm) cc_final: 0.7315 (mmm) REVERT: C 43 ILE cc_start: 0.7678 (OUTLIER) cc_final: 0.7126 (mt) REVERT: C 61 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8774 (ppp) REVERT: C 175 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7574 (mm-40) REVERT: E 230 MET cc_start: 0.8368 (ttp) cc_final: 0.7829 (tmm) outliers start: 40 outliers final: 16 residues processed: 127 average time/residue: 0.9916 time to fit residues: 136.1142 Evaluate side-chains 121 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 25 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS C 259 GLN E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 8554 Z= 0.219 Angle : 0.577 8.824 11576 Z= 0.299 Chirality : 0.042 0.143 1308 Planarity : 0.004 0.052 1460 Dihedral : 4.792 50.157 1150 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.84 % Allowed : 23.49 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.05 (0.27), residues: 1048 helix: 2.16 (0.28), residues: 324 sheet: 0.69 (0.31), residues: 267 loop : -0.35 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.020 0.002 PHE A 21 TYR 0.014 0.001 TYR E 103 ARG 0.003 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 106 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5278 (OUTLIER) cc_final: 0.4999 (t) REVERT: A 36 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.5983 (pp) REVERT: A 75 LEU cc_start: 0.7033 (mp) cc_final: 0.6813 (mp) REVERT: A 76 LEU cc_start: 0.6867 (OUTLIER) cc_final: 0.6618 (tp) REVERT: A 106 MET cc_start: 0.5092 (OUTLIER) cc_final: 0.4151 (ttp) REVERT: A 109 MET cc_start: 0.5428 (OUTLIER) cc_final: 0.5129 (pp-130) REVERT: A 141 ASN cc_start: 0.6977 (OUTLIER) cc_final: 0.6664 (m-40) REVERT: A 150 LEU cc_start: 0.7009 (tp) cc_final: 0.6785 (tt) REVERT: A 166 LYS cc_start: 0.6205 (tppt) cc_final: 0.5983 (tmtt) REVERT: A 167 MET cc_start: 0.3359 (tpp) cc_final: 0.3076 (tpp) REVERT: A 222 ARG cc_start: 0.7926 (ptp-170) cc_final: 0.6676 (mmt90) REVERT: A 227 LYS cc_start: 0.6435 (ttpt) cc_final: 0.6118 (pptt) REVERT: A 228 ARG cc_start: 0.6264 (ttm-80) cc_final: 0.5747 (ptt180) REVERT: B 198 MET cc_start: 0.7788 (mmm) cc_final: 0.7442 (mmm) REVERT: C 43 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7032 (mt) REVERT: C 175 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7585 (mm-40) REVERT: C 314 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7657 (ttp-110) REVERT: E 39 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8319 (tt0) outliers start: 35 outliers final: 15 residues processed: 130 average time/residue: 1.0775 time to fit residues: 150.4196 Evaluate side-chains 128 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 106 MET Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.0170 chunk 8 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 52 optimal weight: 0.0040 chunk 97 optimal weight: 0.2980 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS C 75 GLN C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8554 Z= 0.151 Angle : 0.530 7.037 11576 Z= 0.275 Chirality : 0.041 0.148 1308 Planarity : 0.004 0.048 1460 Dihedral : 4.425 42.522 1148 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.29 % Allowed : 24.92 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.22 (0.27), residues: 1048 helix: 2.15 (0.28), residues: 336 sheet: 0.72 (0.31), residues: 268 loop : -0.11 (0.32), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.002 0.000 HIS E 35 PHE 0.017 0.001 PHE A 197 TYR 0.012 0.001 TYR E 190 ARG 0.003 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 110 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5048 (OUTLIER) cc_final: 0.4770 (t) REVERT: A 109 MET cc_start: 0.5354 (OUTLIER) cc_final: 0.5083 (pp-130) REVERT: A 141 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6626 (m-40) REVERT: A 150 LEU cc_start: 0.6968 (tp) cc_final: 0.6762 (tt) REVERT: A 165 LYS cc_start: 0.7382 (tptt) cc_final: 0.6402 (mtmm) REVERT: A 166 LYS cc_start: 0.6197 (tppt) cc_final: 0.5897 (pttp) REVERT: A 216 ARG cc_start: 0.6467 (mtp85) cc_final: 0.6221 (mtp85) REVERT: A 222 ARG cc_start: 0.7956 (ptp-170) cc_final: 0.6772 (mmt90) REVERT: A 225 LYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5369 (mmpt) REVERT: A 227 LYS cc_start: 0.6436 (ttpt) cc_final: 0.6029 (pptt) REVERT: A 228 ARG cc_start: 0.6330 (ttm-80) cc_final: 0.5827 (ptt180) REVERT: A 285 MET cc_start: 0.6175 (ttp) cc_final: 0.5396 (tpt) REVERT: B 198 MET cc_start: 0.7840 (mmm) cc_final: 0.7444 (mmm) REVERT: C 175 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7560 (mm-40) REVERT: E 39 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8205 (tt0) outliers start: 30 outliers final: 10 residues processed: 133 average time/residue: 1.1527 time to fit residues: 163.9405 Evaluate side-chains 120 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 61 optimal weight: 0.4980 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 HIS B 195 HIS B 269 ASN C 259 GLN E 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 8554 Z= 0.323 Angle : 0.649 10.365 11576 Z= 0.333 Chirality : 0.045 0.151 1308 Planarity : 0.005 0.049 1460 Dihedral : 4.854 48.820 1148 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.72 % Allowed : 23.38 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.12 (0.27), residues: 1048 helix: 2.23 (0.28), residues: 325 sheet: 0.73 (0.31), residues: 272 loop : -0.32 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 47 HIS 0.007 0.001 HIS E 35 PHE 0.016 0.002 PHE A 197 TYR 0.016 0.002 TYR E 103 ARG 0.002 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 108 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 CYS cc_start: 0.6044 (OUTLIER) cc_final: 0.5763 (m) REVERT: A 29 VAL cc_start: 0.5283 (OUTLIER) cc_final: 0.4971 (t) REVERT: A 36 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.5794 (pp) REVERT: A 141 ASN cc_start: 0.6836 (OUTLIER) cc_final: 0.6553 (m-40) REVERT: A 150 LEU cc_start: 0.7001 (tp) cc_final: 0.6767 (tt) REVERT: A 166 LYS cc_start: 0.6285 (tppt) cc_final: 0.6050 (pttp) REVERT: A 167 MET cc_start: 0.3401 (tpp) cc_final: 0.2077 (ptt) REVERT: A 222 ARG cc_start: 0.7890 (ptp-170) cc_final: 0.6733 (mmt90) REVERT: A 225 LYS cc_start: 0.5981 (OUTLIER) cc_final: 0.5650 (mmpt) REVERT: A 227 LYS cc_start: 0.6449 (ttpt) cc_final: 0.5988 (pptt) REVERT: A 228 ARG cc_start: 0.6358 (ttm-80) cc_final: 0.5738 (ptt180) REVERT: A 285 MET cc_start: 0.6170 (ttp) cc_final: 0.5369 (tpt) REVERT: B 198 MET cc_start: 0.7792 (mmm) cc_final: 0.7430 (mmm) REVERT: C 61 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8743 (ppp) REVERT: C 175 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.7584 (mm-40) REVERT: C 295 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7772 (p0) REVERT: C 314 ARG cc_start: 0.8378 (OUTLIER) cc_final: 0.7664 (ttp-110) outliers start: 43 outliers final: 20 residues processed: 138 average time/residue: 1.0343 time to fit residues: 153.5034 Evaluate side-chains 134 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 105 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 19 CYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 75 GLN Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 39 GLN Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 8554 Z= 0.261 Angle : 0.628 9.694 11576 Z= 0.321 Chirality : 0.044 0.162 1308 Planarity : 0.004 0.048 1460 Dihedral : 4.864 48.012 1148 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.06 % Allowed : 24.15 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.10 (0.27), residues: 1048 helix: 2.23 (0.28), residues: 324 sheet: 0.70 (0.31), residues: 267 loop : -0.32 (0.31), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.016 0.002 PHE A 197 TYR 0.015 0.002 TYR E 103 ARG 0.002 0.000 ARG A 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 108 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5345 (OUTLIER) cc_final: 0.5016 (t) REVERT: A 36 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.5789 (pp) REVERT: A 141 ASN cc_start: 0.6913 (OUTLIER) cc_final: 0.6636 (m-40) REVERT: A 150 LEU cc_start: 0.6981 (tp) cc_final: 0.6748 (tt) REVERT: A 166 LYS cc_start: 0.6256 (tppt) cc_final: 0.6035 (pttp) REVERT: A 167 MET cc_start: 0.3461 (tpp) cc_final: 0.2133 (ptt) REVERT: A 222 ARG cc_start: 0.7996 (ptp-170) cc_final: 0.6850 (mmt90) REVERT: A 225 LYS cc_start: 0.5754 (OUTLIER) cc_final: 0.5037 (mmpt) REVERT: A 227 LYS cc_start: 0.6556 (ttpt) cc_final: 0.6047 (pptt) REVERT: A 228 ARG cc_start: 0.6437 (ttm-80) cc_final: 0.5832 (ptt180) REVERT: A 285 MET cc_start: 0.6186 (ttp) cc_final: 0.5386 (tpt) REVERT: B 198 MET cc_start: 0.7835 (mmm) cc_final: 0.7487 (mmm) REVERT: C 43 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7107 (mt) REVERT: C 175 GLN cc_start: 0.8304 (OUTLIER) cc_final: 0.7612 (mm-40) REVERT: C 295 ASN cc_start: 0.8221 (OUTLIER) cc_final: 0.7860 (p0) REVERT: C 314 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7609 (ttp-110) REVERT: E 230 MET cc_start: 0.8388 (ttp) cc_final: 0.7801 (tmm) outliers start: 37 outliers final: 17 residues processed: 133 average time/residue: 1.1200 time to fit residues: 160.0196 Evaluate side-chains 131 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 106 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 295 ASN Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 40 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 195 HIS C 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8554 Z= 0.173 Angle : 0.583 10.141 11576 Z= 0.294 Chirality : 0.042 0.168 1308 Planarity : 0.004 0.047 1460 Dihedral : 4.563 40.753 1148 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.52 % Allowed : 25.80 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.23 (0.27), residues: 1048 helix: 2.27 (0.28), residues: 329 sheet: 0.72 (0.31), residues: 267 loop : -0.17 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE A 197 TYR 0.012 0.001 TYR E 190 ARG 0.002 0.000 ARG A 253 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 115 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5498 (OUTLIER) cc_final: 0.5086 (t) REVERT: A 36 LEU cc_start: 0.6563 (OUTLIER) cc_final: 0.5883 (pp) REVERT: A 141 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6806 (m-40) REVERT: A 150 LEU cc_start: 0.6991 (tp) cc_final: 0.6764 (tt) REVERT: A 166 LYS cc_start: 0.6135 (tppt) cc_final: 0.5837 (pttp) REVERT: A 167 MET cc_start: 0.3232 (tpp) cc_final: 0.2109 (ptt) REVERT: A 216 ARG cc_start: 0.6517 (mtp85) cc_final: 0.6267 (mtp85) REVERT: A 222 ARG cc_start: 0.7992 (ptp-170) cc_final: 0.6797 (mmt90) REVERT: A 225 LYS cc_start: 0.5683 (OUTLIER) cc_final: 0.5112 (mmpt) REVERT: A 227 LYS cc_start: 0.6547 (ttpt) cc_final: 0.6091 (pptt) REVERT: A 228 ARG cc_start: 0.6505 (ttm-80) cc_final: 0.5860 (ptt180) REVERT: A 285 MET cc_start: 0.6174 (ttp) cc_final: 0.5412 (tpt) REVERT: B 198 MET cc_start: 0.7845 (mmm) cc_final: 0.7505 (mmm) REVERT: C 175 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.7588 (mm-40) outliers start: 23 outliers final: 13 residues processed: 129 average time/residue: 1.1887 time to fit residues: 163.6031 Evaluate side-chains 127 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 82 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 8554 Z= 0.445 Angle : 0.756 12.568 11576 Z= 0.384 Chirality : 0.049 0.196 1308 Planarity : 0.005 0.049 1460 Dihedral : 5.251 50.553 1148 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.29 % Allowed : 25.36 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.94 (0.26), residues: 1048 helix: 2.04 (0.28), residues: 324 sheet: 0.66 (0.30), residues: 285 loop : -0.45 (0.31), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP E 47 HIS 0.008 0.001 HIS E 35 PHE 0.021 0.003 PHE A 95 TYR 0.020 0.003 TYR E 103 ARG 0.005 0.000 ARG E 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2096 Ramachandran restraints generated. 1048 Oldfield, 0 Emsley, 1048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 VAL cc_start: 0.5335 (OUTLIER) cc_final: 0.4942 (t) REVERT: A 36 LEU cc_start: 0.6470 (OUTLIER) cc_final: 0.5807 (pp) REVERT: A 102 LEU cc_start: 0.6839 (mm) cc_final: 0.6457 (pp) REVERT: A 141 ASN cc_start: 0.7044 (t0) cc_final: 0.6818 (m-40) REVERT: A 150 LEU cc_start: 0.6854 (tp) cc_final: 0.6622 (tt) REVERT: A 165 LYS cc_start: 0.7318 (tptt) cc_final: 0.7050 (tptt) REVERT: A 167 MET cc_start: 0.3355 (tpp) cc_final: 0.2153 (ptt) REVERT: A 222 ARG cc_start: 0.7843 (ptp-170) cc_final: 0.6871 (mmt90) REVERT: A 225 LYS cc_start: 0.5803 (OUTLIER) cc_final: 0.5195 (mmpt) REVERT: A 227 LYS cc_start: 0.6403 (ttpt) cc_final: 0.5986 (pptt) REVERT: A 228 ARG cc_start: 0.6509 (ttm-80) cc_final: 0.5903 (ttt-90) REVERT: A 285 MET cc_start: 0.6171 (ttp) cc_final: 0.5388 (tpt) REVERT: B 198 MET cc_start: 0.7756 (mmm) cc_final: 0.7365 (mmm) REVERT: B 345 LYS cc_start: 0.7543 (mptm) cc_final: 0.7054 (mptt) REVERT: C 43 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7217 (mt) REVERT: C 61 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8638 (ppp) REVERT: C 175 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7646 (mm-40) REVERT: E 230 MET cc_start: 0.8563 (ttp) cc_final: 0.8096 (tmm) outliers start: 30 outliers final: 20 residues processed: 135 average time/residue: 1.1240 time to fit residues: 162.7326 Evaluate side-chains 139 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 113 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 94 LYS Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 242 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 43 ILE Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 175 GLN Chi-restraints excluded: chain C residue 243 THR Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 327 VAL Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 85 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 169 ASN Chi-restraints excluded: chain E residue 188 LEU Chi-restraints excluded: chain E residue 199 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 4 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 HIS C 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.233891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.158863 restraints weight = 8408.259| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 1.81 r_work: 0.3609 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8554 Z= 0.193 Angle : 0.608 9.682 11576 Z= 0.308 Chirality : 0.043 0.188 1308 Planarity : 0.004 0.048 1460 Dihedral : 4.777 42.065 1148 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.52 % Allowed : 26.13 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.07 (0.27), residues: 1048 helix: 2.09 (0.28), residues: 328 sheet: 0.73 (0.31), residues: 264 loop : -0.29 (0.31), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE A 21 TYR 0.013 0.001 TYR E 190 ARG 0.003 0.000 ARG A 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3380.13 seconds wall clock time: 60 minutes 54.64 seconds (3654.64 seconds total)