Starting phenix.real_space_refine on Thu Feb 15 04:54:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f0t_31404/02_2024/7f0t_31404_updated.pdb" } resolution = 3.1 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= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3052 atoms to isotropic. 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 56 5.16 5 C 5176 2.51 5 N 1432 2.21 5 O 1500 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 50": "NH1" <-> "NH2" Residue "F ARG 52": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 130": "NH1" <-> "NH2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "F ARG 226": "NH1" <-> "NH2" Residue "F ARG 227": "NH1" <-> "NH2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "F ARG 266": "NH1" <-> "NH2" Residue "F ARG 338": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 22": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" 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: 8164 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 2242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2242 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 3 Chain: "A" Number of atoms: 1888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1888 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2619 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Conformer: "B" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} bond proxies already assigned to first conformer: 2640 Chain: "D" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'LDP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ACYS B 233 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 233 " occ=0.50 residue: pdb=" N ACYS B 271 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 271 " occ=0.50 Time building chain proxies: 5.84, per 1000 atoms: 0.72 Number of scatterers: 8164 At special positions: 0 Unit cell: (78.264, 97.83, 127.179, 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 56 16.00 O 1500 8.00 N 1432 7.00 C 5176 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS F 96 " - pdb=" SG CYS F 186 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 99 " - pdb=" SG CYS E 107 " 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: 3.04 Conformation dependent library (CDL) restraints added in 2.0 seconds 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1960 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 40.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'F' and resid 22 through 50 Processing helix chain 'F' and resid 59 through 87 Proline residue: F 79 - end of helix Processing helix chain 'F' and resid 93 through 126 removed outlier: 4.234A pdb=" N ASN F 97 " --> pdb=" O SER F 94 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N SER F 110 " --> pdb=" O SER F 107 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE F 111 " --> pdb=" O THR F 108 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LEU F 112 " --> pdb=" O ALA F 109 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER F 126 " --> pdb=" O TRP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 134 Processing helix chain 'F' and resid 137 through 160 Proline residue: F 158 - end of helix Processing helix chain 'F' and resid 192 through 202 Processing helix chain 'F' and resid 204 through 240 Processing helix chain 'F' and resid 265 through 298 Proline residue: F 287 - end of helix Proline residue: F 296 - end of helix Processing helix chain 'F' and resid 310 through 331 removed outlier: 3.878A pdb=" N GLY F 320 " --> pdb=" O PHE F 316 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TRP F 321 " --> pdb=" O VAL F 317 " (cutoff:3.500A) Proline residue: F 328 - end of helix Processing helix chain 'F' and resid 335 through 345 Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 53 through 60 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 352 removed outlier: 3.967A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.152A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 45 through 47 No H-bonds generated for 'chain 'D' and resid 45 through 47' Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.240A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS A 41 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS A 220 " --> pdb=" O HIS A 41 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.905A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.918A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.710A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.809A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 232 removed outlier: 6.846A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.211A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.694A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (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 93 through 98 removed outlier: 3.589A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) 397 hydrogen bonds defined for protein. 1080 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: 2.27 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1361 1.32 - 1.45: 2350 1.45 - 1.57: 4547 1.57 - 1.70: 0 1.70 - 1.83: 75 Bond restraints: 8333 Sorted by residual: bond pdb=" CA PHE F 288 " pdb=" C PHE F 288 " ideal model delta sigma weight residual 1.524 1.443 0.080 1.27e-02 6.20e+03 4.01e+01 bond pdb=" CA ASN F 292 " pdb=" C ASN F 292 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.39e-02 5.18e+03 1.61e+01 bond pdb=" C ASN F 292 " pdb=" O ASN F 292 " ideal model delta sigma weight residual 1.236 1.189 0.047 1.24e-02 6.50e+03 1.44e+01 bond pdb=" C LEU F 291 " pdb=" O LEU F 291 " ideal model delta sigma weight residual 1.237 1.192 0.044 1.19e-02 7.06e+03 1.38e+01 bond pdb=" C PHE F 288 " pdb=" N PHE F 289 " ideal model delta sigma weight residual 1.335 1.293 0.042 1.38e-02 5.25e+03 9.40e+00 ... (remaining 8328 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.01: 143 106.01 - 113.05: 4497 113.05 - 120.09: 3163 120.09 - 127.13: 3381 127.13 - 134.16: 101 Bond angle restraints: 11285 Sorted by residual: angle pdb=" N ASN F 292 " pdb=" CA ASN F 292 " pdb=" C ASN F 292 " ideal model delta sigma weight residual 111.75 103.61 8.14 1.28e+00 6.10e-01 4.05e+01 angle pdb=" N PHE F 288 " pdb=" CA PHE F 288 " pdb=" C PHE F 288 " ideal model delta sigma weight residual 111.07 104.91 6.16 1.07e+00 8.73e-01 3.31e+01 angle pdb=" C LYS A 233 " pdb=" N TRP A 234 " pdb=" CA TRP A 234 " ideal model delta sigma weight residual 121.94 110.63 11.31 2.00e+00 2.50e-01 3.20e+01 angle pdb=" C PHE A 222 " pdb=" CA PHE A 222 " pdb=" CB PHE A 222 " ideal model delta sigma weight residual 109.35 98.97 10.38 1.98e+00 2.55e-01 2.75e+01 angle pdb=" C ARG A 232 " pdb=" N LYS A 233 " pdb=" CA LYS A 233 " ideal model delta sigma weight residual 122.42 114.43 7.99 1.77e+00 3.19e-01 2.04e+01 ... (remaining 11280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 4439 17.24 - 34.48: 420 34.48 - 51.72: 91 51.72 - 68.95: 11 68.95 - 86.19: 10 Dihedral angle restraints: 4971 sinusoidal: 1952 harmonic: 3019 Sorted by residual: dihedral pdb=" CB CYS E 99 " pdb=" SG CYS E 99 " pdb=" SG CYS E 107 " pdb=" CB CYS E 107 " ideal model delta sinusoidal sigma weight residual 93.00 9.83 83.17 1 1.00e+01 1.00e-02 8.46e+01 dihedral pdb=" C PHE F 289 " pdb=" N PHE F 289 " pdb=" CA PHE F 289 " pdb=" CB PHE F 289 " ideal model delta harmonic sigma weight residual -122.60 -137.04 14.44 0 2.50e+00 1.60e-01 3.34e+01 dihedral pdb=" CA PHE F 95 " pdb=" C PHE F 95 " pdb=" N CYS F 96 " pdb=" CA CYS F 96 " ideal model delta harmonic sigma weight residual -180.00 -152.30 -27.70 0 5.00e+00 4.00e-02 3.07e+01 ... (remaining 4968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1225 0.133 - 0.266: 43 0.266 - 0.399: 0 0.399 - 0.532: 0 0.532 - 0.665: 1 Chirality restraints: 1269 Sorted by residual: chirality pdb=" CA PHE F 289 " pdb=" N PHE F 289 " pdb=" C PHE F 289 " pdb=" CB PHE F 289 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA ILE F 290 " pdb=" N ILE F 290 " pdb=" C ILE F 290 " pdb=" CB ILE F 290 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA ASP B 290 " pdb=" N ASP B 290 " pdb=" C ASP B 290 " pdb=" CB ASP B 290 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 1266 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 28 " 0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C LYS A 28 " -0.061 2.00e-02 2.50e+03 pdb=" O LYS A 28 " 0.023 2.00e-02 2.50e+03 pdb=" N GLN A 29 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE F 201 " 0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ILE F 201 " -0.060 2.00e-02 2.50e+03 pdb=" O ILE F 201 " 0.022 2.00e-02 2.50e+03 pdb=" N SER F 202 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 25 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C LYS A 25 " 0.049 2.00e-02 2.50e+03 pdb=" O LYS A 25 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE A 26 " -0.016 2.00e-02 2.50e+03 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 142 2.63 - 3.20: 7867 3.20 - 3.77: 12602 3.77 - 4.33: 17552 4.33 - 4.90: 29179 Nonbonded interactions: 67342 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.065 2.440 nonbonded pdb=" OG SER B 227 " pdb=" O PRO E 100 " model vdw 2.074 2.440 nonbonded pdb=" OE2 GLU A 27 " pdb=" NZ LYS B 89 " model vdw 2.126 2.520 nonbonded pdb=" OD1 ASP B 205 " pdb=" OG SER B 207 " model vdw 2.126 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.143 2.440 ... (remaining 67337 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=0.50 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: 0.010 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 1.730 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 26.920 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 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 0.080 8333 Z= 0.662 Angle : 1.015 14.375 11285 Z= 0.590 Chirality : 0.062 0.665 1269 Planarity : 0.006 0.057 1437 Dihedral : 14.291 86.194 3002 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 0.57 % Allowed : 14.04 % Favored : 85.39 % Cbeta Deviations : 0.20 % 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: -2.51 (0.22), residues: 1021 helix: -1.79 (0.20), residues: 416 sheet: -1.31 (0.31), residues: 228 loop : -1.44 (0.28), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 169 HIS 0.022 0.003 HIS A 357 PHE 0.031 0.003 PHE B 199 TYR 0.020 0.003 TYR A 311 ARG 0.006 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 187 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7853 (mmt90) cc_final: 0.6895 (tpm170) REVERT: F 57 LYS cc_start: 0.8526 (mppt) cc_final: 0.8263 (mtpt) REVERT: F 90 TRP cc_start: 0.8475 (t-100) cc_final: 0.8260 (t-100) REVERT: F 225 ILE cc_start: 0.8918 (mm) cc_final: 0.8612 (mt) REVERT: A 13 ARG cc_start: 0.8037 (pmt170) cc_final: 0.7799 (ptt-90) REVERT: A 211 LYS cc_start: 0.8732 (mttm) cc_final: 0.8481 (mttp) REVERT: A 221 MET cc_start: 0.8366 (ttp) cc_final: 0.8062 (ttp) REVERT: A 229 ASP cc_start: 0.7786 (m-30) cc_final: 0.6766 (t70) REVERT: A 317 ARG cc_start: 0.7519 (mtm110) cc_final: 0.7252 (mtm110) REVERT: A 318 TYR cc_start: 0.7433 (t80) cc_final: 0.7206 (t80) REVERT: B 68 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7433 (ttt-90) REVERT: B 325 MET cc_start: 0.7570 (tpp) cc_final: 0.7277 (tpp) REVERT: D 59 ASN cc_start: 0.8676 (t0) cc_final: 0.8219 (t0) REVERT: E 82 GLN cc_start: 0.7516 (tm-30) cc_final: 0.7257 (tm-30) outliers start: 5 outliers final: 4 residues processed: 192 average time/residue: 0.2673 time to fit residues: 66.1640 Evaluate side-chains 152 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 148 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain D residue 9 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.2980 chunk 75 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 113 ASN F 164 HIS F 240 ASN F 323 ASN F 327 ASN A 357 HIS A 371 ASN B 9 GLN B 88 ASN B 155 ASN B 175 GLN B 340 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8333 Z= 0.183 Angle : 0.560 8.665 11285 Z= 0.302 Chirality : 0.043 0.146 1269 Planarity : 0.004 0.037 1437 Dihedral : 5.331 40.853 1139 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.72 % Allowed : 15.63 % Favored : 81.65 % 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: -0.72 (0.25), residues: 1021 helix: 0.22 (0.25), residues: 410 sheet: -0.69 (0.33), residues: 225 loop : -0.92 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 169 HIS 0.009 0.001 HIS A 357 PHE 0.011 0.001 PHE F 289 TYR 0.014 0.001 TYR A 37 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7775 (mmt90) cc_final: 0.6840 (tpm170) REVERT: F 85 GLU cc_start: 0.8445 (mm-30) cc_final: 0.8217 (mm-30) REVERT: F 90 TRP cc_start: 0.8389 (t-100) cc_final: 0.8104 (t-100) REVERT: F 190 LEU cc_start: 0.8883 (mt) cc_final: 0.8547 (mp) REVERT: F 319 PHE cc_start: 0.8357 (OUTLIER) cc_final: 0.7411 (m-10) REVERT: A 17 LYS cc_start: 0.9038 (tptt) cc_final: 0.8795 (tppt) REVERT: A 229 ASP cc_start: 0.7791 (m-30) cc_final: 0.7411 (m-30) REVERT: A 252 ASP cc_start: 0.7393 (OUTLIER) cc_final: 0.6526 (t70) REVERT: A 317 ARG cc_start: 0.7580 (mtm110) cc_final: 0.7283 (mtm110) REVERT: A 318 TYR cc_start: 0.7339 (t80) cc_final: 0.7133 (t80) REVERT: A 370 GLU cc_start: 0.8197 (pm20) cc_final: 0.7776 (pm20) REVERT: B 61 MET cc_start: 0.8396 (ppp) cc_final: 0.8121 (ppp) REVERT: B 68 ARG cc_start: 0.7951 (ttt180) cc_final: 0.7322 (ttt-90) REVERT: B 105 TYR cc_start: 0.8885 (t80) cc_final: 0.8627 (t80) REVERT: B 132 ASN cc_start: 0.7605 (m-40) cc_final: 0.6989 (p0) REVERT: B 156 GLN cc_start: 0.7619 (mt0) cc_final: 0.7417 (mt0) REVERT: B 289 TYR cc_start: 0.8284 (m-80) cc_final: 0.8040 (m-80) REVERT: B 292 PHE cc_start: 0.8581 (m-80) cc_final: 0.8378 (m-80) REVERT: B 298 ASP cc_start: 0.8042 (t0) cc_final: 0.6884 (p0) REVERT: B 325 MET cc_start: 0.7463 (tpp) cc_final: 0.7243 (tpp) REVERT: E 80 TYR cc_start: 0.8262 (m-80) cc_final: 0.7711 (m-80) REVERT: E 82 GLN cc_start: 0.7481 (tm-30) cc_final: 0.7097 (tm-30) REVERT: E 120 GLN cc_start: 0.7932 (mm-40) cc_final: 0.7330 (mt0) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.2392 time to fit residues: 57.0226 Evaluate side-chains 160 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 140 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 96 CYS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 325 SER Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 107 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 72 optimal weight: 0.7980 chunk 89 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8333 Z= 0.162 Angle : 0.518 9.931 11285 Z= 0.275 Chirality : 0.042 0.194 1269 Planarity : 0.004 0.035 1437 Dihedral : 4.649 35.919 1135 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.94 % Allowed : 17.78 % Favored : 79.28 % 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: 0.03 (0.25), residues: 1021 helix: 1.05 (0.25), residues: 409 sheet: -0.57 (0.32), residues: 232 loop : -0.60 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 169 HIS 0.007 0.001 HIS F 53 PHE 0.013 0.001 PHE F 289 TYR 0.013 0.001 TYR B 111 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7625 (mmt90) cc_final: 0.6694 (tpm170) REVERT: F 85 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8087 (mm-30) REVERT: F 90 TRP cc_start: 0.8299 (t-100) cc_final: 0.8005 (t-100) REVERT: F 190 LEU cc_start: 0.8851 (mt) cc_final: 0.8513 (mp) REVERT: F 225 ILE cc_start: 0.8931 (OUTLIER) cc_final: 0.8701 (mt) REVERT: A 17 LYS cc_start: 0.9045 (tptt) cc_final: 0.8790 (tppt) REVERT: A 229 ASP cc_start: 0.7898 (m-30) cc_final: 0.7513 (m-30) REVERT: A 252 ASP cc_start: 0.7353 (OUTLIER) cc_final: 0.6444 (t70) REVERT: A 317 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7280 (mtm110) REVERT: A 358 TYR cc_start: 0.8649 (m-80) cc_final: 0.8430 (m-10) REVERT: A 370 GLU cc_start: 0.8081 (pm20) cc_final: 0.7710 (pm20) REVERT: B 68 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7267 (ttt-90) REVERT: B 105 TYR cc_start: 0.8851 (t80) cc_final: 0.8394 (t80) REVERT: B 132 ASN cc_start: 0.7507 (m-40) cc_final: 0.6883 (p0) REVERT: B 292 PHE cc_start: 0.8476 (m-80) cc_final: 0.8209 (m-80) REVERT: B 325 MET cc_start: 0.7505 (tpp) cc_final: 0.7236 (tpp) REVERT: E 80 TYR cc_start: 0.8270 (m-80) cc_final: 0.7546 (m-80) REVERT: E 82 GLN cc_start: 0.7571 (tm-30) cc_final: 0.7161 (tm-30) outliers start: 26 outliers final: 17 residues processed: 172 average time/residue: 0.2235 time to fit residues: 50.9486 Evaluate side-chains 161 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 80 optimal weight: 0.6980 chunk 54 optimal weight: 6.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN A 23 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8333 Z= 0.145 Angle : 0.501 10.936 11285 Z= 0.261 Chirality : 0.042 0.226 1269 Planarity : 0.004 0.037 1437 Dihedral : 4.358 30.864 1132 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.94 % Allowed : 18.91 % Favored : 78.14 % 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: 0.37 (0.26), residues: 1021 helix: 1.44 (0.25), residues: 409 sheet: -0.29 (0.34), residues: 216 loop : -0.62 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 169 HIS 0.006 0.001 HIS F 53 PHE 0.010 0.001 PHE F 289 TYR 0.011 0.001 TYR A 37 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7514 (mmt90) cc_final: 0.6650 (tpm170) REVERT: F 57 LYS cc_start: 0.8549 (mppt) cc_final: 0.8196 (mtpt) REVERT: F 85 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8072 (mm-30) REVERT: F 90 TRP cc_start: 0.8300 (t-100) cc_final: 0.7982 (t-100) REVERT: F 190 LEU cc_start: 0.8823 (mt) cc_final: 0.8507 (mp) REVERT: F 225 ILE cc_start: 0.8910 (mt) cc_final: 0.8683 (mt) REVERT: F 319 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7275 (m-10) REVERT: A 229 ASP cc_start: 0.7912 (m-30) cc_final: 0.7513 (m-30) REVERT: A 239 ASN cc_start: 0.8878 (OUTLIER) cc_final: 0.8567 (p0) REVERT: A 317 ARG cc_start: 0.7605 (mtm110) cc_final: 0.7299 (mtm110) REVERT: A 318 TYR cc_start: 0.6577 (t80) cc_final: 0.6080 (t80) REVERT: A 370 GLU cc_start: 0.8026 (pm20) cc_final: 0.7659 (pm20) REVERT: A 390 GLN cc_start: 0.8898 (tp-100) cc_final: 0.8413 (tp-100) REVERT: B 68 ARG cc_start: 0.8017 (ttt180) cc_final: 0.7410 (ttt-90) REVERT: B 105 TYR cc_start: 0.8785 (t80) cc_final: 0.8330 (t80) REVERT: B 132 ASN cc_start: 0.7381 (m-40) cc_final: 0.6781 (p0) REVERT: B 292 PHE cc_start: 0.8350 (m-80) cc_final: 0.8083 (m-80) REVERT: B 297 TRP cc_start: 0.8286 (m100) cc_final: 0.7782 (m100) REVERT: B 325 MET cc_start: 0.7460 (tpp) cc_final: 0.7184 (tpp) REVERT: E 82 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7266 (tm-30) outliers start: 26 outliers final: 17 residues processed: 176 average time/residue: 0.2160 time to fit residues: 50.7888 Evaluate side-chains 166 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 66 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN A 19 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8333 Z= 0.284 Angle : 0.551 9.694 11285 Z= 0.291 Chirality : 0.044 0.181 1269 Planarity : 0.004 0.036 1437 Dihedral : 4.492 32.700 1132 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.87 % Allowed : 19.37 % Favored : 75.76 % 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: 0.39 (0.26), residues: 1021 helix: 1.49 (0.25), residues: 410 sheet: -0.38 (0.33), residues: 216 loop : -0.59 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE B 199 TYR 0.011 0.002 TYR A 253 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 140 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7600 (mmt90) cc_final: 0.6713 (tpm170) REVERT: F 57 LYS cc_start: 0.8697 (mppt) cc_final: 0.8292 (mtmt) REVERT: F 85 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8119 (mm-30) REVERT: F 90 TRP cc_start: 0.8265 (t-100) cc_final: 0.7972 (t-100) REVERT: F 210 MET cc_start: 0.8127 (mtp) cc_final: 0.7800 (mtm) REVERT: F 225 ILE cc_start: 0.8945 (mt) cc_final: 0.8724 (mt) REVERT: F 319 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7460 (m-10) REVERT: A 229 ASP cc_start: 0.7909 (m-30) cc_final: 0.7513 (m-30) REVERT: A 239 ASN cc_start: 0.8981 (OUTLIER) cc_final: 0.8734 (p0) REVERT: A 252 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6332 (t70) REVERT: A 317 ARG cc_start: 0.7630 (mtm110) cc_final: 0.7333 (mtm110) REVERT: A 318 TYR cc_start: 0.7167 (t80) cc_final: 0.6484 (t80) REVERT: A 370 GLU cc_start: 0.8124 (pm20) cc_final: 0.7744 (pm20) REVERT: B 68 ARG cc_start: 0.8050 (ttt180) cc_final: 0.7343 (ttt-90) REVERT: B 105 TYR cc_start: 0.8891 (t80) cc_final: 0.8468 (t80) REVERT: B 111 TYR cc_start: 0.8821 (m-80) cc_final: 0.8601 (m-80) REVERT: B 292 PHE cc_start: 0.8589 (m-80) cc_final: 0.8344 (m-80) REVERT: B 297 TRP cc_start: 0.8487 (m100) cc_final: 0.7729 (m100) REVERT: B 325 MET cc_start: 0.7629 (tpp) cc_final: 0.7232 (tpp) REVERT: E 65 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7899 (ttpt) REVERT: E 80 TYR cc_start: 0.8120 (m-80) cc_final: 0.7437 (m-80) outliers start: 43 outliers final: 37 residues processed: 170 average time/residue: 0.2123 time to fit residues: 48.9586 Evaluate side-chains 174 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 134 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 83 VAL Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 35 ASN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8333 Z= 0.213 Angle : 0.522 10.087 11285 Z= 0.273 Chirality : 0.042 0.135 1269 Planarity : 0.004 0.036 1437 Dihedral : 4.435 31.643 1132 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.64 % Allowed : 20.84 % Favored : 74.52 % 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: 0.46 (0.26), residues: 1021 helix: 1.64 (0.26), residues: 404 sheet: -0.44 (0.32), residues: 219 loop : -0.56 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.005 0.001 HIS F 53 PHE 0.012 0.001 PHE F 289 TYR 0.010 0.001 TYR A 391 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 145 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7597 (mmt90) cc_final: 0.6707 (tpm170) REVERT: F 57 LYS cc_start: 0.8686 (mppt) cc_final: 0.8358 (mtpt) REVERT: F 85 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 90 TRP cc_start: 0.8215 (t-100) cc_final: 0.7931 (t-100) REVERT: F 210 MET cc_start: 0.8117 (mtp) cc_final: 0.7761 (mtm) REVERT: F 225 ILE cc_start: 0.8927 (mt) cc_final: 0.8711 (mt) REVERT: F 319 PHE cc_start: 0.8300 (OUTLIER) cc_final: 0.7383 (m-10) REVERT: A 229 ASP cc_start: 0.7906 (m-30) cc_final: 0.7467 (m-30) REVERT: A 239 ASN cc_start: 0.8952 (OUTLIER) cc_final: 0.8696 (p0) REVERT: A 252 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6682 (t70) REVERT: A 317 ARG cc_start: 0.7609 (mtm110) cc_final: 0.7302 (mtm110) REVERT: A 318 TYR cc_start: 0.7150 (t80) cc_final: 0.6472 (t80) REVERT: A 370 GLU cc_start: 0.8113 (pm20) cc_final: 0.7735 (pm20) REVERT: A 390 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8405 (tp-100) REVERT: B 68 ARG cc_start: 0.8065 (ttt180) cc_final: 0.7295 (ttt-90) REVERT: B 105 TYR cc_start: 0.8871 (t80) cc_final: 0.8408 (t80) REVERT: B 111 TYR cc_start: 0.8828 (m-80) cc_final: 0.8591 (m-80) REVERT: B 292 PHE cc_start: 0.8530 (m-80) cc_final: 0.8283 (m-80) REVERT: B 297 TRP cc_start: 0.8457 (m100) cc_final: 0.7673 (m100) REVERT: B 325 MET cc_start: 0.7618 (tpp) cc_final: 0.7206 (tpp) REVERT: E 65 LYS cc_start: 0.8361 (ttpt) cc_final: 0.7929 (ttpt) REVERT: E 80 TYR cc_start: 0.8079 (m-80) cc_final: 0.7397 (m-80) outliers start: 41 outliers final: 36 residues processed: 174 average time/residue: 0.2243 time to fit residues: 51.5988 Evaluate side-chains 182 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 143 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 200 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 107 CYS Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 6.9990 chunk 59 optimal weight: 0.0670 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8333 Z= 0.195 Angle : 0.513 10.155 11285 Z= 0.269 Chirality : 0.042 0.131 1269 Planarity : 0.004 0.037 1437 Dihedral : 4.366 30.272 1132 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.87 % Allowed : 20.72 % Favored : 74.41 % 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: 0.54 (0.26), residues: 1021 helix: 1.73 (0.26), residues: 407 sheet: -0.47 (0.33), residues: 220 loop : -0.52 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.010 0.001 HIS F 53 PHE 0.012 0.001 PHE F 289 TYR 0.011 0.001 TYR A 391 ARG 0.007 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7577 (mmt90) cc_final: 0.6653 (tpm170) REVERT: F 57 LYS cc_start: 0.8626 (mppt) cc_final: 0.8214 (mtpt) REVERT: F 85 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8115 (mm-30) REVERT: F 90 TRP cc_start: 0.8205 (t-100) cc_final: 0.7896 (t-100) REVERT: F 225 ILE cc_start: 0.8916 (mt) cc_final: 0.8691 (mt) REVERT: F 233 ARG cc_start: 0.7461 (ttp-110) cc_final: 0.6873 (mtm-85) REVERT: F 319 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: A 229 ASP cc_start: 0.7884 (m-30) cc_final: 0.7406 (m-30) REVERT: A 239 ASN cc_start: 0.8960 (OUTLIER) cc_final: 0.8710 (p0) REVERT: A 252 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.6669 (t70) REVERT: A 317 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7322 (mtm110) REVERT: A 318 TYR cc_start: 0.7140 (t80) cc_final: 0.6472 (t80) REVERT: A 358 TYR cc_start: 0.8582 (m-80) cc_final: 0.8304 (m-10) REVERT: A 370 GLU cc_start: 0.8166 (pm20) cc_final: 0.7790 (pm20) REVERT: A 390 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8384 (tp-100) REVERT: B 59 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7698 (m-80) REVERT: B 68 ARG cc_start: 0.8084 (ttt180) cc_final: 0.7311 (ttt-90) REVERT: B 105 TYR cc_start: 0.8864 (t80) cc_final: 0.8393 (t80) REVERT: B 111 TYR cc_start: 0.8827 (m-80) cc_final: 0.8573 (m-80) REVERT: B 292 PHE cc_start: 0.8485 (m-80) cc_final: 0.8240 (m-80) REVERT: B 297 TRP cc_start: 0.8444 (m100) cc_final: 0.7673 (m100) REVERT: B 325 MET cc_start: 0.7589 (tpp) cc_final: 0.7145 (tpp) REVERT: E 65 LYS cc_start: 0.8362 (ttpt) cc_final: 0.7923 (ttpt) REVERT: E 80 TYR cc_start: 0.8023 (m-80) cc_final: 0.7269 (m-80) outliers start: 43 outliers final: 35 residues processed: 177 average time/residue: 0.2189 time to fit residues: 51.1922 Evaluate side-chains 186 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 147 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 284 CYS Chi-restraints excluded: chain F residue 315 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 15 GLU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 LEU Chi-restraints excluded: chain E residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 0.0060 chunk 87 optimal weight: 0.0470 chunk 92 optimal weight: 5.9990 chunk 84 optimal weight: 30.0000 chunk 89 optimal weight: 0.8980 overall best weight: 0.4094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 53 HIS F 327 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8333 Z= 0.132 Angle : 0.486 11.256 11285 Z= 0.254 Chirality : 0.041 0.130 1269 Planarity : 0.004 0.039 1437 Dihedral : 4.161 24.192 1132 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.30 % Allowed : 21.86 % Favored : 73.84 % 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: 0.73 (0.26), residues: 1021 helix: 1.88 (0.26), residues: 407 sheet: -0.30 (0.33), residues: 218 loop : -0.45 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.011 0.001 HIS F 53 PHE 0.009 0.001 PHE F 289 TYR 0.010 0.001 TYR A 37 ARG 0.007 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 156 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7552 (mmt90) cc_final: 0.6628 (tpm170) REVERT: F 57 LYS cc_start: 0.8564 (mppt) cc_final: 0.8140 (mtpt) REVERT: F 85 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8126 (mm-30) REVERT: F 90 TRP cc_start: 0.8151 (t-100) cc_final: 0.7862 (t-100) REVERT: F 190 LEU cc_start: 0.8823 (mt) cc_final: 0.8560 (mp) REVERT: F 225 ILE cc_start: 0.8900 (mt) cc_final: 0.8567 (mt) REVERT: F 319 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: A 229 ASP cc_start: 0.7895 (m-30) cc_final: 0.7410 (m-30) REVERT: A 239 ASN cc_start: 0.8926 (OUTLIER) cc_final: 0.8656 (p0) REVERT: A 252 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6755 (t70) REVERT: A 283 ARG cc_start: 0.7924 (ttp-110) cc_final: 0.7591 (ttp80) REVERT: A 317 ARG cc_start: 0.7587 (mtm110) cc_final: 0.7277 (mtm110) REVERT: A 318 TYR cc_start: 0.6989 (t80) cc_final: 0.6324 (t80) REVERT: A 358 TYR cc_start: 0.8523 (m-80) cc_final: 0.8239 (m-10) REVERT: A 370 GLU cc_start: 0.8106 (pm20) cc_final: 0.7710 (pm20) REVERT: A 390 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8305 (tp-100) REVERT: B 68 ARG cc_start: 0.8109 (ttt180) cc_final: 0.7550 (ttt-90) REVERT: B 105 TYR cc_start: 0.8725 (t80) cc_final: 0.8452 (t80) REVERT: B 175 GLN cc_start: 0.7453 (mm-40) cc_final: 0.7244 (mm-40) REVERT: B 292 PHE cc_start: 0.8377 (m-80) cc_final: 0.8136 (m-80) REVERT: B 297 TRP cc_start: 0.8313 (m100) cc_final: 0.7719 (m100) REVERT: B 325 MET cc_start: 0.7488 (tpp) cc_final: 0.7078 (tpp) REVERT: E 65 LYS cc_start: 0.8344 (ttpt) cc_final: 0.7932 (ttpt) REVERT: E 120 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7621 (mm-40) outliers start: 38 outliers final: 29 residues processed: 183 average time/residue: 0.2243 time to fit residues: 54.5087 Evaluate side-chains 184 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 152 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 53 HIS Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 8.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 0.3980 chunk 57 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8333 Z= 0.169 Angle : 0.513 10.842 11285 Z= 0.267 Chirality : 0.041 0.184 1269 Planarity : 0.004 0.041 1437 Dihedral : 4.151 22.956 1132 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.96 % Allowed : 22.65 % Favored : 73.39 % 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: 0.77 (0.26), residues: 1021 helix: 1.98 (0.26), residues: 401 sheet: -0.32 (0.33), residues: 221 loop : -0.45 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.012 0.001 HIS F 53 PHE 0.010 0.001 PHE F 289 TYR 0.014 0.001 TYR B 59 ARG 0.008 0.000 ARG F 233 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7608 (mmt90) cc_final: 0.6603 (tpm170) REVERT: F 57 LYS cc_start: 0.8544 (mppt) cc_final: 0.8131 (mtpt) REVERT: F 85 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8098 (mm-30) REVERT: F 90 TRP cc_start: 0.8160 (t-100) cc_final: 0.7864 (t-100) REVERT: F 190 LEU cc_start: 0.8828 (mt) cc_final: 0.8564 (mp) REVERT: F 225 ILE cc_start: 0.8914 (mt) cc_final: 0.8581 (mt) REVERT: F 319 PHE cc_start: 0.8235 (OUTLIER) cc_final: 0.7393 (m-10) REVERT: A 229 ASP cc_start: 0.7897 (m-30) cc_final: 0.7408 (m-30) REVERT: A 239 ASN cc_start: 0.8961 (OUTLIER) cc_final: 0.8671 (p0) REVERT: A 252 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6754 (t70) REVERT: A 283 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7565 (ttp80) REVERT: A 317 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7267 (mtm110) REVERT: A 318 TYR cc_start: 0.7070 (t80) cc_final: 0.6384 (t80) REVERT: A 358 TYR cc_start: 0.8534 (m-80) cc_final: 0.8230 (m-10) REVERT: A 370 GLU cc_start: 0.8078 (pm20) cc_final: 0.7695 (pm20) REVERT: A 390 GLN cc_start: 0.8856 (tp-100) cc_final: 0.8289 (tp-100) REVERT: B 68 ARG cc_start: 0.8137 (ttt180) cc_final: 0.7681 (ttt-90) REVERT: B 175 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7280 (mm-40) REVERT: B 292 PHE cc_start: 0.8395 (m-80) cc_final: 0.8128 (m-80) REVERT: B 297 TRP cc_start: 0.8332 (m100) cc_final: 0.7739 (m100) REVERT: B 325 MET cc_start: 0.7511 (tpp) cc_final: 0.7088 (tpp) REVERT: D 47 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7388 (mp0) REVERT: E 34 MET cc_start: 0.8391 (mmm) cc_final: 0.8052 (mmm) REVERT: E 65 LYS cc_start: 0.8373 (ttpt) cc_final: 0.7949 (ttpt) REVERT: E 120 GLN cc_start: 0.7946 (mm-40) cc_final: 0.7618 (mm-40) outliers start: 35 outliers final: 31 residues processed: 176 average time/residue: 0.2211 time to fit residues: 51.7313 Evaluate side-chains 183 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 327 ASN ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8333 Z= 0.170 Angle : 0.507 10.844 11285 Z= 0.264 Chirality : 0.041 0.167 1269 Planarity : 0.004 0.041 1437 Dihedral : 4.150 22.373 1132 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.08 % Allowed : 22.76 % Favored : 73.16 % 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: 0.80 (0.26), residues: 1021 helix: 2.00 (0.26), residues: 401 sheet: -0.36 (0.34), residues: 211 loop : -0.39 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.010 0.001 HIS F 53 PHE 0.009 0.001 PHE F 289 TYR 0.010 0.001 TYR B 59 ARG 0.008 0.000 ARG F 233 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2042 Ramachandran restraints generated. 1021 Oldfield, 0 Emsley, 1021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 154 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 50 ARG cc_start: 0.7623 (mmt90) cc_final: 0.6599 (tpm170) REVERT: F 57 LYS cc_start: 0.8543 (mppt) cc_final: 0.8140 (mtpt) REVERT: F 85 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8100 (mm-30) REVERT: F 90 TRP cc_start: 0.8165 (t-100) cc_final: 0.7862 (t-100) REVERT: F 190 LEU cc_start: 0.8851 (mt) cc_final: 0.8590 (mp) REVERT: F 225 ILE cc_start: 0.8917 (mt) cc_final: 0.8583 (mt) REVERT: F 319 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: A 38 ARG cc_start: 0.8150 (mmm-85) cc_final: 0.7704 (ttp-110) REVERT: A 229 ASP cc_start: 0.7919 (m-30) cc_final: 0.7444 (m-30) REVERT: A 239 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8700 (p0) REVERT: A 252 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6797 (t70) REVERT: A 283 ARG cc_start: 0.7915 (ttp-110) cc_final: 0.7538 (ttp80) REVERT: A 317 ARG cc_start: 0.7585 (mtm110) cc_final: 0.7266 (mtm110) REVERT: A 318 TYR cc_start: 0.7136 (t80) cc_final: 0.6503 (t80) REVERT: A 358 TYR cc_start: 0.8537 (m-80) cc_final: 0.8263 (m-10) REVERT: A 370 GLU cc_start: 0.8074 (pm20) cc_final: 0.7694 (pm20) REVERT: A 390 GLN cc_start: 0.8824 (tp-100) cc_final: 0.8266 (tp-100) REVERT: B 68 ARG cc_start: 0.8119 (ttt180) cc_final: 0.7629 (ttt-90) REVERT: B 124 TYR cc_start: 0.8253 (m-80) cc_final: 0.7771 (m-80) REVERT: B 292 PHE cc_start: 0.8416 (m-80) cc_final: 0.8135 (m-80) REVERT: B 297 TRP cc_start: 0.8347 (m100) cc_final: 0.7758 (m100) REVERT: B 325 MET cc_start: 0.7510 (tpp) cc_final: 0.7093 (tpp) REVERT: D 47 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7324 (mp0) REVERT: E 38 ARG cc_start: 0.8112 (ptt180) cc_final: 0.7799 (ptm-80) REVERT: E 65 LYS cc_start: 0.8358 (ttpt) cc_final: 0.7898 (ttpt) REVERT: E 120 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7618 (mm-40) outliers start: 36 outliers final: 33 residues processed: 177 average time/residue: 0.2315 time to fit residues: 54.0605 Evaluate side-chains 187 residues out of total 886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 24 ILE Chi-restraints excluded: chain F residue 126 SER Chi-restraints excluded: chain F residue 136 THR Chi-restraints excluded: chain F residue 145 SER Chi-restraints excluded: chain F residue 185 ASN Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 319 PHE Chi-restraints excluded: chain F residue 327 ASN Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 333 PHE Chi-restraints excluded: chain F residue 336 ASP Chi-restraints excluded: chain A residue 59 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 239 ASN Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 252 ASP Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 79 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.0870 chunk 11 optimal weight: 8.9990 chunk 22 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 14 optimal weight: 0.0270 chunk 69 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 59 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.149457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.111770 restraints weight = 28207.988| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 4.90 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3451 r_free = 0.3451 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 8333 Z= 0.247 Angle : 0.998 59.195 11285 Z= 0.577 Chirality : 0.044 0.544 1269 Planarity : 0.005 0.152 1437 Dihedral : 4.162 22.374 1132 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.08 % Allowed : 22.88 % Favored : 73.05 % Cbeta Deviations : 0.20 % 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: 0.81 (0.26), residues: 1021 helix: 2.01 (0.26), residues: 401 sheet: -0.37 (0.34), residues: 211 loop : -0.39 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 169 HIS 0.010 0.001 HIS F 53 PHE 0.009 0.001 PHE F 289 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2054.22 seconds wall clock time: 37 minutes 56.39 seconds (2276.39 seconds total)