Starting phenix.real_space_refine on Wed Sep 17 06:37:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.map" model { file = "/net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e91_47739/09_2025/9e91_47739.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 18 5.16 5 C 3949 2.51 5 N 1056 2.21 5 O 1209 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6238 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3094 Classifications: {'peptide': 390} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 13, 'TRANS': 376} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 3082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3082 Classifications: {'peptide': 392} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 378} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.78, per 1000 atoms: 0.29 Number of scatterers: 6238 At special positions: 0 Unit cell: (68.67, 86.11, 140.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 6 15.00 O 1209 8.00 N 1056 7.00 C 3949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.39 Conformation dependent library (CDL) restraints added in 246.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1472 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 7 sheets defined 40.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.544A pdb=" N ILE A 13 " --> pdb=" O THR A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 30 removed outlier: 3.814A pdb=" N TYR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS A 29 " --> pdb=" O TYR A 25 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 30 " --> pdb=" O GLN A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 52 removed outlier: 3.820A pdb=" N ASP A 46 " --> pdb=" O GLU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 117 removed outlier: 4.259A pdb=" N HIS A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 187 removed outlier: 3.841A pdb=" N ASN A 174 " --> pdb=" O TYR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 230 removed outlier: 3.584A pdb=" N TYR A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 257 removed outlier: 3.906A pdb=" N ASN A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 332 removed outlier: 3.569A pdb=" N MET A 328 " --> pdb=" O VAL A 324 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N PHE A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 383 removed outlier: 3.940A pdb=" N ILE A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 421 removed outlier: 4.079A pdb=" N ASN A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ILE A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 432 through 437 removed outlier: 4.001A pdb=" N HIS A 437 " --> pdb=" O GLN A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 444 removed outlier: 3.753A pdb=" N ILE A 444 " --> pdb=" O SER A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.575A pdb=" N THR B 10 " --> pdb=" O PRO B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 98 through 117 removed outlier: 4.108A pdb=" N ALA B 104 " --> pdb=" O THR B 100 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS B 107 " --> pdb=" O ASP B 103 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY B 108 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 115 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 131 removed outlier: 3.675A pdb=" N LEU B 131 " --> pdb=" O LYS B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 3.649A pdb=" N GLY B 177 " --> pdb=" O ILE B 173 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER B 178 " --> pdb=" O ASN B 174 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 203 removed outlier: 3.532A pdb=" N ARG B 202 " --> pdb=" O THR B 199 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA B 203 " --> pdb=" O VAL B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 203' Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 238 through 254 Processing helix chain 'B' and resid 316 through 331 removed outlier: 4.373A pdb=" N THR B 320 " --> pdb=" O VAL B 316 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 321 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET B 328 " --> pdb=" O VAL B 324 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 383 Processing helix chain 'B' and resid 388 through 392 removed outlier: 3.838A pdb=" N GLY B 392 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 421 Processing helix chain 'B' and resid 432 through 439 removed outlier: 4.163A pdb=" N THR B 438 " --> pdb=" O VAL B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.808A pdb=" N MET A 79 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL A 63 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP A 145 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 80 removed outlier: 3.808A pdb=" N MET A 79 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL A 63 " --> pdb=" O ASP A 145 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP A 145 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP A 65 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 91 Processing sheet with id=AA4, first strand: chain 'A' and resid 197 through 198 Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 340 removed outlier: 5.244A pdb=" N ASN A 337 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP A 350 " --> pdb=" O ASN A 337 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 77 through 80 removed outlier: 5.645A pdb=" N VAL B 63 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP B 145 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP B 65 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 194 through 198 removed outlier: 3.515A pdb=" N GLN B 425 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE B 427 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 398 " --> pdb=" O ILE B 427 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N THR B 88 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N THR B 430 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU B 90 " --> pdb=" O THR B 430 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N TRP B 445 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE B 89 " --> pdb=" O TRP B 445 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N LEU B 447 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 91 " --> pdb=" O LEU B 447 " (cutoff:3.500A) 237 hydrogen bonds defined for protein. 648 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: 0.94 Time building geometry restraints manager: 0.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2027 1.34 - 1.46: 1195 1.46 - 1.58: 3093 1.58 - 1.69: 14 1.69 - 1.81: 32 Bond restraints: 6361 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.264 0.267 1.20e-02 6.94e+03 4.96e+02 bond pdb=" C2' ATP A 601 " pdb=" C3' ATP A 601 " ideal model delta sigma weight residual 1.531 1.266 0.265 1.20e-02 6.94e+03 4.86e+02 bond pdb=" C6 ATP B 601 " pdb=" N6 ATP B 601 " ideal model delta sigma weight residual 1.337 1.479 -0.142 1.10e-02 8.26e+03 1.67e+02 bond pdb=" C6 ATP A 601 " pdb=" N6 ATP A 601 " ideal model delta sigma weight residual 1.337 1.479 -0.142 1.10e-02 8.26e+03 1.66e+02 bond pdb=" C1' ATP A 601 " pdb=" C2' ATP A 601 " ideal model delta sigma weight residual 1.531 1.662 -0.131 1.20e-02 6.94e+03 1.18e+02 ... (remaining 6356 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.28: 8503 3.28 - 6.56: 80 6.56 - 9.84: 19 9.84 - 13.12: 1 13.12 - 16.40: 3 Bond angle restraints: 8606 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 123.47 16.40 1.00e+00 1.00e+00 2.69e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 124.17 15.70 1.00e+00 1.00e+00 2.47e+02 angle pdb=" PA ATP A 601 " pdb=" O3A ATP A 601 " pdb=" PB ATP A 601 " ideal model delta sigma weight residual 136.83 121.99 14.84 1.00e+00 1.00e+00 2.20e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 123.81 13.02 1.00e+00 1.00e+00 1.70e+02 angle pdb=" C5 ATP A 601 " pdb=" C4 ATP A 601 " pdb=" N3 ATP A 601 " ideal model delta sigma weight residual 126.80 118.97 7.83 1.00e+00 1.00e+00 6.13e+01 ... (remaining 8601 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.04: 3422 16.04 - 32.08: 337 32.08 - 48.12: 75 48.12 - 64.17: 37 64.17 - 80.21: 7 Dihedral angle restraints: 3878 sinusoidal: 1602 harmonic: 2276 Sorted by residual: dihedral pdb=" CA LEU B 332 " pdb=" C LEU B 332 " pdb=" N PRO B 333 " pdb=" CA PRO B 333 " ideal model delta harmonic sigma weight residual -180.00 -159.12 -20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA GLY B 97 " pdb=" C GLY B 97 " pdb=" N LYS B 98 " pdb=" CA LYS B 98 " ideal model delta harmonic sigma weight residual 180.00 161.35 18.65 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA HIS A 406 " pdb=" C HIS A 406 " pdb=" N PRO A 407 " pdb=" CA PRO A 407 " ideal model delta harmonic sigma weight residual 180.00 161.53 18.47 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 3875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 825 0.061 - 0.123: 123 0.123 - 0.184: 5 0.184 - 0.246: 7 0.246 - 0.307: 3 Chirality restraints: 963 Sorted by residual: chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' ATP B 601 " pdb=" C2' ATP B 601 " pdb=" C4' ATP B 601 " pdb=" O3' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C2' ATP A 601 " pdb=" C1' ATP A 601 " pdb=" C3' ATP A 601 " pdb=" O2' ATP A 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.43 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 960 not shown) Planarity restraints: 1093 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 119 " 0.365 9.50e-02 1.11e+02 1.64e-01 1.64e+01 pdb=" NE ARG A 119 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 119 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 119 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 119 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 118 " -0.012 2.00e-02 2.50e+03 2.57e-02 6.59e+00 pdb=" C THR A 118 " 0.044 2.00e-02 2.50e+03 pdb=" O THR A 118 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG A 119 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 39 " -0.040 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO A 40 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 40 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 40 " -0.033 5.00e-02 4.00e+02 ... (remaining 1090 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1127 2.77 - 3.31: 6109 3.31 - 3.84: 9864 3.84 - 4.37: 11887 4.37 - 4.90: 19933 Nonbonded interactions: 48920 Sorted by model distance: nonbonded pdb=" NH1 ARG A 244 " pdb=" OE2 GLU A 248 " model vdw 2.243 3.120 nonbonded pdb=" O2' ATP B 601 " pdb=" O3' ATP B 601 " model vdw 2.265 2.432 nonbonded pdb=" O2' ATP A 601 " pdb=" O3' ATP A 601 " model vdw 2.269 2.432 nonbonded pdb=" O THR B 182 " pdb=" OG SER B 185 " model vdw 2.271 3.040 nonbonded pdb=" OG SER A 87 " pdb=" OE2 GLU A 418 " model vdw 2.286 3.040 ... (remaining 48915 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 10 or (resid 11 through 12 and (name N or name CA or name C \ or name O or name CB )) or resid 13 or (resid 14 through 15 and (name N or name \ CA or name C or name O or name CB )) or resid 16 through 33 or (resid 34 and (n \ ame N or name CA or name C or name O or name CB )) or resid 35 through 49 or (re \ sid 50 and (name N or name CA or name C or name O or name CB )) or resid 51 thro \ ugh 53 or (resid 54 and (name N or name CA or name C or name O or name CB )) or \ resid 55 through 129 or (resid 130 and (name N or name CA or name C or name O or \ name CB )) or resid 131 through 243 or (resid 244 and (name N or name CA or nam \ e C or name O or name CB )) or resid 245 through 255 or resid 257 through 454 or \ resid 601)) selection = (chain 'B' and (resid 8 through 120 or (resid 121 through 122 and (name N or nam \ e CA or name C or name O or name CB )) or resid 123 through 315 or resid 317 thr \ ough 415 or (resid 416 and (name N or name CA or name C or name O or name CB )) \ or resid 417 through 418 or (resid 419 and (name N or name CA or name C or name \ O or name CB )) or resid 420 through 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.620 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 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 : 0.008 0.267 6361 Z= 0.650 Angle : 0.887 16.399 8606 Z= 0.592 Chirality : 0.049 0.307 963 Planarity : 0.008 0.164 1093 Dihedral : 14.864 80.208 2406 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.02 % Favored : 87.98 % Rotamer: Outliers : 1.47 % Allowed : 3.81 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.29), residues: 774 helix: 0.05 (0.32), residues: 246 sheet: -1.84 (0.45), residues: 130 loop : -2.26 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 62 TYR 0.013 0.002 TYR B 71 PHE 0.025 0.001 PHE B 242 TRP 0.014 0.002 TRP B 445 HIS 0.005 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00829 ( 6361) covalent geometry : angle 0.88689 ( 8606) hydrogen bonds : bond 0.21208 ( 229) hydrogen bonds : angle 6.97741 ( 648) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 159 time to evaluate : 0.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7753 (mtmt) REVERT: A 17 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 42 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7578 (mm-30) REVERT: A 75 GLU cc_start: 0.5751 (tm-30) cc_final: 0.5384 (tm-30) REVERT: A 124 ASP cc_start: 0.7187 (m-30) cc_final: 0.6985 (m-30) REVERT: A 190 VAL cc_start: 0.8145 (m) cc_final: 0.7784 (t) REVERT: A 240 LYS cc_start: 0.7675 (mmtm) cc_final: 0.7439 (mptt) REVERT: A 247 LYS cc_start: 0.7396 (tttt) cc_final: 0.7192 (ttmm) REVERT: A 374 ASP cc_start: 0.6910 (t70) cc_final: 0.6677 (t0) REVERT: A 412 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6856 (t0) REVERT: B 60 GLN cc_start: 0.7716 (mp10) cc_final: 0.7439 (mp10) REVERT: B 114 SER cc_start: 0.8272 (m) cc_final: 0.7702 (t) REVERT: B 139 SER cc_start: 0.8154 (t) cc_final: 0.7724 (p) REVERT: B 146 TYR cc_start: 0.7937 (t80) cc_final: 0.7710 (t80) REVERT: B 195 ILE cc_start: 0.7491 (mt) cc_final: 0.7132 (mm) REVERT: B 210 ASP cc_start: 0.6605 (p0) cc_final: 0.6338 (t70) REVERT: B 439 ILE cc_start: 0.8301 (mm) cc_final: 0.7927 (mm) outliers start: 10 outliers final: 5 residues processed: 167 average time/residue: 0.0880 time to fit residues: 18.8936 Evaluate side-chains 140 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 134 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 119 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.0000 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.0570 overall best weight: 0.2502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 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 = 0.4287 r_free = 0.4287 target = 0.174704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152980 restraints weight = 8195.149| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 2.31 r_work: 0.3920 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6361 Z= 0.128 Angle : 0.616 6.099 8606 Z= 0.316 Chirality : 0.044 0.185 963 Planarity : 0.005 0.045 1093 Dihedral : 9.135 84.368 912 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 2.35 % Allowed : 10.26 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.92 (0.29), residues: 774 helix: 0.14 (0.31), residues: 257 sheet: -1.66 (0.44), residues: 134 loop : -2.15 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 62 TYR 0.009 0.001 TYR B 146 PHE 0.019 0.002 PHE B 242 TRP 0.016 0.001 TRP A 245 HIS 0.008 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6361) covalent geometry : angle 0.61570 ( 8606) hydrogen bonds : bond 0.04315 ( 229) hydrogen bonds : angle 4.85626 ( 648) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8025 (mtmt) cc_final: 0.7773 (mtmt) REVERT: A 21 PHE cc_start: 0.7457 (t80) cc_final: 0.7198 (t80) REVERT: A 49 LYS cc_start: 0.7640 (mmtm) cc_final: 0.7235 (tppt) REVERT: A 75 GLU cc_start: 0.5968 (tm-30) cc_final: 0.5482 (tm-30) REVERT: A 190 VAL cc_start: 0.8166 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 197 MET cc_start: 0.6870 (ttt) cc_final: 0.6439 (ttt) REVERT: A 247 LYS cc_start: 0.7480 (tttt) cc_final: 0.7270 (ttmm) REVERT: A 412 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.6837 (t0) REVERT: B 9 ILE cc_start: 0.6966 (OUTLIER) cc_final: 0.6674 (mt) REVERT: B 44 MET cc_start: 0.7106 (ptm) cc_final: 0.6896 (ptm) REVERT: B 69 GLU cc_start: 0.7770 (tt0) cc_final: 0.7557 (tt0) REVERT: B 114 SER cc_start: 0.8316 (m) cc_final: 0.7862 (t) REVERT: B 139 SER cc_start: 0.8524 (t) cc_final: 0.8107 (p) REVERT: B 230 ASN cc_start: 0.6966 (m-40) cc_final: 0.6728 (t0) REVERT: B 391 ASP cc_start: 0.7089 (m-30) cc_final: 0.6853 (m-30) REVERT: B 400 GLU cc_start: 0.7563 (tp30) cc_final: 0.7096 (mm-30) REVERT: B 439 ILE cc_start: 0.8228 (mm) cc_final: 0.7816 (mm) outliers start: 16 outliers final: 9 residues processed: 161 average time/residue: 0.0860 time to fit residues: 17.8403 Evaluate side-chains 157 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 145 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 363 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 49 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 HIS ** A 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.169816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148375 restraints weight = 8078.077| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.28 r_work: 0.3845 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6361 Z= 0.172 Angle : 0.645 6.371 8606 Z= 0.333 Chirality : 0.045 0.196 963 Planarity : 0.005 0.047 1093 Dihedral : 9.118 80.276 911 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 3.37 % Allowed : 12.90 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.03 (0.29), residues: 774 helix: 0.24 (0.30), residues: 255 sheet: -1.75 (0.42), residues: 134 loop : -2.34 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 377 TYR 0.014 0.001 TYR B 71 PHE 0.028 0.002 PHE B 192 TRP 0.007 0.002 TRP A 245 HIS 0.007 0.001 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 6361) covalent geometry : angle 0.64522 ( 8606) hydrogen bonds : bond 0.04674 ( 229) hydrogen bonds : angle 4.41404 ( 648) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7720 (mtmt) REVERT: A 75 GLU cc_start: 0.6011 (tm-30) cc_final: 0.5533 (tm-30) REVERT: A 167 LYS cc_start: 0.8215 (mttt) cc_final: 0.7800 (mtpp) REVERT: A 201 GLU cc_start: 0.8162 (pt0) cc_final: 0.7898 (mt-10) REVERT: A 247 LYS cc_start: 0.7656 (tttt) cc_final: 0.7368 (ttmm) REVERT: A 248 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6974 (mm-30) REVERT: A 353 ASN cc_start: 0.8324 (t0) cc_final: 0.8107 (t0) REVERT: A 412 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.6702 (t0) REVERT: B 9 ILE cc_start: 0.6997 (OUTLIER) cc_final: 0.6672 (mt) REVERT: B 44 MET cc_start: 0.7097 (ptm) cc_final: 0.6879 (ptm) REVERT: B 60 GLN cc_start: 0.7535 (mp10) cc_final: 0.7274 (mp10) REVERT: B 93 ASN cc_start: 0.7125 (m-40) cc_final: 0.6900 (m-40) REVERT: B 114 SER cc_start: 0.8477 (m) cc_final: 0.8032 (t) REVERT: B 128 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7998 (mtmm) REVERT: B 139 SER cc_start: 0.8508 (t) cc_final: 0.8055 (p) REVERT: B 204 ASN cc_start: 0.7260 (m-40) cc_final: 0.6985 (m-40) REVERT: B 363 GLN cc_start: 0.7321 (OUTLIER) cc_final: 0.6949 (tt0) REVERT: B 391 ASP cc_start: 0.7341 (m-30) cc_final: 0.6973 (m-30) REVERT: B 400 GLU cc_start: 0.7372 (tp30) cc_final: 0.7011 (mm-30) REVERT: B 439 ILE cc_start: 0.8250 (mm) cc_final: 0.7949 (mm) outliers start: 23 outliers final: 10 residues processed: 171 average time/residue: 0.0755 time to fit residues: 16.7972 Evaluate side-chains 160 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 147 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 21 optimal weight: 0.0060 chunk 10 optimal weight: 0.5980 chunk 12 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 20 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.172140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.150834 restraints weight = 8202.581| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 2.28 r_work: 0.3881 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6361 Z= 0.123 Angle : 0.575 6.566 8606 Z= 0.299 Chirality : 0.043 0.170 963 Planarity : 0.004 0.052 1093 Dihedral : 8.840 78.764 911 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 2.79 % Allowed : 15.40 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.66 (0.29), residues: 774 helix: 0.55 (0.31), residues: 251 sheet: -1.55 (0.43), residues: 130 loop : -2.10 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 115 TYR 0.016 0.001 TYR B 71 PHE 0.012 0.001 PHE B 192 TRP 0.005 0.001 TRP B 445 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 6361) covalent geometry : angle 0.57531 ( 8606) hydrogen bonds : bond 0.03961 ( 229) hydrogen bonds : angle 4.12050 ( 648) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7934 (mtmt) cc_final: 0.7665 (mtmt) REVERT: A 49 LYS cc_start: 0.7952 (mmmm) cc_final: 0.7495 (ttmm) REVERT: A 75 GLU cc_start: 0.5963 (tm-30) cc_final: 0.5500 (tm-30) REVERT: A 79 MET cc_start: 0.8048 (mtm) cc_final: 0.7807 (mtm) REVERT: A 167 LYS cc_start: 0.8194 (mttt) cc_final: 0.7748 (mtpp) REVERT: A 247 LYS cc_start: 0.7663 (tttt) cc_final: 0.7366 (ttmm) REVERT: A 248 GLU cc_start: 0.7074 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 412 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.6756 (t0) REVERT: B 9 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6670 (mt) REVERT: B 69 GLU cc_start: 0.7799 (tt0) cc_final: 0.7390 (tt0) REVERT: B 93 ASN cc_start: 0.7103 (m-40) cc_final: 0.6612 (m110) REVERT: B 114 SER cc_start: 0.8388 (m) cc_final: 0.8026 (t) REVERT: B 128 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7959 (mtmm) REVERT: B 139 SER cc_start: 0.8497 (t) cc_final: 0.8045 (p) REVERT: B 374 ASP cc_start: 0.6474 (t70) cc_final: 0.5438 (m-30) REVERT: B 391 ASP cc_start: 0.7343 (m-30) cc_final: 0.6984 (m-30) REVERT: B 400 GLU cc_start: 0.7331 (tp30) cc_final: 0.7128 (tp30) REVERT: B 439 ILE cc_start: 0.8198 (mm) cc_final: 0.7875 (mm) outliers start: 19 outliers final: 14 residues processed: 165 average time/residue: 0.0840 time to fit residues: 17.7817 Evaluate side-chains 155 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 423 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 61 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 60 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 411 GLN ** B 431 HIS ** 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 = 0.4218 r_free = 0.4218 target = 0.170043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.148609 restraints weight = 8273.716| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.28 r_work: 0.3852 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6361 Z= 0.153 Angle : 0.602 6.575 8606 Z= 0.314 Chirality : 0.044 0.143 963 Planarity : 0.005 0.056 1093 Dihedral : 8.931 79.715 911 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 2.79 % Allowed : 17.89 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.71 (0.29), residues: 774 helix: 0.53 (0.31), residues: 254 sheet: -1.71 (0.42), residues: 132 loop : -2.11 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 377 TYR 0.014 0.001 TYR B 71 PHE 0.017 0.002 PHE B 192 TRP 0.007 0.001 TRP B 445 HIS 0.005 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6361) covalent geometry : angle 0.60201 ( 8606) hydrogen bonds : bond 0.04190 ( 229) hydrogen bonds : angle 4.09194 ( 648) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7925 (mtmt) cc_final: 0.7662 (mtmt) REVERT: A 28 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.6502 (t80) REVERT: A 49 LYS cc_start: 0.7946 (mmmm) cc_final: 0.7500 (ttmm) REVERT: A 75 GLU cc_start: 0.5972 (tm-30) cc_final: 0.5512 (tm-30) REVERT: A 167 LYS cc_start: 0.8211 (mttt) cc_final: 0.7785 (mtpp) REVERT: A 200 VAL cc_start: 0.8547 (t) cc_final: 0.8061 (t) REVERT: A 247 LYS cc_start: 0.7682 (tttt) cc_final: 0.7386 (ttmm) REVERT: A 248 GLU cc_start: 0.7040 (mm-30) cc_final: 0.6808 (mm-30) REVERT: B 9 ILE cc_start: 0.7066 (OUTLIER) cc_final: 0.6722 (mt) REVERT: B 74 PHE cc_start: 0.6077 (m-10) cc_final: 0.5776 (m-10) REVERT: B 93 ASN cc_start: 0.7160 (m-40) cc_final: 0.6709 (m-40) REVERT: B 114 SER cc_start: 0.8395 (m) cc_final: 0.8040 (t) REVERT: B 139 SER cc_start: 0.8499 (t) cc_final: 0.8035 (p) REVERT: B 363 GLN cc_start: 0.7258 (OUTLIER) cc_final: 0.6947 (tt0) REVERT: B 374 ASP cc_start: 0.6596 (t70) cc_final: 0.5484 (m-30) REVERT: B 391 ASP cc_start: 0.7375 (m-30) cc_final: 0.6955 (m-30) REVERT: B 400 GLU cc_start: 0.7306 (tp30) cc_final: 0.7088 (tp30) REVERT: B 439 ILE cc_start: 0.8087 (mm) cc_final: 0.7781 (mm) outliers start: 19 outliers final: 14 residues processed: 161 average time/residue: 0.0795 time to fit residues: 16.5816 Evaluate side-chains 160 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 423 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 63 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 56 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 11 optimal weight: 0.0170 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 411 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.171290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.149838 restraints weight = 8069.264| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.27 r_work: 0.3866 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6361 Z= 0.128 Angle : 0.567 7.319 8606 Z= 0.296 Chirality : 0.043 0.138 963 Planarity : 0.004 0.054 1093 Dihedral : 8.746 80.231 909 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.49 % Allowed : 17.45 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.30), residues: 774 helix: 0.78 (0.31), residues: 251 sheet: -1.60 (0.43), residues: 130 loop : -2.04 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 115 TYR 0.015 0.001 TYR B 146 PHE 0.014 0.001 PHE B 180 TRP 0.005 0.001 TRP B 445 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 6361) covalent geometry : angle 0.56704 ( 8606) hydrogen bonds : bond 0.03850 ( 229) hydrogen bonds : angle 3.93475 ( 648) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 0.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7601 (mt) cc_final: 0.7040 (pp) REVERT: A 15 LYS cc_start: 0.7913 (mtmt) cc_final: 0.7634 (mtmt) REVERT: A 28 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.6914 (t80) REVERT: A 42 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7257 (mm-30) REVERT: A 49 LYS cc_start: 0.7962 (mmmm) cc_final: 0.7687 (mmmm) REVERT: A 79 MET cc_start: 0.8067 (mtm) cc_final: 0.7755 (mtm) REVERT: A 135 GLN cc_start: 0.7331 (mm-40) cc_final: 0.7043 (mm-40) REVERT: A 167 LYS cc_start: 0.8207 (mttt) cc_final: 0.7792 (mtpp) REVERT: A 247 LYS cc_start: 0.7663 (tttt) cc_final: 0.7412 (ttmm) REVERT: A 248 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6645 (mt-10) REVERT: A 374 ASP cc_start: 0.6778 (t0) cc_final: 0.6418 (t0) REVERT: A 452 LYS cc_start: 0.7940 (pttp) cc_final: 0.7678 (ptpp) REVERT: B 9 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6730 (mt) REVERT: B 69 GLU cc_start: 0.7812 (tt0) cc_final: 0.7198 (tt0) REVERT: B 93 ASN cc_start: 0.7146 (m-40) cc_final: 0.6641 (m-40) REVERT: B 114 SER cc_start: 0.8377 (m) cc_final: 0.7932 (p) REVERT: B 137 TYR cc_start: 0.6984 (p90) cc_final: 0.6682 (p90) REVERT: B 139 SER cc_start: 0.8486 (t) cc_final: 0.7947 (p) REVERT: B 363 GLN cc_start: 0.7327 (OUTLIER) cc_final: 0.7017 (tp40) REVERT: B 374 ASP cc_start: 0.6490 (t70) cc_final: 0.5397 (m-30) REVERT: B 391 ASP cc_start: 0.7378 (m-30) cc_final: 0.6960 (m-30) REVERT: B 400 GLU cc_start: 0.7316 (tp30) cc_final: 0.7064 (mm-30) REVERT: B 439 ILE cc_start: 0.8080 (mm) cc_final: 0.7810 (mm) outliers start: 17 outliers final: 11 residues processed: 153 average time/residue: 0.0799 time to fit residues: 15.9710 Evaluate side-chains 151 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 48 optimal weight: 0.0870 chunk 8 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 28 optimal weight: 0.1980 chunk 66 optimal weight: 0.0970 chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 overall best weight: 0.3756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.149829 restraints weight = 8054.902| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 2.28 r_work: 0.3864 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6361 Z= 0.130 Angle : 0.575 7.892 8606 Z= 0.300 Chirality : 0.043 0.160 963 Planarity : 0.004 0.053 1093 Dihedral : 8.718 80.007 909 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.49 % Allowed : 17.60 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.30), residues: 774 helix: 0.87 (0.31), residues: 254 sheet: -1.53 (0.43), residues: 134 loop : -2.04 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 115 TYR 0.011 0.001 TYR B 71 PHE 0.013 0.001 PHE B 421 TRP 0.006 0.001 TRP B 445 HIS 0.004 0.001 HIS B 404 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 6361) covalent geometry : angle 0.57474 ( 8606) hydrogen bonds : bond 0.03860 ( 229) hydrogen bonds : angle 3.91273 ( 648) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7650 (mt) cc_final: 0.7093 (pp) REVERT: A 15 LYS cc_start: 0.7857 (mtmt) cc_final: 0.7587 (mtmt) REVERT: A 28 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7028 (t80) REVERT: A 42 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7233 (mm-30) REVERT: A 49 LYS cc_start: 0.7981 (mmmm) cc_final: 0.7691 (ttmm) REVERT: A 60 GLN cc_start: 0.7821 (mm-40) cc_final: 0.7513 (mm-40) REVERT: A 79 MET cc_start: 0.8072 (mtm) cc_final: 0.7762 (mtm) REVERT: A 135 GLN cc_start: 0.7285 (mm-40) cc_final: 0.7000 (mm-40) REVERT: A 167 LYS cc_start: 0.8242 (mttt) cc_final: 0.7806 (mtpp) REVERT: A 247 LYS cc_start: 0.7672 (tttt) cc_final: 0.7376 (ttmm) REVERT: A 248 GLU cc_start: 0.7053 (mm-30) cc_final: 0.6677 (mt-10) REVERT: A 452 LYS cc_start: 0.7973 (pttp) cc_final: 0.7695 (ptpp) REVERT: B 9 ILE cc_start: 0.7069 (OUTLIER) cc_final: 0.6722 (mt) REVERT: B 69 GLU cc_start: 0.7855 (tt0) cc_final: 0.7504 (tt0) REVERT: B 74 PHE cc_start: 0.6107 (m-10) cc_final: 0.5668 (m-10) REVERT: B 77 LEU cc_start: 0.7079 (tp) cc_final: 0.6632 (tp) REVERT: B 93 ASN cc_start: 0.7118 (m-40) cc_final: 0.6912 (p0) REVERT: B 114 SER cc_start: 0.8366 (m) cc_final: 0.7968 (p) REVERT: B 139 SER cc_start: 0.8479 (t) cc_final: 0.8018 (p) REVERT: B 363 GLN cc_start: 0.7378 (OUTLIER) cc_final: 0.7176 (tp40) REVERT: B 391 ASP cc_start: 0.7402 (m-30) cc_final: 0.6988 (m-30) REVERT: B 439 ILE cc_start: 0.8065 (mm) cc_final: 0.7808 (mm) outliers start: 17 outliers final: 13 residues processed: 151 average time/residue: 0.0927 time to fit residues: 18.0073 Evaluate side-chains 156 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 423 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 2 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 56 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 70 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.169778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.148315 restraints weight = 8112.938| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.28 r_work: 0.3842 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6361 Z= 0.154 Angle : 0.600 8.312 8606 Z= 0.313 Chirality : 0.044 0.158 963 Planarity : 0.005 0.066 1093 Dihedral : 8.808 81.270 909 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.49 % Allowed : 17.89 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.30), residues: 774 helix: 0.80 (0.31), residues: 256 sheet: -1.54 (0.43), residues: 136 loop : -2.05 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 115 TYR 0.013 0.001 TYR B 137 PHE 0.014 0.002 PHE B 421 TRP 0.007 0.001 TRP B 445 HIS 0.004 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 6361) covalent geometry : angle 0.59994 ( 8606) hydrogen bonds : bond 0.04101 ( 229) hydrogen bonds : angle 3.95511 ( 648) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7673 (mt) cc_final: 0.7035 (pp) REVERT: A 15 LYS cc_start: 0.7853 (mtmt) cc_final: 0.7571 (mtmt) REVERT: A 28 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 42 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7166 (mp0) REVERT: A 49 LYS cc_start: 0.8022 (mmmm) cc_final: 0.7739 (ttmm) REVERT: A 75 GLU cc_start: 0.5913 (tm-30) cc_final: 0.5482 (tm-30) REVERT: A 79 MET cc_start: 0.8057 (mtm) cc_final: 0.7763 (mtm) REVERT: A 167 LYS cc_start: 0.8239 (mttt) cc_final: 0.7811 (mtpp) REVERT: A 247 LYS cc_start: 0.7688 (tttt) cc_final: 0.7376 (ttmm) REVERT: A 248 GLU cc_start: 0.7080 (mm-30) cc_final: 0.6688 (mt-10) REVERT: A 374 ASP cc_start: 0.6734 (t0) cc_final: 0.6314 (t70) REVERT: B 9 ILE cc_start: 0.7101 (OUTLIER) cc_final: 0.6762 (mt) REVERT: B 69 GLU cc_start: 0.7742 (tt0) cc_final: 0.7454 (tt0) REVERT: B 114 SER cc_start: 0.8354 (m) cc_final: 0.7968 (p) REVERT: B 139 SER cc_start: 0.8504 (t) cc_final: 0.7947 (p) REVERT: B 363 GLN cc_start: 0.7449 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: B 374 ASP cc_start: 0.6643 (t70) cc_final: 0.5464 (m-30) REVERT: B 391 ASP cc_start: 0.7453 (m-30) cc_final: 0.7049 (m-30) REVERT: B 439 ILE cc_start: 0.8054 (mm) cc_final: 0.7789 (mm) outliers start: 17 outliers final: 12 residues processed: 156 average time/residue: 0.0951 time to fit residues: 18.7928 Evaluate side-chains 159 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 0 optimal weight: 5.9990 chunk 71 optimal weight: 0.2980 chunk 73 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 434 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148959 restraints weight = 8082.094| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 2.28 r_work: 0.3854 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6361 Z= 0.144 Angle : 0.598 8.933 8606 Z= 0.312 Chirality : 0.043 0.167 963 Planarity : 0.005 0.062 1093 Dihedral : 8.791 81.685 909 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 2.49 % Allowed : 18.62 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.49 (0.30), residues: 774 helix: 0.78 (0.31), residues: 262 sheet: -1.37 (0.46), residues: 122 loop : -2.17 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 62 TYR 0.014 0.001 TYR B 146 PHE 0.015 0.001 PHE B 421 TRP 0.010 0.001 TRP B 445 HIS 0.004 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 6361) covalent geometry : angle 0.59834 ( 8606) hydrogen bonds : bond 0.03923 ( 229) hydrogen bonds : angle 3.92606 ( 648) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 147 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7674 (mt) cc_final: 0.7037 (pp) REVERT: A 15 LYS cc_start: 0.7831 (mtmt) cc_final: 0.7554 (mtmt) REVERT: A 28 TYR cc_start: 0.8043 (OUTLIER) cc_final: 0.7412 (t80) REVERT: A 60 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7561 (mm-40) REVERT: A 79 MET cc_start: 0.7943 (mtm) cc_final: 0.7652 (mtm) REVERT: A 135 GLN cc_start: 0.7283 (mm-40) cc_final: 0.7059 (mm-40) REVERT: A 167 LYS cc_start: 0.8264 (mttt) cc_final: 0.7833 (mtpp) REVERT: A 198 TYR cc_start: 0.8061 (m-80) cc_final: 0.7819 (m-80) REVERT: A 247 LYS cc_start: 0.7700 (tttt) cc_final: 0.7352 (ttmm) REVERT: A 248 GLU cc_start: 0.7075 (mm-30) cc_final: 0.6678 (mt-10) REVERT: A 374 ASP cc_start: 0.6723 (t0) cc_final: 0.6325 (t70) REVERT: B 9 ILE cc_start: 0.7105 (OUTLIER) cc_final: 0.6765 (mt) REVERT: B 114 SER cc_start: 0.8330 (m) cc_final: 0.7969 (p) REVERT: B 139 SER cc_start: 0.8512 (t) cc_final: 0.8012 (p) REVERT: B 146 TYR cc_start: 0.7890 (t80) cc_final: 0.7673 (t80) REVERT: B 169 ASN cc_start: 0.7548 (t0) cc_final: 0.7296 (t0) REVERT: B 363 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7068 (tt0) REVERT: B 374 ASP cc_start: 0.6618 (t70) cc_final: 0.5415 (m-30) REVERT: B 391 ASP cc_start: 0.7445 (m-30) cc_final: 0.7035 (m-30) REVERT: B 439 ILE cc_start: 0.8026 (mm) cc_final: 0.7773 (mm) outliers start: 17 outliers final: 13 residues processed: 158 average time/residue: 0.0881 time to fit residues: 17.8246 Evaluate side-chains 159 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 143 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TYR Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 44 MET Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 363 GLN Chi-restraints excluded: chain B residue 417 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 50 optimal weight: 0.0050 chunk 77 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 73 optimal weight: 0.0970 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 overall best weight: 0.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.171821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.150483 restraints weight = 8057.324| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 2.29 r_work: 0.3869 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6739 moved from start: 0.3602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6361 Z= 0.124 Angle : 0.584 9.106 8606 Z= 0.307 Chirality : 0.043 0.156 963 Planarity : 0.005 0.056 1093 Dihedral : 8.627 81.100 909 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.98 % Favored : 89.02 % Rotamer: Outliers : 2.20 % Allowed : 18.62 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.30), residues: 774 helix: 0.94 (0.31), residues: 259 sheet: -1.32 (0.47), residues: 122 loop : -2.16 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 62 TYR 0.018 0.001 TYR B 71 PHE 0.015 0.001 PHE B 421 TRP 0.011 0.001 TRP B 445 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 6361) covalent geometry : angle 0.58423 ( 8606) hydrogen bonds : bond 0.03713 ( 229) hydrogen bonds : angle 3.85060 ( 648) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1548 Ramachandran restraints generated. 774 Oldfield, 0 Emsley, 774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7645 (mt) cc_final: 0.6984 (pp) REVERT: A 15 LYS cc_start: 0.7834 (mtmt) cc_final: 0.7547 (mtmt) REVERT: A 60 GLN cc_start: 0.7759 (mm-40) cc_final: 0.7529 (mm-40) REVERT: A 135 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6991 (mm-40) REVERT: A 167 LYS cc_start: 0.8220 (mttt) cc_final: 0.7795 (mtpp) REVERT: A 197 MET cc_start: 0.6843 (ttt) cc_final: 0.6462 (ttt) REVERT: A 198 TYR cc_start: 0.7972 (m-80) cc_final: 0.7705 (m-80) REVERT: A 247 LYS cc_start: 0.7691 (tttt) cc_final: 0.7430 (tttm) REVERT: A 374 ASP cc_start: 0.6682 (t0) cc_final: 0.6316 (t70) REVERT: B 9 ILE cc_start: 0.7097 (OUTLIER) cc_final: 0.6755 (mt) REVERT: B 77 LEU cc_start: 0.6985 (tp) cc_final: 0.6523 (tp) REVERT: B 114 SER cc_start: 0.8317 (m) cc_final: 0.7986 (p) REVERT: B 139 SER cc_start: 0.8513 (t) cc_final: 0.8010 (p) REVERT: B 391 ASP cc_start: 0.7398 (m-30) cc_final: 0.6999 (m-30) outliers start: 15 outliers final: 10 residues processed: 142 average time/residue: 0.0876 time to fit residues: 16.0960 Evaluate side-chains 142 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 241 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 27 optimal weight: 0.0870 chunk 42 optimal weight: 0.2980 chunk 76 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 overall best weight: 0.2816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.172760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.151534 restraints weight = 8098.304| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.31 r_work: 0.3876 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6361 Z= 0.122 Angle : 0.575 9.050 8606 Z= 0.303 Chirality : 0.043 0.146 963 Planarity : 0.004 0.056 1093 Dihedral : 8.426 79.279 907 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 1.61 % Allowed : 18.91 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.29 (0.30), residues: 774 helix: 1.11 (0.31), residues: 254 sheet: -1.28 (0.47), residues: 122 loop : -2.12 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 62 TYR 0.016 0.001 TYR B 71 PHE 0.017 0.001 PHE A 21 TRP 0.014 0.001 TRP B 445 HIS 0.003 0.001 HIS B 406 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 6361) covalent geometry : angle 0.57515 ( 8606) hydrogen bonds : bond 0.03639 ( 229) hydrogen bonds : angle 3.82959 ( 648) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1367.98 seconds wall clock time: 24 minutes 14.55 seconds (1454.55 seconds total)