Starting phenix.real_space_refine on Thu Jul 24 13:12:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e91_47739/07_2025/9e91_47739.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e91_47739/07_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_47739/07_2025/9e91_47739.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e91_47739/07_2025/9e91_47739.map" model { file = "/net/cci-nas-00/data/ceres_data/9e91_47739/07_2025/9e91_47739.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e91_47739/07_2025/9e91_47739.cif" } resolution = 3.31 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'ARG:plan': 1, 'ASN:plan1': 1, 'HIS: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: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG: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: 4.37, per 1000 atoms: 0.70 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: 1.47 Conformation dependent library (CDL) restraints added in 887.6 milliseconds 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: 0.64 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: 1.70 Time building geometry restraints manager: 1.75 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 454 or resid 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: 0.730 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 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: 22.140 ------------------------------------------------------------------------------- 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 (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: -2.13 (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 TRP 0.014 0.002 TRP B 445 HIS 0.005 0.001 HIS B 406 PHE 0.025 0.001 PHE B 242 TYR 0.013 0.002 TYR B 71 ARG 0.005 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.21208 ( 229) hydrogen bonds : angle 6.97741 ( 648) covalent geometry : bond 0.00829 ( 6361) covalent geometry : angle 0.88689 ( 8606) *********************** 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 : 0.712 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: 0.2088 time to fit residues: 44.4063 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 : 0.654 ------------------------------------------------------------------------------- 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 65 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 0.0870 chunk 20 optimal weight: 0.0070 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.0670 chunk 45 optimal weight: 0.0970 chunk 70 optimal weight: 0.5980 overall best weight: 0.1112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 383 ASN ** 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 = 0.4318 r_free = 0.4318 target = 0.177549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.156248 restraints weight = 8079.561| |-----------------------------------------------------------------------------| r_work (start): 0.4072 rms_B_bonded: 2.25 r_work: 0.3965 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6361 Z= 0.115 Angle : 0.603 6.533 8606 Z= 0.309 Chirality : 0.044 0.174 963 Planarity : 0.005 0.045 1093 Dihedral : 9.050 83.269 912 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 2.35 % Allowed : 9.82 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.29), residues: 774 helix: 0.20 (0.31), residues: 257 sheet: -1.60 (0.44), residues: 134 loop : -2.11 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 245 HIS 0.007 0.001 HIS B 404 PHE 0.020 0.001 PHE B 242 TYR 0.009 0.001 TYR B 198 ARG 0.004 0.000 ARG B 132 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 229) hydrogen bonds : angle 4.78164 ( 648) covalent geometry : bond 0.00245 ( 6361) covalent geometry : angle 0.60312 ( 8606) *********************** 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 155 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.8006 (mtmt) cc_final: 0.7751 (mtmt) REVERT: A 21 PHE cc_start: 0.7401 (t80) cc_final: 0.7148 (t80) REVERT: A 49 LYS cc_start: 0.7602 (mmtm) cc_final: 0.7217 (tppt) REVERT: A 75 GLU cc_start: 0.5954 (tm-30) cc_final: 0.5434 (tm-30) REVERT: A 190 VAL cc_start: 0.8097 (OUTLIER) cc_final: 0.7740 (t) REVERT: A 247 LYS cc_start: 0.7427 (tttt) cc_final: 0.7224 (ttmm) REVERT: A 365 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7698 (mt-10) REVERT: B 9 ILE cc_start: 0.6940 (OUTLIER) cc_final: 0.6647 (mt) REVERT: B 44 MET cc_start: 0.7132 (ptm) cc_final: 0.6916 (ptm) REVERT: B 69 GLU cc_start: 0.7680 (tt0) cc_final: 0.7279 (tt0) REVERT: B 114 SER cc_start: 0.8138 (m) cc_final: 0.7733 (t) REVERT: B 137 TYR cc_start: 0.6458 (p90) cc_final: 0.6221 (p90) REVERT: B 139 SER cc_start: 0.8508 (t) cc_final: 0.8049 (p) REVERT: B 197 MET cc_start: 0.7172 (tpp) cc_final: 0.6334 (tpp) REVERT: B 210 ASP cc_start: 0.6536 (p0) cc_final: 0.6294 (t70) REVERT: B 363 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.6860 (tt0) REVERT: B 391 ASP cc_start: 0.7030 (m-30) cc_final: 0.6748 (m-30) REVERT: B 400 GLU cc_start: 0.7522 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 439 ILE cc_start: 0.8186 (mm) cc_final: 0.7812 (mm) outliers start: 16 outliers final: 8 residues processed: 151 average time/residue: 0.2028 time to fit residues: 39.0573 Evaluate side-chains 141 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.734 ------------------------------------------------------------------------------- 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 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 65 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 111 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.169705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.148485 restraints weight = 8216.242| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 2.27 r_work: 0.3855 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6757 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6361 Z= 0.179 Angle : 0.648 7.250 8606 Z= 0.333 Chirality : 0.045 0.148 963 Planarity : 0.005 0.047 1093 Dihedral : 9.020 80.736 909 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.63 % Favored : 88.37 % Rotamer: Outliers : 3.37 % Allowed : 11.00 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.29), residues: 774 helix: 0.24 (0.30), residues: 257 sheet: -1.65 (0.42), residues: 134 loop : -2.29 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 245 HIS 0.006 0.001 HIS A 406 PHE 0.029 0.002 PHE B 192 TYR 0.010 0.001 TYR A 162 ARG 0.005 0.001 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04705 ( 229) hydrogen bonds : angle 4.42972 ( 648) covalent geometry : bond 0.00417 ( 6361) covalent geometry : angle 0.64840 ( 8606) *********************** 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 176 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7728 (mtmt) REVERT: A 75 GLU cc_start: 0.6018 (tm-30) cc_final: 0.5529 (tm-30) REVERT: A 167 LYS cc_start: 0.8211 (mttt) cc_final: 0.7792 (mtpp) REVERT: A 201 GLU cc_start: 0.8150 (pt0) cc_final: 0.7883 (mt-10) REVERT: A 247 LYS cc_start: 0.7630 (tttt) cc_final: 0.7333 (ttmm) REVERT: A 353 ASN cc_start: 0.8339 (t0) cc_final: 0.8117 (t0) REVERT: B 9 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6678 (mt) REVERT: B 44 MET cc_start: 0.7158 (ptm) cc_final: 0.6941 (ptm) REVERT: B 60 GLN cc_start: 0.7534 (mp10) cc_final: 0.7280 (mp10) REVERT: B 69 GLU cc_start: 0.7755 (tt0) cc_final: 0.7534 (tt0) REVERT: B 77 LEU cc_start: 0.6876 (tp) cc_final: 0.6429 (tp) REVERT: B 114 SER cc_start: 0.8437 (m) cc_final: 0.8014 (t) REVERT: B 128 LYS cc_start: 0.8320 (ttmm) cc_final: 0.7997 (mtmm) REVERT: B 139 SER cc_start: 0.8478 (t) cc_final: 0.7964 (p) REVERT: B 204 ASN cc_start: 0.7290 (m-40) cc_final: 0.7062 (m-40) REVERT: B 391 ASP cc_start: 0.7358 (m-30) cc_final: 0.6977 (m-30) REVERT: B 439 ILE cc_start: 0.8257 (mm) cc_final: 0.7926 (mm) outliers start: 23 outliers final: 11 residues processed: 164 average time/residue: 0.2174 time to fit residues: 45.7175 Evaluate side-chains 159 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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 60 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.0470 chunk 77 optimal weight: 0.4980 chunk 9 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 GLN B 322 HIS ** B 431 HIS ** 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 = 0.169910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.148628 restraints weight = 8254.287| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.28 r_work: 0.3856 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6361 Z= 0.154 Angle : 0.605 6.257 8606 Z= 0.314 Chirality : 0.044 0.145 963 Planarity : 0.005 0.054 1093 Dihedral : 8.947 81.007 909 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 2.20 % Allowed : 15.25 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.29), residues: 774 helix: 0.45 (0.31), residues: 250 sheet: -1.53 (0.43), residues: 132 loop : -2.07 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 223 HIS 0.004 0.001 HIS B 406 PHE 0.019 0.002 PHE B 192 TYR 0.014 0.001 TYR B 71 ARG 0.006 0.001 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04244 ( 229) hydrogen bonds : angle 4.19529 ( 648) covalent geometry : bond 0.00357 ( 6361) covalent geometry : angle 0.60544 ( 8606) *********************** 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 166 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7978 (mtmt) cc_final: 0.7713 (mtmt) REVERT: A 49 LYS cc_start: 0.7957 (mmmm) cc_final: 0.7493 (ttmm) REVERT: A 75 GLU cc_start: 0.5989 (tm-30) cc_final: 0.5532 (tm-30) REVERT: A 79 MET cc_start: 0.8138 (mtm) cc_final: 0.7898 (mtm) REVERT: A 167 LYS cc_start: 0.8182 (mttt) cc_final: 0.7773 (mtpp) REVERT: A 247 LYS cc_start: 0.7693 (tttt) cc_final: 0.7387 (ttmm) REVERT: A 365 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7720 (mt-10) REVERT: B 9 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6662 (mt) REVERT: B 77 LEU cc_start: 0.6819 (tp) cc_final: 0.6444 (tp) REVERT: B 94 ASN cc_start: 0.7495 (m110) cc_final: 0.7202 (m110) REVERT: B 114 SER cc_start: 0.8420 (m) cc_final: 0.8040 (t) REVERT: B 128 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7994 (mtmm) REVERT: B 139 SER cc_start: 0.8481 (t) cc_final: 0.8030 (p) REVERT: B 204 ASN cc_start: 0.7253 (m-40) cc_final: 0.7037 (m-40) REVERT: B 374 ASP cc_start: 0.6604 (t70) cc_final: 0.5522 (m-30) REVERT: B 391 ASP cc_start: 0.7387 (m-30) cc_final: 0.6952 (m-30) REVERT: B 400 GLU cc_start: 0.7373 (tp30) cc_final: 0.7126 (mm-30) REVERT: B 439 ILE cc_start: 0.8250 (mm) cc_final: 0.7944 (mm) outliers start: 15 outliers final: 11 residues processed: 161 average time/residue: 0.2188 time to fit residues: 44.7027 Evaluate side-chains 152 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 19 optimal weight: 0.0170 chunk 12 optimal weight: 0.0980 chunk 53 optimal weight: 0.0980 chunk 64 optimal weight: 0.9980 chunk 45 optimal weight: 0.0370 chunk 34 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 77 optimal weight: 0.0980 chunk 29 optimal weight: 0.6980 overall best weight: 0.0696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.155166 restraints weight = 8114.189| |-----------------------------------------------------------------------------| r_work (start): 0.4042 rms_B_bonded: 2.29 r_work: 0.3933 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6361 Z= 0.099 Angle : 0.535 7.524 8606 Z= 0.280 Chirality : 0.042 0.138 963 Planarity : 0.004 0.048 1093 Dihedral : 8.428 79.070 907 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.61 % Allowed : 17.60 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.30), residues: 774 helix: 0.95 (0.32), residues: 249 sheet: -1.30 (0.45), residues: 130 loop : -1.94 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 445 HIS 0.004 0.001 HIS B 406 PHE 0.011 0.001 PHE B 421 TYR 0.011 0.001 TYR B 71 ARG 0.004 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.03391 ( 229) hydrogen bonds : angle 3.89870 ( 648) covalent geometry : bond 0.00209 ( 6361) covalent geometry : angle 0.53534 ( 8606) *********************** 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 143 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7593 (mt) cc_final: 0.7038 (pp) REVERT: A 15 LYS cc_start: 0.7882 (mtmt) cc_final: 0.7615 (mtmt) REVERT: A 49 LYS cc_start: 0.7982 (mmmm) cc_final: 0.7742 (mmmm) REVERT: A 75 GLU cc_start: 0.5937 (tm-30) cc_final: 0.5474 (tm-30) REVERT: A 169 ASN cc_start: 0.7431 (t0) cc_final: 0.7101 (p0) REVERT: A 197 MET cc_start: 0.6856 (ttt) cc_final: 0.6480 (ttt) REVERT: A 247 LYS cc_start: 0.7585 (tttt) cc_final: 0.7333 (ttmm) REVERT: B 69 GLU cc_start: 0.7807 (tt0) cc_final: 0.7554 (tt0) REVERT: B 114 SER cc_start: 0.8300 (m) cc_final: 0.8028 (t) REVERT: B 128 LYS cc_start: 0.8383 (ttmm) cc_final: 0.8024 (mtmm) REVERT: B 139 SER cc_start: 0.8473 (t) cc_final: 0.7983 (p) REVERT: B 391 ASP cc_start: 0.7356 (m-30) cc_final: 0.7005 (m-30) REVERT: B 400 GLU cc_start: 0.7350 (tp30) cc_final: 0.7066 (mm-30) REVERT: B 439 ILE cc_start: 0.8079 (mm) cc_final: 0.7865 (mm) outliers start: 11 outliers final: 6 residues processed: 140 average time/residue: 0.1996 time to fit residues: 36.2957 Evaluate side-chains 131 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 98 LYS Chi-restraints excluded: chain B residue 118 THR Chi-restraints excluded: chain B residue 119 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 20 optimal weight: 0.7980 chunk 66 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.0870 chunk 45 optimal weight: 0.0470 chunk 10 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 76 optimal weight: 0.0870 overall best weight: 0.2034 ------------------------------------------------------------------------------- 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 ** 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 = 0.4280 r_free = 0.4280 target = 0.175583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.154253 restraints weight = 8167.579| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 2.31 r_work: 0.3916 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6361 Z= 0.106 Angle : 0.536 7.741 8606 Z= 0.280 Chirality : 0.042 0.136 963 Planarity : 0.004 0.053 1093 Dihedral : 8.284 77.778 907 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.47 % Allowed : 17.89 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.30), residues: 774 helix: 1.21 (0.32), residues: 249 sheet: -1.24 (0.44), residues: 130 loop : -1.88 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 445 HIS 0.003 0.001 HIS B 406 PHE 0.010 0.001 PHE B 421 TYR 0.012 0.001 TYR B 71 ARG 0.003 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.03503 ( 229) hydrogen bonds : angle 3.78651 ( 648) covalent geometry : bond 0.00233 ( 6361) covalent geometry : angle 0.53648 ( 8606) *********************** 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 145 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7593 (mt) cc_final: 0.7038 (pp) REVERT: A 15 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7551 (mtmt) REVERT: A 42 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7184 (mm-30) REVERT: A 49 LYS cc_start: 0.7960 (mmmm) cc_final: 0.7661 (ttmt) REVERT: A 75 GLU cc_start: 0.5918 (tm-30) cc_final: 0.5456 (tm-30) REVERT: A 135 GLN cc_start: 0.7248 (mm-40) cc_final: 0.6962 (mm-40) REVERT: A 169 ASN cc_start: 0.7434 (t0) cc_final: 0.7117 (p0) REVERT: A 197 MET cc_start: 0.6875 (ttt) cc_final: 0.6541 (ttt) REVERT: A 236 LYS cc_start: 0.8213 (OUTLIER) cc_final: 0.7902 (mtpt) REVERT: A 247 LYS cc_start: 0.7616 (tttt) cc_final: 0.7362 (tttm) REVERT: B 9 ILE cc_start: 0.7031 (OUTLIER) cc_final: 0.6709 (mt) REVERT: B 93 ASN cc_start: 0.7016 (m-40) cc_final: 0.6508 (m-40) REVERT: B 94 ASN cc_start: 0.7662 (m110) cc_final: 0.7200 (m110) REVERT: B 114 SER cc_start: 0.8299 (m) cc_final: 0.7994 (t) REVERT: B 128 LYS cc_start: 0.8375 (ttmm) cc_final: 0.8010 (mtmm) REVERT: B 139 SER cc_start: 0.8453 (t) cc_final: 0.8001 (p) REVERT: B 391 ASP cc_start: 0.7341 (m-30) cc_final: 0.7020 (m-30) REVERT: B 400 GLU cc_start: 0.7295 (tp30) cc_final: 0.7011 (tp30) REVERT: B 439 ILE cc_start: 0.8105 (mm) cc_final: 0.7850 (mm) outliers start: 10 outliers final: 7 residues processed: 145 average time/residue: 0.2015 time to fit residues: 38.0729 Evaluate side-chains 139 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 236 LYS Chi-restraints excluded: chain A residue 336 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.0870 chunk 41 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 overall best weight: 0.5560 ------------------------------------------------------------------------------- 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 = 0.4213 r_free = 0.4213 target = 0.169853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.148749 restraints weight = 8074.653| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.26 r_work: 0.3851 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6361 Z= 0.162 Angle : 0.603 7.874 8606 Z= 0.314 Chirality : 0.044 0.146 963 Planarity : 0.005 0.055 1093 Dihedral : 8.675 79.290 907 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.17 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.30), residues: 774 helix: 0.92 (0.31), residues: 256 sheet: -1.10 (0.45), residues: 134 loop : -1.99 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 445 HIS 0.003 0.001 HIS B 404 PHE 0.018 0.002 PHE B 192 TYR 0.017 0.001 TYR B 71 ARG 0.003 0.000 ARG B 377 Details of bonding type rmsd hydrogen bonds : bond 0.04154 ( 229) hydrogen bonds : angle 3.90026 ( 648) covalent geometry : bond 0.00376 ( 6361) covalent geometry : angle 0.60319 ( 8606) *********************** 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 166 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7664 (mt) cc_final: 0.7099 (pp) REVERT: A 15 LYS cc_start: 0.7840 (mtmt) cc_final: 0.7566 (mtmt) REVERT: A 42 GLU cc_start: 0.7374 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 49 LYS cc_start: 0.7990 (mmmm) cc_final: 0.7689 (ttmm) REVERT: A 75 GLU cc_start: 0.5899 (tm-30) cc_final: 0.5450 (tm-30) REVERT: A 135 GLN cc_start: 0.7353 (mm-40) cc_final: 0.7116 (mm-40) REVERT: A 167 LYS cc_start: 0.8186 (mttt) cc_final: 0.7780 (mtpp) REVERT: A 247 LYS cc_start: 0.7648 (tttt) cc_final: 0.7339 (ttmm) REVERT: A 396 VAL cc_start: 0.7714 (t) cc_final: 0.7293 (m) REVERT: B 9 ILE cc_start: 0.7075 (OUTLIER) cc_final: 0.6726 (mt) REVERT: B 114 SER cc_start: 0.8375 (m) cc_final: 0.8078 (t) REVERT: B 128 LYS cc_start: 0.8406 (ttmm) cc_final: 0.8032 (mtmm) REVERT: B 139 SER cc_start: 0.8481 (t) cc_final: 0.8066 (p) REVERT: B 374 ASP cc_start: 0.6645 (t70) cc_final: 0.5451 (m-30) REVERT: B 391 ASP cc_start: 0.7389 (m-30) cc_final: 0.6981 (m-30) REVERT: B 439 ILE cc_start: 0.8129 (mm) cc_final: 0.7852 (mm) outliers start: 17 outliers final: 11 residues processed: 160 average time/residue: 0.1968 time to fit residues: 40.7035 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 : 0.655 ------------------------------------------------------------------------------- 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 336 SER Chi-restraints excluded: chain A residue 353 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 241 LEU 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 31 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 21 optimal weight: 0.0170 chunk 25 optimal weight: 0.0170 chunk 62 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- 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 94 ASN ** 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 = 0.4245 r_free = 0.4245 target = 0.172913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.151864 restraints weight = 8023.994| |-----------------------------------------------------------------------------| r_work (start): 0.3996 rms_B_bonded: 2.25 r_work: 0.3886 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3419 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= 0.121 Angle : 0.569 8.099 8606 Z= 0.295 Chirality : 0.043 0.218 963 Planarity : 0.004 0.054 1093 Dihedral : 8.569 80.407 907 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 1.91 % Allowed : 18.33 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.30), residues: 774 helix: 1.06 (0.31), residues: 256 sheet: -1.01 (0.46), residues: 134 loop : -1.98 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 445 HIS 0.002 0.001 HIS B 404 PHE 0.014 0.001 PHE B 421 TYR 0.020 0.001 TYR B 71 ARG 0.005 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 229) hydrogen bonds : angle 3.81901 ( 648) covalent geometry : bond 0.00271 ( 6361) covalent geometry : angle 0.56888 ( 8606) *********************** 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 154 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 141 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7610 (mt) cc_final: 0.7041 (pp) REVERT: A 15 LYS cc_start: 0.7720 (mtmt) cc_final: 0.7425 (mtmt) REVERT: A 49 LYS cc_start: 0.7947 (mmmm) cc_final: 0.7636 (ttmm) REVERT: A 60 GLN cc_start: 0.7804 (mm-40) cc_final: 0.7496 (mm-40) REVERT: A 75 GLU cc_start: 0.5848 (tm-30) cc_final: 0.5419 (tm-30) REVERT: A 135 GLN cc_start: 0.7296 (mm-40) cc_final: 0.7041 (mm-40) REVERT: A 167 LYS cc_start: 0.8163 (mttt) cc_final: 0.7750 (mtpp) REVERT: A 247 LYS cc_start: 0.7632 (tttt) cc_final: 0.7365 (ttmm) REVERT: A 374 ASP cc_start: 0.6712 (t0) cc_final: 0.6499 (t0) REVERT: A 396 VAL cc_start: 0.7706 (t) cc_final: 0.7281 (m) REVERT: A 452 LYS cc_start: 0.7854 (pttp) cc_final: 0.7604 (ptpp) REVERT: B 9 ILE cc_start: 0.7067 (OUTLIER) cc_final: 0.6739 (mt) REVERT: B 94 ASN cc_start: 0.7327 (m110) cc_final: 0.6873 (m110) REVERT: B 114 SER cc_start: 0.8337 (m) cc_final: 0.7949 (p) REVERT: B 128 LYS cc_start: 0.8389 (ttmm) cc_final: 0.8035 (mtmm) REVERT: B 139 SER cc_start: 0.8488 (t) cc_final: 0.8055 (p) REVERT: B 225 LYS cc_start: 0.7853 (mtmm) cc_final: 0.7482 (mmtm) REVERT: B 391 ASP cc_start: 0.7410 (m-30) cc_final: 0.6991 (m-30) REVERT: B 439 ILE cc_start: 0.8087 (mm) cc_final: 0.7823 (mm) outliers start: 13 outliers final: 9 residues processed: 152 average time/residue: 0.2621 time to fit residues: 50.3006 Evaluate side-chains 146 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 136 time to evaluate : 0.703 ------------------------------------------------------------------------------- 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 353 ASN 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 417 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 47 optimal weight: 1.9990 chunk 32 optimal weight: 0.0270 chunk 34 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.0980 chunk 74 optimal weight: 0.0970 chunk 11 optimal weight: 0.0870 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 overall best weight: 0.1614 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.175620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.155012 restraints weight = 8089.601| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 2.31 r_work: 0.3912 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6361 Z= 0.105 Angle : 0.556 8.467 8606 Z= 0.288 Chirality : 0.043 0.155 963 Planarity : 0.004 0.060 1093 Dihedral : 8.331 79.861 907 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 1.76 % Allowed : 18.77 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.31), residues: 774 helix: 1.39 (0.32), residues: 250 sheet: -0.94 (0.47), residues: 134 loop : -1.93 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 445 HIS 0.003 0.001 HIS B 67 PHE 0.012 0.001 PHE B 421 TYR 0.014 0.001 TYR B 71 ARG 0.005 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 229) hydrogen bonds : angle 3.72566 ( 648) covalent geometry : bond 0.00227 ( 6361) covalent geometry : angle 0.55624 ( 8606) *********************** 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 148 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7548 (mtmt) cc_final: 0.7267 (mtmt) REVERT: A 49 LYS cc_start: 0.7929 (mmmm) cc_final: 0.7517 (ttmm) REVERT: A 60 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7462 (mm-40) REVERT: A 75 GLU cc_start: 0.5866 (tm-30) cc_final: 0.5430 (tm-30) REVERT: A 135 GLN cc_start: 0.7229 (mm-40) cc_final: 0.6966 (mm-40) REVERT: A 167 LYS cc_start: 0.8182 (mttt) cc_final: 0.7766 (mtpp) REVERT: A 197 MET cc_start: 0.6795 (ttt) cc_final: 0.6405 (ttt) REVERT: A 247 LYS cc_start: 0.7622 (tttt) cc_final: 0.7351 (ttmm) REVERT: A 396 VAL cc_start: 0.7770 (t) cc_final: 0.7353 (m) REVERT: B 9 ILE cc_start: 0.7073 (OUTLIER) cc_final: 0.6745 (mt) REVERT: B 77 LEU cc_start: 0.6843 (tp) cc_final: 0.6576 (tp) REVERT: B 94 ASN cc_start: 0.7384 (m110) cc_final: 0.6895 (m110) REVERT: B 114 SER cc_start: 0.8282 (m) cc_final: 0.7940 (p) REVERT: B 128 LYS cc_start: 0.8391 (ttmm) cc_final: 0.8026 (mtmm) REVERT: B 139 SER cc_start: 0.8323 (t) cc_final: 0.7959 (p) REVERT: B 157 THR cc_start: 0.8542 (m) cc_final: 0.8295 (t) REVERT: B 197 MET cc_start: 0.7159 (tpp) cc_final: 0.6375 (tpp) REVERT: B 225 LYS cc_start: 0.7805 (mtmm) cc_final: 0.7499 (mmtm) REVERT: B 391 ASP cc_start: 0.7382 (m-30) cc_final: 0.6964 (m-30) REVERT: B 439 ILE cc_start: 0.8044 (mm) cc_final: 0.7825 (mm) outliers start: 12 outliers final: 8 residues processed: 146 average time/residue: 0.2596 time to fit residues: 49.6747 Evaluate side-chains 145 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 136 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 15 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 61 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 42 optimal weight: 0.1980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 94 ASN ** 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 = 0.4221 r_free = 0.4221 target = 0.170688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.149426 restraints weight = 8055.244| |-----------------------------------------------------------------------------| r_work (start): 0.3966 rms_B_bonded: 2.28 r_work: 0.3852 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6361 Z= 0.165 Angle : 0.622 9.066 8606 Z= 0.322 Chirality : 0.045 0.223 963 Planarity : 0.005 0.057 1093 Dihedral : 8.643 80.319 907 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer: Outliers : 1.61 % Allowed : 19.06 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.30), residues: 774 helix: 0.99 (0.31), residues: 256 sheet: -1.07 (0.45), residues: 134 loop : -2.00 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 445 HIS 0.004 0.001 HIS B 406 PHE 0.016 0.002 PHE B 226 TYR 0.022 0.001 TYR B 71 ARG 0.003 0.000 ARG B 115 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 229) hydrogen bonds : angle 3.85203 ( 648) covalent geometry : bond 0.00381 ( 6361) covalent geometry : angle 0.62221 ( 8606) ********************** 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 152 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.7841 (mt) cc_final: 0.7056 (pp) REVERT: A 15 LYS cc_start: 0.7649 (mtmt) cc_final: 0.7372 (mtmt) REVERT: A 49 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7652 (ttmm) REVERT: A 60 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7475 (mm-40) REVERT: A 75 GLU cc_start: 0.5826 (tm-30) cc_final: 0.5398 (tm-30) REVERT: A 135 GLN cc_start: 0.7250 (mm-40) cc_final: 0.6961 (mm-40) REVERT: A 167 LYS cc_start: 0.8240 (mttt) cc_final: 0.7676 (mmmm) REVERT: A 247 LYS cc_start: 0.7717 (tttt) cc_final: 0.7329 (ttmm) REVERT: A 396 VAL cc_start: 0.7709 (t) cc_final: 0.7260 (m) REVERT: A 452 LYS cc_start: 0.7971 (pttp) cc_final: 0.7766 (ptpp) REVERT: B 9 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6753 (mt) REVERT: B 114 SER cc_start: 0.8312 (m) cc_final: 0.7975 (p) REVERT: B 128 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8056 (mtmm) REVERT: B 139 SER cc_start: 0.8435 (t) cc_final: 0.8049 (p) REVERT: B 374 ASP cc_start: 0.6642 (t70) cc_final: 0.5450 (m-30) REVERT: B 391 ASP cc_start: 0.7431 (m-30) cc_final: 0.7037 (m-30) REVERT: B 439 ILE cc_start: 0.8103 (mm) cc_final: 0.7853 (mm) outliers start: 11 outliers final: 9 residues processed: 148 average time/residue: 0.2340 time to fit residues: 44.7228 Evaluate side-chains 145 residues out of total 697 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 135 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 189 ASN Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 93 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 74 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 94 ASN ** 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 = 0.4226 r_free = 0.4226 target = 0.171001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.149629 restraints weight = 8133.501| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.31 r_work: 0.3854 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6361 Z= 0.156 Angle : 0.615 8.829 8606 Z= 0.319 Chirality : 0.044 0.203 963 Planarity : 0.005 0.064 1093 Dihedral : 8.716 82.142 907 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 1.76 % Allowed : 19.50 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.30), residues: 774 helix: 1.01 (0.31), residues: 256 sheet: -1.26 (0.44), residues: 134 loop : -2.04 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 445 HIS 0.003 0.001 HIS A 431 PHE 0.021 0.002 PHE B 226 TYR 0.021 0.001 TYR B 71 ARG 0.007 0.001 ARG A 62 Details of bonding type rmsd hydrogen bonds : bond 0.03949 ( 229) hydrogen bonds : angle 3.81564 ( 648) covalent geometry : bond 0.00358 ( 6361) covalent geometry : angle 0.61462 ( 8606) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3523.48 seconds wall clock time: 63 minutes 26.45 seconds (3806.45 seconds total)