Starting phenix.real_space_refine on Wed Jul 30 08:53:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597.map" model { file = "/net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fih_31597/07_2025/7fih_31597_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1455 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 6885 2.51 5 N 1872 2.21 5 O 2005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10853 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1972 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 550, 4314 Classifications: {'peptide': 550} Incomplete info: {'backbone_only': 9} Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 525} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "X" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 679 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "Y" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 816 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'55Z': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.62 Number of scatterers: 10853 At special positions: 0 Unit cell: (82.612, 97.83, 186.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 2005 8.00 N 1872 7.00 C 6885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 156 " distance=2.05 Simple disulfide: pdb=" SG CYS R 279 " - pdb=" SG CYS R 343 " distance=2.03 Simple disulfide: pdb=" SG CYS R 280 " - pdb=" SG CYS R 353 " distance=2.03 Simple disulfide: pdb=" SG CYS R 439 " - pdb=" SG CYS R 514 " distance=2.03 Simple disulfide: pdb=" SG CYS X 7 " - pdb=" SG CYS X 31 " distance=2.03 Simple disulfide: pdb=" SG CYS X 10 " - pdb=" SG CYS X 60 " distance=2.03 Simple disulfide: pdb=" SG CYS X 28 " - pdb=" SG CYS X 82 " distance=2.03 Simple disulfide: pdb=" SG CYS X 32 " - pdb=" SG CYS X 84 " distance=2.03 Simple disulfide: pdb=" SG CYS X 59 " - pdb=" SG CYS X 87 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 9 " - pdb=" SG CYS Y 57 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 23 " - pdb=" SG CYS Y 72 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 26 " - pdb=" SG CYS Y 110 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 34 " - pdb=" SG CYS Y 88 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 38 " - pdb=" SG CYS Y 90 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 93 " - pdb=" SG CYS Y 100 " distance=2.04 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: 2.57 Conformation dependent library (CDL) restraints added in 1.5 seconds 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2604 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 18 sheets defined 32.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 234 through 239 Processing helix chain 'A' and resid 254 through 268 Processing helix chain 'A' and resid 283 through 293 Processing helix chain 'A' and resid 297 through 302 removed outlier: 3.563A pdb=" N TYR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 306 Processing helix chain 'A' and resid 321 through 342 removed outlier: 3.637A pdb=" N ILE A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N SER A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 381 removed outlier: 3.600A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.631A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.526A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 241 through 245 removed outlier: 3.773A pdb=" N SER R 244 " --> pdb=" O GLY R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 261 through 265 Processing helix chain 'R' and resid 275 through 283 Processing helix chain 'R' and resid 359 through 373 removed outlier: 3.751A pdb=" N ARG R 363 " --> pdb=" O TYR R 359 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL R 364 " --> pdb=" O ASP R 360 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N TRP R 367 " --> pdb=" O ARG R 363 " (cutoff:3.500A) Processing helix chain 'R' and resid 374 through 386 Processing helix chain 'R' and resid 392 through 422 Processing helix chain 'R' and resid 425 through 435 removed outlier: 4.238A pdb=" N HIS R 429 " --> pdb=" O GLN R 425 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE R 431 " --> pdb=" O TYR R 427 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASP R 432 " --> pdb=" O ASN R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 436 through 470 removed outlier: 3.674A pdb=" N SER R 440 " --> pdb=" O GLY R 436 " (cutoff:3.500A) Processing helix chain 'R' and resid 479 through 498 Processing helix chain 'R' and resid 499 through 504 removed outlier: 3.671A pdb=" N GLY R 504 " --> pdb=" O PRO R 501 " (cutoff:3.500A) Processing helix chain 'R' and resid 521 through 554 Processing helix chain 'R' and resid 563 through 594 Proline residue: R 584 - end of helix Processing helix chain 'R' and resid 600 through 612 removed outlier: 3.634A pdb=" N LYS R 605 " --> pdb=" O VAL R 601 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL R 606 " --> pdb=" O THR R 602 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU R 607 " --> pdb=" O ASN R 603 " (cutoff:3.500A) Processing helix chain 'R' and resid 613 through 624 Proline residue: R 620 - end of helix Processing helix chain 'R' and resid 627 through 642 Processing helix chain 'X' and resid 40 through 45 removed outlier: 4.053A pdb=" N LYS X 45 " --> pdb=" O LEU X 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 213 through 214 removed outlier: 6.304A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 244 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE A 280 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 246 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N ASN A 282 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 248 " --> pdb=" O ASN A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.731A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.678A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 103 removed outlier: 3.869A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.666A pdb=" N SER B 160 " --> pdb=" O CYS B 148 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.669A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.614A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.698A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 53 through 57 removed outlier: 3.755A pdb=" N SER R 81 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLY R 220 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N THR R 197 " --> pdb=" O GLY R 220 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 53 through 57 removed outlier: 3.755A pdb=" N SER R 81 " --> pdb=" O LEU R 56 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE R 103 " --> pdb=" O SER R 129 " (cutoff:3.500A) removed outlier: 8.198A pdb=" N CYS R 131 " --> pdb=" O ILE R 103 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE R 105 " --> pdb=" O CYS R 131 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU R 128 " --> pdb=" O GLU R 154 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N CYS R 156 " --> pdb=" O LEU R 128 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE R 130 " --> pdb=" O CYS R 156 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL R 177 " --> pdb=" O LEU R 199 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER R 201 " --> pdb=" O VAL R 177 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N LEU R 227 " --> pdb=" O ILE R 249 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 63 through 64 removed outlier: 4.370A pdb=" N ILE R 89 " --> pdb=" O TYR R 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'R' and resid 163 through 164 removed outlier: 3.558A pdb=" N ILE R 164 " --> pdb=" O GLU R 188 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'R' and resid 271 through 272 removed outlier: 6.905A pdb=" N ALA R 271 " --> pdb=" O ALA R 344 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'X' and resid 11 through 14 removed outlier: 3.728A pdb=" N GLY X 30 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N CYS X 32 " --> pdb=" O CYS Y 38 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N CYS Y 38 " --> pdb=" O CYS X 32 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N CYS Y 34 " --> pdb=" O ALA X 36 " (cutoff:3.500A) removed outlier: 10.709A pdb=" N THR Y 32 " --> pdb=" O PRO X 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'X' and resid 11 through 14 Processing sheet with id=AB7, first strand: chain 'X' and resid 59 through 69 removed outlier: 6.031A pdb=" N CYS X 60 " --> pdb=" O CYS X 84 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N CYS X 84 " --> pdb=" O CYS X 60 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA X 62 " --> pdb=" O CYS X 82 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N CYS X 82 " --> pdb=" O ALA X 62 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N SER X 64 " --> pdb=" O THR X 80 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'X' and resid 91 through 92 removed outlier: 3.660A pdb=" N SER X 92 " --> pdb=" O CYS Y 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'Y' and resid 56 through 68 removed outlier: 5.657A pdb=" N CYS Y 57 " --> pdb=" O CYS Y 90 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N CYS Y 90 " --> pdb=" O CYS Y 57 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N TYR Y 59 " --> pdb=" O CYS Y 88 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N CYS Y 88 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASP Y 61 " --> pdb=" O LEU Y 86 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1308 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: 3.76 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 1762 1.25 - 1.40: 2700 1.40 - 1.54: 6355 1.54 - 1.68: 136 1.68 - 1.83: 123 Bond restraints: 11076 Sorted by residual: bond pdb=" C33 55Z R 801 " pdb=" C34 55Z R 801 " ideal model delta sigma weight residual 1.517 1.300 0.217 2.00e-02 2.50e+03 1.18e+02 bond pdb=" C30 55Z R 801 " pdb=" C31 55Z R 801 " ideal model delta sigma weight residual 1.516 1.319 0.197 2.00e-02 2.50e+03 9.67e+01 bond pdb=" C6 55Z R 801 " pdb=" O7 55Z R 801 " ideal model delta sigma weight residual 1.234 1.110 0.124 2.00e-02 2.50e+03 3.86e+01 bond pdb=" C8 55Z R 801 " pdb=" C9 55Z R 801 " ideal model delta sigma weight residual 1.382 1.271 0.111 2.00e-02 2.50e+03 3.07e+01 bond pdb=" C34 55Z R 801 " pdb=" N29 55Z R 801 " ideal model delta sigma weight residual 1.458 1.349 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 11071 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14914 3.37 - 6.74: 79 6.74 - 10.10: 17 10.10 - 13.47: 3 13.47 - 16.84: 2 Bond angle restraints: 15015 Sorted by residual: angle pdb=" N ARG A 255 " pdb=" CA ARG A 255 " pdb=" C ARG A 255 " ideal model delta sigma weight residual 112.38 98.44 13.94 1.22e+00 6.72e-01 1.31e+02 angle pdb=" CA ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 115.89 103.49 12.40 1.40e+00 5.10e-01 7.85e+01 angle pdb=" C13 55Z R 801 " pdb=" S17 55Z R 801 " pdb=" C18 55Z R 801 " ideal model delta sigma weight residual 102.86 119.70 -16.84 3.00e+00 1.11e-01 3.15e+01 angle pdb=" CA ASN A 254 " pdb=" C ASN A 254 " pdb=" O ASN A 254 " ideal model delta sigma weight residual 120.51 112.58 7.93 1.43e+00 4.89e-01 3.07e+01 angle pdb=" O ASP A 252 " pdb=" C ASP A 252 " pdb=" N TYR A 253 " ideal model delta sigma weight residual 122.43 128.93 -6.50 1.30e+00 5.92e-01 2.50e+01 ... (remaining 15010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6057 17.62 - 35.24: 530 35.24 - 52.85: 94 52.85 - 70.47: 18 70.47 - 88.09: 15 Dihedral angle restraints: 6714 sinusoidal: 2692 harmonic: 4022 Sorted by residual: dihedral pdb=" C ASN A 254 " pdb=" N ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual -122.60 -153.16 30.56 0 2.50e+00 1.60e-01 1.49e+02 dihedral pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CA ASN A 254 " pdb=" CB ASN A 254 " ideal model delta harmonic sigma weight residual 122.80 152.93 -30.13 0 2.50e+00 1.60e-01 1.45e+02 dihedral pdb=" CB CYS X 10 " pdb=" SG CYS X 10 " pdb=" SG CYS X 60 " pdb=" CB CYS X 60 " ideal model delta sinusoidal sigma weight residual 93.00 168.78 -75.78 1 1.00e+01 1.00e-02 7.24e+01 ... (remaining 6711 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.247: 1711 0.247 - 0.495: 2 0.495 - 0.742: 0 0.742 - 0.989: 0 0.989 - 1.236: 1 Chirality restraints: 1714 Sorted by residual: chirality pdb=" CA ASN A 254 " pdb=" N ASN A 254 " pdb=" C ASN A 254 " pdb=" CB ASN A 254 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.82e+01 chirality pdb=" CA ARG A 255 " pdb=" N ARG A 255 " pdb=" C ARG A 255 " pdb=" CB ARG A 255 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" CA CYS X 84 " pdb=" N CYS X 84 " pdb=" C CYS X 84 " pdb=" CB CYS X 84 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1711 not shown) Planarity restraints: 1917 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 252 " -0.034 2.00e-02 2.50e+03 7.69e-02 5.91e+01 pdb=" C ASP A 252 " 0.133 2.00e-02 2.50e+03 pdb=" O ASP A 252 " -0.055 2.00e-02 2.50e+03 pdb=" N TYR A 253 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU R 354 " 0.018 2.00e-02 2.50e+03 3.83e-02 1.47e+01 pdb=" CD GLU R 354 " -0.066 2.00e-02 2.50e+03 pdb=" OE1 GLU R 354 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU R 354 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 55Z R 801 " -0.005 2.00e-02 2.50e+03 1.78e-02 1.03e+01 pdb=" C11 55Z R 801 " -0.007 2.00e-02 2.50e+03 pdb=" C13 55Z R 801 " -0.015 2.00e-02 2.50e+03 pdb=" C15 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" C19 55Z R 801 " 0.021 2.00e-02 2.50e+03 pdb=" C6 55Z R 801 " 0.044 2.00e-02 2.50e+03 pdb=" C8 55Z R 801 " -0.025 2.00e-02 2.50e+03 pdb=" C9 55Z R 801 " -0.018 2.00e-02 2.50e+03 pdb=" N12 55Z R 801 " 0.004 2.00e-02 2.50e+03 pdb=" N14 55Z R 801 " -0.003 2.00e-02 2.50e+03 pdb=" N35 55Z R 801 " -0.013 2.00e-02 2.50e+03 pdb=" S16 55Z R 801 " -0.001 2.00e-02 2.50e+03 pdb=" S17 55Z R 801 " 0.017 2.00e-02 2.50e+03 ... (remaining 1914 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 114 2.55 - 3.14: 9019 3.14 - 3.72: 16588 3.72 - 4.31: 22348 4.31 - 4.90: 38527 Nonbonded interactions: 86596 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 1.962 3.040 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.079 3.040 nonbonded pdb=" O ASP R 518 " pdb=" OG SER R 524 " model vdw 2.114 3.040 nonbonded pdb=" OH TYR R 359 " pdb=" OD1 ASN R 603 " model vdw 2.128 3.040 nonbonded pdb=" ND2 ASN R 507 " pdb=" OD2 ASP R 518 " model vdw 2.160 3.120 ... (remaining 86591 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 28.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.005 0.217 11091 Z= 0.280 Angle : 0.766 16.837 15045 Z= 0.437 Chirality : 0.052 1.236 1714 Planarity : 0.005 0.077 1917 Dihedral : 13.977 88.091 4065 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.30 % Favored : 96.63 % Rotamer: Outliers : 0.17 % Allowed : 0.33 % Favored : 99.50 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.51 % 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: -0.18 (0.24), residues: 1365 helix: 1.38 (0.27), residues: 385 sheet: -1.69 (0.28), residues: 301 loop : -0.11 (0.26), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.005 0.001 HIS B 54 PHE 0.013 0.001 PHE B 234 TYR 0.032 0.001 TYR R 389 ARG 0.017 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.15466 ( 449) hydrogen bonds : angle 6.72350 ( 1308) SS BOND : bond 0.00532 ( 15) SS BOND : angle 2.26265 ( 30) covalent geometry : bond 0.00543 (11076) covalent geometry : angle 0.75976 (15015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 ASP cc_start: 0.7711 (t0) cc_final: 0.7453 (t0) REVERT: A 273 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7797 (ttm-80) REVERT: B 127 LYS cc_start: 0.7346 (mttp) cc_final: 0.6987 (mttp) REVERT: B 315 VAL cc_start: 0.8258 (t) cc_final: 0.8006 (p) REVERT: R 228 ASP cc_start: 0.7393 (t0) cc_final: 0.7172 (t0) REVERT: X 29 MET cc_start: 0.4549 (mtm) cc_final: 0.4333 (mtm) REVERT: X 46 THR cc_start: 0.7606 (m) cc_final: 0.7379 (t) REVERT: Y 7 PRO cc_start: 0.6142 (Cg_endo) cc_final: 0.5907 (Cg_exo) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.2917 time to fit residues: 115.4674 Evaluate side-chains 249 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS R 158 ASN ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN R 615 ASN Y 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.134697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.121678 restraints weight = 21493.341| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 2.59 r_work: 0.3687 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3687 r_free = 0.3687 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11091 Z= 0.172 Angle : 0.693 8.274 15045 Z= 0.362 Chirality : 0.047 0.180 1714 Planarity : 0.005 0.058 1917 Dihedral : 5.585 41.665 1526 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.75 % Allowed : 11.03 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: -0.01 (0.23), residues: 1365 helix: 1.60 (0.26), residues: 407 sheet: -1.42 (0.27), residues: 301 loop : -0.22 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.004 0.001 HIS B 183 PHE 0.014 0.002 PHE R 403 TYR 0.022 0.002 TYR R 389 ARG 0.006 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04531 ( 449) hydrogen bonds : angle 4.82876 ( 1308) SS BOND : bond 0.00498 ( 15) SS BOND : angle 1.57428 ( 30) covalent geometry : bond 0.00390 (11076) covalent geometry : angle 0.68963 (15015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 309 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7993 (tp30) cc_final: 0.7389 (tp30) REVERT: A 51 SER cc_start: 0.8243 (p) cc_final: 0.8014 (m) REVERT: A 249 ASP cc_start: 0.7980 (t70) cc_final: 0.7718 (t0) REVERT: A 262 ASP cc_start: 0.7943 (t0) cc_final: 0.7496 (t0) REVERT: A 265 SER cc_start: 0.8976 (t) cc_final: 0.8767 (t) REVERT: A 273 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8127 (ttm-80) REVERT: A 285 ASP cc_start: 0.7003 (p0) cc_final: 0.6204 (t0) REVERT: B 51 LEU cc_start: 0.8986 (mp) cc_final: 0.8785 (mp) REVERT: B 155 ASN cc_start: 0.8338 (t0) cc_final: 0.7456 (t0) REVERT: B 160 SER cc_start: 0.8424 (p) cc_final: 0.8223 (p) REVERT: B 163 ASP cc_start: 0.8096 (t70) cc_final: 0.7708 (t0) REVERT: B 175 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7422 (mm-40) REVERT: B 200 VAL cc_start: 0.9081 (m) cc_final: 0.8813 (p) REVERT: B 315 VAL cc_start: 0.8253 (t) cc_final: 0.7965 (p) REVERT: R 81 SER cc_start: 0.8639 (p) cc_final: 0.8272 (t) REVERT: R 108 THR cc_start: 0.8121 (m) cc_final: 0.7288 (p) REVERT: R 203 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7395 (mp0) REVERT: R 262 ARG cc_start: 0.7711 (tpt90) cc_final: 0.7506 (tpt90) REVERT: R 342 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7991 (ptp-110) REVERT: R 419 ASP cc_start: 0.7827 (t0) cc_final: 0.7546 (t0) REVERT: R 545 CYS cc_start: 0.7581 (m) cc_final: 0.7360 (m) REVERT: R 559 MET cc_start: 0.5854 (tpt) cc_final: 0.5295 (tpt) REVERT: R 571 MET cc_start: 0.7802 (mtp) cc_final: 0.7577 (mtp) outliers start: 21 outliers final: 9 residues processed: 316 average time/residue: 0.2622 time to fit residues: 112.5950 Evaluate side-chains 287 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 277 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 203 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 628 LYS Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 69 optimal weight: 0.0010 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 118 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 26 optimal weight: 0.0050 chunk 85 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 126 optimal weight: 0.0030 overall best weight: 0.3410 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.134783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121795 restraints weight = 21702.148| |-----------------------------------------------------------------------------| r_work (start): 0.3778 rms_B_bonded: 2.59 r_work: 0.3690 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3693 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11091 Z= 0.119 Angle : 0.616 9.530 15045 Z= 0.321 Chirality : 0.044 0.203 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.166 39.109 1524 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.51 % Allowed : 14.04 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.18 (0.23), residues: 1365 helix: 1.86 (0.26), residues: 408 sheet: -1.25 (0.28), residues: 299 loop : -0.22 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 267 HIS 0.006 0.001 HIS A 347 PHE 0.011 0.001 PHE R 186 TYR 0.014 0.001 TYR R 389 ARG 0.007 0.001 ARG R 342 Details of bonding type rmsd hydrogen bonds : bond 0.04138 ( 449) hydrogen bonds : angle 4.62300 ( 1308) SS BOND : bond 0.00278 ( 15) SS BOND : angle 1.62441 ( 30) covalent geometry : bond 0.00262 (11076) covalent geometry : angle 0.61206 (15015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.7946 (tp30) cc_final: 0.7375 (tp30) REVERT: A 233 LYS cc_start: 0.7281 (ttmm) cc_final: 0.7001 (tppp) REVERT: A 262 ASP cc_start: 0.7937 (t0) cc_final: 0.7603 (t0) REVERT: A 267 TRP cc_start: 0.8715 (t-100) cc_final: 0.8272 (t-100) REVERT: A 273 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7815 (ttm-80) REVERT: A 358 ASP cc_start: 0.7248 (t0) cc_final: 0.6970 (t0) REVERT: B 175 GLN cc_start: 0.7902 (mm-40) cc_final: 0.7473 (mm-40) REVERT: B 189 SER cc_start: 0.7852 (p) cc_final: 0.7366 (t) REVERT: B 214 ARG cc_start: 0.8159 (mtm-85) cc_final: 0.7916 (mtt90) REVERT: B 315 VAL cc_start: 0.8212 (t) cc_final: 0.7972 (p) REVERT: G 16 VAL cc_start: 0.7446 (t) cc_final: 0.7212 (p) REVERT: R 81 SER cc_start: 0.8586 (p) cc_final: 0.8317 (t) REVERT: R 108 THR cc_start: 0.8019 (m) cc_final: 0.7327 (p) REVERT: R 262 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7333 (tpt90) REVERT: R 377 ASN cc_start: 0.7332 (m-40) cc_final: 0.7041 (t0) REVERT: R 405 ASP cc_start: 0.8253 (m-30) cc_final: 0.7964 (t0) REVERT: R 632 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7775 (tmm-80) outliers start: 30 outliers final: 13 residues processed: 288 average time/residue: 0.2962 time to fit residues: 117.1396 Evaluate side-chains 285 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 271 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 632 ARG Chi-restraints excluded: chain X residue 84 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 183 HIS ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 400 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 = 0.3929 r_free = 0.3929 target = 0.133089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120047 restraints weight = 21288.923| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.65 r_work: 0.3662 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11091 Z= 0.130 Angle : 0.615 8.916 15045 Z= 0.319 Chirality : 0.044 0.194 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.102 35.759 1524 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.59 % Allowed : 16.04 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.26 (0.23), residues: 1365 helix: 2.00 (0.26), residues: 402 sheet: -1.20 (0.28), residues: 298 loop : -0.21 (0.25), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 267 HIS 0.007 0.001 HIS A 347 PHE 0.026 0.001 PHE R 493 TYR 0.014 0.001 TYR R 389 ARG 0.005 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 449) hydrogen bonds : angle 4.41711 ( 1308) SS BOND : bond 0.00275 ( 15) SS BOND : angle 1.49676 ( 30) covalent geometry : bond 0.00296 (11076) covalent geometry : angle 0.61157 (15015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 266 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8001 (tp30) cc_final: 0.7352 (tp30) REVERT: A 262 ASP cc_start: 0.8018 (t0) cc_final: 0.7677 (t0) REVERT: A 267 TRP cc_start: 0.8745 (t-100) cc_final: 0.8171 (t-100) REVERT: A 273 ARG cc_start: 0.8336 (ttm-80) cc_final: 0.8048 (ttm-80) REVERT: A 333 ASP cc_start: 0.8324 (t0) cc_final: 0.7950 (t0) REVERT: A 358 ASP cc_start: 0.7296 (t0) cc_final: 0.7055 (t0) REVERT: A 360 GLU cc_start: 0.8004 (mp0) cc_final: 0.7541 (mp0) REVERT: B 163 ASP cc_start: 0.8087 (t70) cc_final: 0.7638 (t0) REVERT: B 164 THR cc_start: 0.8128 (p) cc_final: 0.7863 (p) REVERT: B 175 GLN cc_start: 0.8004 (mm-40) cc_final: 0.7533 (mm-40) REVERT: B 189 SER cc_start: 0.8126 (p) cc_final: 0.7574 (t) REVERT: B 214 ARG cc_start: 0.8267 (mtm-85) cc_final: 0.8000 (mtt90) REVERT: B 291 ASP cc_start: 0.7079 (t0) cc_final: 0.6867 (t0) REVERT: B 315 VAL cc_start: 0.8124 (t) cc_final: 0.7872 (p) REVERT: R 108 THR cc_start: 0.8056 (m) cc_final: 0.7361 (p) REVERT: R 136 ARG cc_start: 0.5297 (mpt180) cc_final: 0.4979 (mmt180) REVERT: R 262 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7273 (tpt90) REVERT: R 398 MET cc_start: 0.7979 (tpp) cc_final: 0.7632 (tpp) REVERT: R 582 MET cc_start: 0.7592 (tmm) cc_final: 0.7376 (tmm) REVERT: R 632 ARG cc_start: 0.8268 (OUTLIER) cc_final: 0.8016 (tmm-80) REVERT: X 46 THR cc_start: 0.7941 (OUTLIER) cc_final: 0.7480 (t) outliers start: 31 outliers final: 16 residues processed: 276 average time/residue: 0.2576 time to fit residues: 95.5003 Evaluate side-chains 271 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 520 GLU Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 632 ARG Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 33 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 84 optimal weight: 0.0040 chunk 115 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.5574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.132080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119301 restraints weight = 21153.691| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.56 r_work: 0.3656 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3659 r_free = 0.3659 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11091 Z= 0.129 Angle : 0.637 11.473 15045 Z= 0.328 Chirality : 0.045 0.204 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.083 37.220 1524 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.34 % Allowed : 18.21 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.26 (0.23), residues: 1365 helix: 2.02 (0.26), residues: 404 sheet: -1.20 (0.28), residues: 300 loop : -0.23 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.027 0.001 PHE R 493 TYR 0.016 0.001 TYR R 389 ARG 0.005 0.001 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 449) hydrogen bonds : angle 4.27651 ( 1308) SS BOND : bond 0.00286 ( 15) SS BOND : angle 2.24108 ( 30) covalent geometry : bond 0.00292 (11076) covalent geometry : angle 0.62951 (15015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 264 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7338 (ttm) cc_final: 0.6896 (mtt) REVERT: A 27 GLU cc_start: 0.7997 (tp30) cc_final: 0.7305 (tp30) REVERT: A 262 ASP cc_start: 0.7997 (t0) cc_final: 0.7706 (t0) REVERT: A 267 TRP cc_start: 0.8663 (t-100) cc_final: 0.8247 (t-100) REVERT: A 273 ARG cc_start: 0.8278 (ttm-80) cc_final: 0.8031 (ttm-80) REVERT: A 360 GLU cc_start: 0.7983 (mp0) cc_final: 0.7561 (mp0) REVERT: A 375 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7493 (mtm-85) REVERT: A 379 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7331 (mtm110) REVERT: B 130 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6300 (mt-10) REVERT: B 155 ASN cc_start: 0.8372 (t0) cc_final: 0.7472 (t0) REVERT: B 175 GLN cc_start: 0.8039 (mm-40) cc_final: 0.7547 (mm-40) REVERT: B 189 SER cc_start: 0.7987 (p) cc_final: 0.7490 (t) REVERT: B 254 ASP cc_start: 0.7815 (t0) cc_final: 0.7583 (t0) REVERT: B 315 VAL cc_start: 0.8096 (t) cc_final: 0.7848 (p) REVERT: R 108 THR cc_start: 0.7944 (m) cc_final: 0.7236 (p) REVERT: R 253 SER cc_start: 0.8552 (t) cc_final: 0.8315 (t) REVERT: R 262 ARG cc_start: 0.7753 (tpt90) cc_final: 0.7319 (tpt90) REVERT: R 375 MET cc_start: 0.7098 (mmm) cc_final: 0.6870 (mmm) REVERT: R 398 MET cc_start: 0.7955 (tpp) cc_final: 0.7708 (tpp) REVERT: R 487 MET cc_start: 0.7815 (mmm) cc_final: 0.7479 (mmm) REVERT: R 632 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7962 (tmm-80) REVERT: X 76 VAL cc_start: 0.6720 (t) cc_final: 0.6329 (p) outliers start: 28 outliers final: 20 residues processed: 276 average time/residue: 0.2679 time to fit residues: 100.2219 Evaluate side-chains 271 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 249 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 632 ARG Chi-restraints excluded: chain X residue 46 THR Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 131 optimal weight: 0.2980 chunk 122 optimal weight: 0.0980 chunk 88 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 156 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 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 = 0.3908 r_free = 0.3908 target = 0.131346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.118615 restraints weight = 21320.271| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.58 r_work: 0.3643 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3647 r_free = 0.3647 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11091 Z= 0.128 Angle : 0.636 10.783 15045 Z= 0.326 Chirality : 0.044 0.184 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.013 34.006 1524 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.51 % Allowed : 19.38 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.31 (0.23), residues: 1365 helix: 2.12 (0.26), residues: 404 sheet: -1.17 (0.28), residues: 305 loop : -0.24 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.026 0.001 PHE R 493 TYR 0.023 0.001 TYR B 105 ARG 0.006 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04024 ( 449) hydrogen bonds : angle 4.22938 ( 1308) SS BOND : bond 0.00250 ( 15) SS BOND : angle 2.14226 ( 30) covalent geometry : bond 0.00291 (11076) covalent geometry : angle 0.62938 (15015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.7318 (ttm) cc_final: 0.6901 (mtt) REVERT: A 27 GLU cc_start: 0.8017 (tp30) cc_final: 0.7344 (tp30) REVERT: A 262 ASP cc_start: 0.7970 (t0) cc_final: 0.7667 (t0) REVERT: A 267 TRP cc_start: 0.8647 (t-100) cc_final: 0.8311 (t-100) REVERT: A 273 ARG cc_start: 0.8202 (ttm-80) cc_final: 0.7954 (ttm-80) REVERT: A 360 GLU cc_start: 0.7848 (mp0) cc_final: 0.7529 (mp0) REVERT: B 130 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6306 (mt-10) REVERT: B 155 ASN cc_start: 0.8395 (t0) cc_final: 0.8099 (t0) REVERT: B 189 SER cc_start: 0.8034 (p) cc_final: 0.7571 (t) REVERT: B 254 ASP cc_start: 0.7834 (t0) cc_final: 0.7618 (t70) REVERT: B 315 VAL cc_start: 0.8059 (t) cc_final: 0.7796 (p) REVERT: R 108 THR cc_start: 0.7808 (m) cc_final: 0.7147 (p) REVERT: R 253 SER cc_start: 0.8627 (t) cc_final: 0.8409 (t) REVERT: R 262 ARG cc_start: 0.7682 (tpt90) cc_final: 0.7221 (tpt90) REVERT: R 487 MET cc_start: 0.7696 (mmm) cc_final: 0.7347 (mmm) REVERT: R 632 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7960 (tmm-80) REVERT: X 76 VAL cc_start: 0.6892 (t) cc_final: 0.6491 (p) outliers start: 30 outliers final: 21 residues processed: 271 average time/residue: 0.2875 time to fit residues: 105.2873 Evaluate side-chains 273 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 251 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 381 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 632 ARG Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain X residue 47 MET Chi-restraints excluded: chain Y residue 26 CYS Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 46 optimal weight: 0.8980 chunk 80 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.0370 chunk 24 optimal weight: 1.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.117959 restraints weight = 21568.633| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.60 r_work: 0.3624 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3626 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3626 r_free = 0.3626 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3626 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11091 Z= 0.132 Angle : 0.650 10.167 15045 Z= 0.334 Chirality : 0.045 0.175 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.138 49.594 1524 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.42 % Allowed : 19.30 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.29 (0.23), residues: 1365 helix: 2.17 (0.26), residues: 398 sheet: -1.10 (0.29), residues: 294 loop : -0.35 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 169 HIS 0.003 0.001 HIS X 83 PHE 0.026 0.001 PHE R 493 TYR 0.019 0.001 TYR B 105 ARG 0.012 0.001 ARG A 346 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 449) hydrogen bonds : angle 4.23274 ( 1308) SS BOND : bond 0.00278 ( 15) SS BOND : angle 2.19531 ( 30) covalent geometry : bond 0.00301 (11076) covalent geometry : angle 0.64323 (15015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 276 time to evaluate : 1.325 Fit side-chains REVERT: A 25 MET cc_start: 0.7306 (ttm) cc_final: 0.6908 (mtt) REVERT: A 27 GLU cc_start: 0.8084 (tp30) cc_final: 0.7374 (tp30) REVERT: A 262 ASP cc_start: 0.8040 (t0) cc_final: 0.7714 (t0) REVERT: A 267 TRP cc_start: 0.8643 (t-100) cc_final: 0.8248 (t-100) REVERT: A 270 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7726 (ttp80) REVERT: A 273 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7927 (ttm-80) REVERT: A 358 ASP cc_start: 0.6555 (t0) cc_final: 0.6328 (t0) REVERT: A 360 GLU cc_start: 0.7848 (mp0) cc_final: 0.7627 (mp0) REVERT: B 130 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6411 (mt-10) REVERT: B 155 ASN cc_start: 0.8378 (t0) cc_final: 0.7735 (t0) REVERT: B 163 ASP cc_start: 0.8088 (t70) cc_final: 0.7710 (t0) REVERT: B 189 SER cc_start: 0.8062 (p) cc_final: 0.7620 (t) REVERT: B 315 VAL cc_start: 0.7967 (t) cc_final: 0.7679 (p) REVERT: G 58 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7265 (mp0) REVERT: R 108 THR cc_start: 0.7817 (OUTLIER) cc_final: 0.7189 (p) REVERT: R 253 SER cc_start: 0.8765 (t) cc_final: 0.8266 (p) REVERT: R 262 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7239 (tpt90) REVERT: R 407 CYS cc_start: 0.8077 (m) cc_final: 0.7871 (t) REVERT: R 487 MET cc_start: 0.7828 (mmm) cc_final: 0.7433 (mmm) REVERT: R 520 GLU cc_start: 0.8247 (mp0) cc_final: 0.7827 (mp0) REVERT: R 632 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7975 (tmm-80) REVERT: Y 72 CYS cc_start: -0.0700 (OUTLIER) cc_final: -0.1127 (p) outliers start: 29 outliers final: 20 residues processed: 288 average time/residue: 0.2629 time to fit residues: 102.4860 Evaluate side-chains 290 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 267 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain R residue 632 ARG Chi-restraints excluded: chain X residue 12 LEU Chi-restraints excluded: chain Y residue 72 CYS Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 59 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 84 optimal weight: 0.3980 chunk 126 optimal weight: 8.9990 chunk 49 optimal weight: 0.0470 chunk 124 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 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 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 106 GLN ** R 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 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 = 0.3883 r_free = 0.3883 target = 0.129637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.116885 restraints weight = 21398.718| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.60 r_work: 0.3620 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3622 r_free = 0.3622 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11091 Z= 0.130 Angle : 0.651 9.901 15045 Z= 0.334 Chirality : 0.044 0.178 1714 Planarity : 0.004 0.056 1917 Dihedral : 5.077 48.982 1524 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.84 % Allowed : 20.55 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.27 (0.23), residues: 1365 helix: 2.07 (0.26), residues: 404 sheet: -1.05 (0.29), residues: 293 loop : -0.35 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.004 0.001 HIS A 347 PHE 0.023 0.001 PHE R 493 TYR 0.018 0.001 TYR R 389 ARG 0.009 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04019 ( 449) hydrogen bonds : angle 4.24860 ( 1308) SS BOND : bond 0.00254 ( 15) SS BOND : angle 2.00955 ( 30) covalent geometry : bond 0.00295 (11076) covalent geometry : angle 0.64499 (15015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 284 time to evaluate : 1.071 Fit side-chains revert: symmetry clash REVERT: A 25 MET cc_start: 0.7305 (ttm) cc_final: 0.6910 (mtt) REVERT: A 27 GLU cc_start: 0.8124 (tp30) cc_final: 0.7447 (tp30) REVERT: A 229 ASP cc_start: 0.8305 (p0) cc_final: 0.8031 (p0) REVERT: A 262 ASP cc_start: 0.8078 (t0) cc_final: 0.7752 (t0) REVERT: A 267 TRP cc_start: 0.8657 (t-100) cc_final: 0.8278 (t-100) REVERT: A 270 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7667 (ttp80) REVERT: A 273 ARG cc_start: 0.8189 (ttm-80) cc_final: 0.7979 (ttm-80) REVERT: A 358 ASP cc_start: 0.6653 (t0) cc_final: 0.6432 (t0) REVERT: A 360 GLU cc_start: 0.7860 (mp0) cc_final: 0.7654 (mp0) REVERT: B 130 GLU cc_start: 0.6929 (mm-30) cc_final: 0.6431 (mt-10) REVERT: B 155 ASN cc_start: 0.8459 (t0) cc_final: 0.8088 (t0) REVERT: B 163 ASP cc_start: 0.8158 (t70) cc_final: 0.7704 (t0) REVERT: B 164 THR cc_start: 0.7964 (p) cc_final: 0.7545 (p) REVERT: B 189 SER cc_start: 0.8072 (p) cc_final: 0.7632 (t) REVERT: B 315 VAL cc_start: 0.7958 (t) cc_final: 0.7675 (p) REVERT: G 58 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7267 (mp0) REVERT: R 108 THR cc_start: 0.7798 (OUTLIER) cc_final: 0.7177 (p) REVERT: R 136 ARG cc_start: 0.4908 (mmt-90) cc_final: 0.4669 (mmt180) REVERT: R 143 LYS cc_start: 0.4023 (pttt) cc_final: 0.3580 (pttm) REVERT: R 253 SER cc_start: 0.8803 (t) cc_final: 0.8304 (p) REVERT: R 262 ARG cc_start: 0.7727 (tpt90) cc_final: 0.7253 (tpt90) REVERT: R 405 ASP cc_start: 0.7654 (t70) cc_final: 0.7355 (t70) REVERT: R 407 CYS cc_start: 0.8096 (m) cc_final: 0.7866 (t) REVERT: R 484 ILE cc_start: 0.8587 (mm) cc_final: 0.8141 (tp) REVERT: R 520 GLU cc_start: 0.8287 (mp0) cc_final: 0.7737 (mp0) outliers start: 34 outliers final: 24 residues processed: 301 average time/residue: 0.2967 time to fit residues: 120.3918 Evaluate side-chains 303 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 278 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 607 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 619 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 = 0.3857 r_free = 0.3857 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115509 restraints weight = 21338.268| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.58 r_work: 0.3585 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3587 r_free = 0.3587 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.4560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11091 Z= 0.164 Angle : 0.697 12.373 15045 Z= 0.354 Chirality : 0.046 0.178 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.265 49.837 1524 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.84 % Allowed : 21.05 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.20 (0.23), residues: 1365 helix: 2.09 (0.26), residues: 398 sheet: -1.17 (0.29), residues: 292 loop : -0.39 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.005 0.001 HIS A 377 PHE 0.023 0.001 PHE R 493 TYR 0.025 0.002 TYR R 546 ARG 0.010 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 449) hydrogen bonds : angle 4.32938 ( 1308) SS BOND : bond 0.00294 ( 15) SS BOND : angle 2.13659 ( 30) covalent geometry : bond 0.00380 (11076) covalent geometry : angle 0.69069 (15015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 280 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7415 (ttm) cc_final: 0.7037 (mtt) REVERT: A 27 GLU cc_start: 0.8233 (tp30) cc_final: 0.8000 (tp30) REVERT: A 262 ASP cc_start: 0.8133 (t0) cc_final: 0.7785 (t0) REVERT: A 267 TRP cc_start: 0.8713 (t-100) cc_final: 0.8293 (t-100) REVERT: A 270 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7741 (ttp80) REVERT: A 273 ARG cc_start: 0.8276 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: B 130 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6484 (mt-10) REVERT: B 155 ASN cc_start: 0.8513 (t0) cc_final: 0.7699 (t0) REVERT: B 163 ASP cc_start: 0.8201 (t70) cc_final: 0.7812 (t0) REVERT: B 189 SER cc_start: 0.8081 (p) cc_final: 0.7647 (t) REVERT: B 291 ASP cc_start: 0.7013 (t0) cc_final: 0.6788 (t70) REVERT: B 315 VAL cc_start: 0.7987 (t) cc_final: 0.7723 (p) REVERT: G 58 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7286 (mp0) REVERT: R 108 THR cc_start: 0.7944 (m) cc_final: 0.7372 (p) REVERT: R 143 LYS cc_start: 0.4168 (pttt) cc_final: 0.3737 (pttm) REVERT: R 253 SER cc_start: 0.8901 (t) cc_final: 0.8433 (p) REVERT: R 262 ARG cc_start: 0.7758 (tpt90) cc_final: 0.7250 (tpt90) REVERT: R 357 MET cc_start: 0.7612 (mmm) cc_final: 0.7383 (mmp) REVERT: R 520 GLU cc_start: 0.8315 (mp0) cc_final: 0.7861 (mp0) outliers start: 34 outliers final: 27 residues processed: 295 average time/residue: 0.2683 time to fit residues: 107.9725 Evaluate side-chains 302 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 1.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 243 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 388 ARG Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 573 ILE Chi-restraints excluded: chain R residue 607 LEU Chi-restraints excluded: chain R residue 622 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Y residue 92 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 7.9990 chunk 41 optimal weight: 0.0870 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 69 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.116656 restraints weight = 21127.480| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.58 r_work: 0.3599 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3602 r_free = 0.3602 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11091 Z= 0.138 Angle : 0.682 12.036 15045 Z= 0.346 Chirality : 0.045 0.177 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.179 47.579 1524 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.17 % Allowed : 22.47 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.22 (0.23), residues: 1365 helix: 2.11 (0.26), residues: 397 sheet: -1.26 (0.29), residues: 296 loop : -0.31 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.022 0.001 PHE R 493 TYR 0.018 0.001 TYR B 105 ARG 0.010 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 449) hydrogen bonds : angle 4.31980 ( 1308) SS BOND : bond 0.00261 ( 15) SS BOND : angle 2.08132 ( 30) covalent geometry : bond 0.00318 (11076) covalent geometry : angle 0.67600 (15015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2730 Ramachandran restraints generated. 1365 Oldfield, 0 Emsley, 1365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 277 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.7407 (ttm) cc_final: 0.7034 (mtt) REVERT: A 27 GLU cc_start: 0.8225 (tp30) cc_final: 0.8006 (tp30) REVERT: A 262 ASP cc_start: 0.8057 (t0) cc_final: 0.7715 (t0) REVERT: A 267 TRP cc_start: 0.8655 (t-100) cc_final: 0.8281 (t-100) REVERT: A 273 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7981 (ttm-80) REVERT: A 285 ASP cc_start: 0.7058 (p0) cc_final: 0.6653 (p0) REVERT: A 360 GLU cc_start: 0.7865 (mp0) cc_final: 0.7632 (mp0) REVERT: A 382 GLU cc_start: 0.7428 (mp0) cc_final: 0.7205 (mp0) REVERT: B 86 THR cc_start: 0.8445 (p) cc_final: 0.8235 (p) REVERT: B 130 GLU cc_start: 0.7043 (mm-30) cc_final: 0.6521 (mt-10) REVERT: B 155 ASN cc_start: 0.8516 (t0) cc_final: 0.7685 (t0) REVERT: B 163 ASP cc_start: 0.8187 (t70) cc_final: 0.7717 (t0) REVERT: B 164 THR cc_start: 0.8115 (p) cc_final: 0.7750 (p) REVERT: B 189 SER cc_start: 0.8061 (p) cc_final: 0.7628 (t) REVERT: B 228 ASP cc_start: 0.8540 (p0) cc_final: 0.8308 (p0) REVERT: B 315 VAL cc_start: 0.7951 (t) cc_final: 0.7678 (p) REVERT: G 58 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7322 (mp0) REVERT: R 108 THR cc_start: 0.7900 (OUTLIER) cc_final: 0.7336 (p) REVERT: R 143 LYS cc_start: 0.3863 (pttt) cc_final: 0.3427 (pttm) REVERT: R 206 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8014 (mt-10) REVERT: R 253 SER cc_start: 0.8882 (t) cc_final: 0.8420 (p) REVERT: R 262 ARG cc_start: 0.7754 (tpt90) cc_final: 0.7305 (tpt90) REVERT: R 357 MET cc_start: 0.7445 (mmm) cc_final: 0.7227 (mmp) REVERT: R 407 CYS cc_start: 0.8138 (m) cc_final: 0.7917 (t) REVERT: R 484 ILE cc_start: 0.8571 (mm) cc_final: 0.8142 (tp) REVERT: R 520 GLU cc_start: 0.8256 (mp0) cc_final: 0.7862 (mp0) outliers start: 26 outliers final: 22 residues processed: 290 average time/residue: 0.3109 time to fit residues: 123.1106 Evaluate side-chains 287 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 264 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain A residue 254 ASN Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 54 HIS Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 130 ILE Chi-restraints excluded: chain R residue 131 CYS Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 263 GLU Chi-restraints excluded: chain R residue 269 LEU Chi-restraints excluded: chain R residue 474 LEU Chi-restraints excluded: chain R residue 509 MET Chi-restraints excluded: chain R residue 522 THR Chi-restraints excluded: chain R residue 607 LEU Chi-restraints excluded: chain X residue 55 SER Chi-restraints excluded: chain Y residue 48 VAL Chi-restraints excluded: chain Y residue 54 GLN Chi-restraints excluded: chain Y residue 76 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 20 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 0.0970 chunk 38 optimal weight: 0.8980 chunk 84 optimal weight: 0.0170 overall best weight: 0.6016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN B 44 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 ASN ** R 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 476 GLN ** R 619 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.128839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.116463 restraints weight = 21258.296| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.64 r_work: 0.3595 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3598 r_free = 0.3598 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11091 Z= 0.140 Angle : 0.687 11.901 15045 Z= 0.351 Chirality : 0.045 0.174 1714 Planarity : 0.004 0.057 1917 Dihedral : 5.216 51.873 1524 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.17 % Allowed : 22.39 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.51 % 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: 0.19 (0.23), residues: 1365 helix: 2.12 (0.26), residues: 397 sheet: -1.28 (0.29), residues: 296 loop : -0.35 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.022 0.001 PHE R 493 TYR 0.017 0.001 TYR B 105 ARG 0.010 0.001 ARG A 307 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 449) hydrogen bonds : angle 4.32679 ( 1308) SS BOND : bond 0.00276 ( 15) SS BOND : angle 2.04924 ( 30) covalent geometry : bond 0.00325 (11076) covalent geometry : angle 0.68199 (15015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6247.89 seconds wall clock time: 111 minutes 9.23 seconds (6669.23 seconds total)