Starting phenix.real_space_refine on Sat Jun 14 16:26:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cxh_27056/06_2025/8cxh_27056.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cxh_27056/06_2025/8cxh_27056.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/8cxh_27056/06_2025/8cxh_27056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cxh_27056/06_2025/8cxh_27056.map" model { file = "/net/cci-nas-00/data/ceres_data/8cxh_27056/06_2025/8cxh_27056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cxh_27056/06_2025/8cxh_27056.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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 10511 2.51 5 N 2866 2.21 5 O 3147 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16634 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3714 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} Chain breaks: 1 Chain: "D" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 3714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3714 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 16, 'TRANS': 474} Chain breaks: 1 Chain: "E" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "h" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "l" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 787 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "C" Number of atoms: 3790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 501, 3790 Classifications: {'peptide': 501} Link IDs: {'PTRANS': 16, 'TRANS': 484} Chain: "F" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 600 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Time building chain proxies: 9.58, per 1000 atoms: 0.58 Number of scatterers: 16634 At special positions: 0 Unit cell: (106, 202.46, 120.84, 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 110 16.00 O 3147 8.00 N 2866 7.00 C 10511 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=19, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.02 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 190 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 339 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=1.69 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 190 " - pdb=" SG CYS B 291 " distance=1.75 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 339 " distance=2.03 Simple disulfide: pdb=" SG CYS h 22 " - pdb=" SG CYS h 92 " distance=2.03 Simple disulfide: pdb=" SG CYS l 23 " - pdb=" SG CYS l 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.02 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.50 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 190 " - pdb=" SG CYS C 291 " distance=1.85 Simple disulfide: pdb=" SG CYS C 308 " - pdb=" SG CYS C 339 " distance=1.47 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.00 Conformation dependent library (CDL) restraints added in 2.2 seconds 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3922 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 30 sheets defined 23.0% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.84 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.868A pdb=" N SER A 86 " --> pdb=" O ASP A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 269 removed outlier: 3.583A pdb=" N THR A 267 " --> pdb=" O GLY A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 425 Processing helix chain 'A' and resid 426 through 431 removed outlier: 3.545A pdb=" N PHE A 431 " --> pdb=" O ALA A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 457 Processing helix chain 'A' and resid 463 through 479 Processing helix chain 'A' and resid 483 through 500 Processing helix chain 'D' and resid 6 through 11 removed outlier: 4.004A pdb=" N THR D 9 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 11 " --> pdb=" O SER D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 39 Processing helix chain 'D' and resid 40 through 53 Processing helix chain 'D' and resid 56 through 74 Proline residue: D 72 - end of helix Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.719A pdb=" N GLN H 64 " --> pdb=" O GLN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'B' and resid 3 through 7 removed outlier: 4.631A pdb=" N SER B 7 " --> pdb=" O ILE B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 86 removed outlier: 3.859A pdb=" N SER B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.549A pdb=" N VAL B 265 " --> pdb=" O GLN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 425 Processing helix chain 'B' and resid 426 through 431 Processing helix chain 'B' and resid 437 through 457 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 482 through 501 removed outlier: 4.351A pdb=" N LEU B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA B 501 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.560A pdb=" N LYS E 11 " --> pdb=" O SER E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 Processing helix chain 'E' and resid 40 through 52 removed outlier: 3.997A pdb=" N LEU E 44 " --> pdb=" O PRO E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 Processing helix chain 'h' and resid 28 through 30 No H-bonds generated for 'chain 'h' and resid 28 through 30' Processing helix chain 'h' and resid 61 through 64 removed outlier: 3.552A pdb=" N GLN h 64 " --> pdb=" O GLN h 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 61 through 64' Processing helix chain 'h' and resid 83 through 87 Processing helix chain 'C' and resid 82 through 86 removed outlier: 3.649A pdb=" N SER C 86 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 153 removed outlier: 3.538A pdb=" N ILE C 152 " --> pdb=" O SER C 149 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N VAL C 153 " --> pdb=" O GLY C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 263 through 269 Processing helix chain 'C' and resid 405 through 425 Processing helix chain 'C' and resid 426 through 431 removed outlier: 3.670A pdb=" N PHE C 431 " --> pdb=" O ALA C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 457 Processing helix chain 'C' and resid 461 through 479 Processing helix chain 'C' and resid 483 through 500 Processing helix chain 'F' and resid 6 through 11 removed outlier: 3.945A pdb=" N THR F 9 " --> pdb=" O SER F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 39 Processing helix chain 'F' and resid 40 through 53 removed outlier: 3.971A pdb=" N LEU F 44 " --> pdb=" O PRO F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 71 Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.509A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N MET A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL A 12 " --> pdb=" O MET A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 41 through 50 current: chain 'A' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 110 through 129 current: chain 'A' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 164 through 169 current: chain 'A' and resid 210 through 214 removed outlier: 4.078A pdb=" N HIS A 210 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 26 removed outlier: 4.332A pdb=" N LYS A 290 " --> pdb=" O GLU A 191 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASP A 296 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N SER A 185 " --> pdb=" O ASP A 296 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 243 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 312 through 314 current: chain 'A' and resid 326 through 332 Processing sheet with id=AA5, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N TYR H 32 " --> pdb=" O ASN H 52 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 18 through 20 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 12 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 96 through 98 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 11 removed outlier: 6.556A pdb=" N ASP B 10 " --> pdb=" O THR B 32 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 41 through 50 current: chain 'B' and resid 126 through 129 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 126 through 129 current: chain 'B' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 164 through 169 current: chain 'B' and resid 210 through 214 removed outlier: 3.964A pdb=" N HIS B 210 " --> pdb=" O ALA B 275 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 281 " --> pdb=" O ASP B 278 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.438A pdb=" N ASP B 296 " --> pdb=" O SER B 185 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N SER B 185 " --> pdb=" O ASP B 296 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 58 through 59 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 73 removed outlier: 5.031A pdb=" N ILE B 65 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 120 " --> pdb=" O ILE B 65 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ASP B 67 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS B 118 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 112 " --> pdb=" O ARG B 73 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 243 through 247 Processing sheet with id=AB8, first strand: chain 'B' and resid 312 through 320 removed outlier: 6.761A pdb=" N THR B 315 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N GLN B 331 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N ILE B 317 " --> pdb=" O GLU B 329 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLU B 329 " --> pdb=" O ILE B 317 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'B' and resid 353 through 354 removed outlier: 4.582A pdb=" N THR B 353 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL B 347 " --> pdb=" O THR B 353 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'h' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'h' and resid 10 through 12 removed outlier: 7.443A pdb=" N TYR h 32 " --> pdb=" O ASN h 52 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASN h 52 " --> pdb=" O TYR h 32 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N MET h 34 " --> pdb=" O TRP h 50 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N TRP h 50 " --> pdb=" O MET h 34 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N TRP h 36 " --> pdb=" O MET h 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC5, first strand: chain 'l' and resid 9 through 12 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 9 through 12 current: chain 'l' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'l' and resid 45 through 48 current: chain 'l' and resid 96 through 98 No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'l' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'C' and resid 10 through 13 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 41 through 50 current: chain 'C' and resid 110 through 129 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 110 through 129 current: chain 'C' and resid 164 through 169 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 164 through 169 current: chain 'C' and resid 210 through 214 removed outlier: 4.346A pdb=" N HIS C 210 " --> pdb=" O ALA C 275 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU C 273 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 21 through 26 removed outlier: 5.398A pdb=" N ASP C 296 " --> pdb=" O SER C 185 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER C 185 " --> pdb=" O ASP C 296 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 243 through 246 Processing sheet with id=AD1, first strand: chain 'C' and resid 312 through 314 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 312 through 314 current: chain 'C' and resid 326 through 332 Processing sheet with id=AD2, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AD3, first strand: chain 'C' and resid 353 through 355 removed outlier: 4.646A pdb=" N THR C 353 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N VAL C 347 " --> pdb=" O THR C 353 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET C 345 " --> pdb=" O VAL C 355 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1557 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: 4.91 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.27: 2706 1.27 - 1.42: 4401 1.42 - 1.56: 9726 1.56 - 1.71: 0 1.71 - 1.86: 173 Bond restraints: 17006 Sorted by residual: bond pdb=" CA ASN C 238 " pdb=" C ASN C 238 " ideal model delta sigma weight residual 1.526 1.378 0.148 9.20e-03 1.18e+04 2.58e+02 bond pdb=" C ASN C 238 " pdb=" O ASN C 238 " ideal model delta sigma weight residual 1.234 1.121 0.113 8.30e-03 1.45e+04 1.86e+02 bond pdb=" CA HIS C 249 " pdb=" C HIS C 249 " ideal model delta sigma weight residual 1.524 1.408 0.115 1.35e-02 5.49e+03 7.28e+01 bond pdb=" CA ARG C 252 " pdb=" C ARG C 252 " ideal model delta sigma weight residual 1.527 1.449 0.079 9.80e-03 1.04e+04 6.43e+01 bond pdb=" C ARG C 252 " pdb=" O ARG C 252 " ideal model delta sigma weight residual 1.238 1.154 0.083 1.06e-02 8.90e+03 6.20e+01 ... (remaining 17001 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 22818 3.42 - 6.83: 195 6.83 - 10.25: 21 10.25 - 13.67: 7 13.67 - 17.08: 5 Bond angle restraints: 23046 Sorted by residual: angle pdb=" N LYS C 251 " pdb=" CA LYS C 251 " pdb=" C LYS C 251 " ideal model delta sigma weight residual 111.36 123.90 -12.54 1.09e+00 8.42e-01 1.32e+02 angle pdb=" C ASN C 362 " pdb=" N PRO C 363 " pdb=" CA PRO C 363 " ideal model delta sigma weight residual 119.84 107.84 12.00 1.25e+00 6.40e-01 9.21e+01 angle pdb=" N THR C 360 " pdb=" CA THR C 360 " pdb=" C THR C 360 " ideal model delta sigma weight residual 107.20 92.33 14.87 1.70e+00 3.46e-01 7.65e+01 angle pdb=" CA TRP C 101 " pdb=" CB TRP C 101 " pdb=" CG TRP C 101 " ideal model delta sigma weight residual 113.60 129.36 -15.76 1.90e+00 2.77e-01 6.88e+01 angle pdb=" N PHE B 463 " pdb=" CA PHE B 463 " pdb=" C PHE B 463 " ideal model delta sigma weight residual 112.72 102.26 10.46 1.28e+00 6.10e-01 6.68e+01 ... (remaining 23041 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 9203 17.53 - 35.05: 634 35.05 - 52.58: 125 52.58 - 70.11: 38 70.11 - 87.63: 16 Dihedral angle restraints: 10016 sinusoidal: 3861 harmonic: 6155 Sorted by residual: dihedral pdb=" CB CYS C 308 " pdb=" SG CYS C 308 " pdb=" SG CYS C 339 " pdb=" CB CYS C 339 " ideal model delta sinusoidal sigma weight residual -86.00 -173.49 87.49 1 1.00e+01 1.00e-02 9.18e+01 dihedral pdb=" CB CYS B 74 " pdb=" SG CYS B 74 " pdb=" SG CYS B 105 " pdb=" CB CYS B 105 " ideal model delta sinusoidal sigma weight residual 93.00 178.76 -85.76 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS C 3 " pdb=" SG CYS C 3 " pdb=" SG CYS C 30 " pdb=" CB CYS C 30 " ideal model delta sinusoidal sigma weight residual -86.00 -149.53 63.53 1 1.00e+01 1.00e-02 5.32e+01 ... (remaining 10013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 2552 0.161 - 0.322: 15 0.322 - 0.483: 9 0.483 - 0.645: 2 0.645 - 0.806: 1 Chirality restraints: 2579 Sorted by residual: chirality pdb=" CA HIS C 249 " pdb=" N HIS C 249 " pdb=" C HIS C 249 " pdb=" CB HIS C 249 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CA PRO B 75 " pdb=" N PRO B 75 " pdb=" C PRO B 75 " pdb=" CB PRO B 75 " both_signs ideal model delta sigma weight residual False 2.72 2.19 0.53 2.00e-01 2.50e+01 7.04e+00 chirality pdb=" CA ILE A 359 " pdb=" N ILE A 359 " pdb=" C ILE A 359 " pdb=" CB ILE A 359 " both_signs ideal model delta sigma weight residual False 2.43 1.91 0.52 2.00e-01 2.50e+01 6.81e+00 ... (remaining 2576 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 101 " -0.089 2.00e-02 2.50e+03 4.41e-02 4.86e+01 pdb=" CG TRP C 101 " 0.096 2.00e-02 2.50e+03 pdb=" CD1 TRP C 101 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 101 " 0.025 2.00e-02 2.50e+03 pdb=" NE1 TRP C 101 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP C 101 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 101 " 0.017 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 101 " -0.030 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 101 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 238 " -0.027 2.00e-02 2.50e+03 5.17e-02 2.67e+01 pdb=" C ASN C 238 " 0.089 2.00e-02 2.50e+03 pdb=" O ASN C 238 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS C 239 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG C 99 " -0.021 2.00e-02 2.50e+03 4.31e-02 1.86e+01 pdb=" C ARG C 99 " 0.074 2.00e-02 2.50e+03 pdb=" O ARG C 99 " -0.029 2.00e-02 2.50e+03 pdb=" N GLY C 100 " -0.025 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 0.94 - 1.73: 7 1.73 - 2.52: 195 2.52 - 3.32: 18690 3.32 - 4.11: 39612 4.11 - 4.90: 74479 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132983 Sorted by model distance: nonbonded pdb=" CD1 LEU A 358 " pdb=" CD2 LEU A 378 " model vdw 0.938 3.880 nonbonded pdb=" CE1 PHE B 463 " pdb=" O SER F 75 " model vdw 1.481 3.340 nonbonded pdb=" OD1 ASP B 220 " pdb=" NH2 ARG F 38 " model vdw 1.541 3.120 nonbonded pdb=" CG LEU A 358 " pdb=" CD2 LEU A 378 " model vdw 1.567 3.890 nonbonded pdb=" CD1 LEU A 358 " pdb=" CG LEU A 378 " model vdw 1.600 3.890 ... (remaining 132978 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 1 through 150 or resid 161 through 501)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'H' selection = chain 'h' } ncs_group { reference = chain 'L' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 36.870 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 42.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 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 : 0.011 0.558 17026 Z= 0.571 Angle : 1.103 62.075 23084 Z= 0.614 Chirality : 0.060 0.806 2579 Planarity : 0.006 0.090 2912 Dihedral : 13.142 87.633 6037 Min Nonbonded Distance : 0.938 Molprobity Statistics. All-atom Clashscore : 26.23 Ramachandran Plot: Outliers : 0.42 % Allowed : 9.56 % Favored : 90.02 % Rotamer: Outliers : 2.74 % Allowed : 9.06 % Favored : 88.20 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.16), residues: 2154 helix: -1.24 (0.21), residues: 435 sheet: -0.33 (0.19), residues: 727 loop : -3.06 (0.16), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.096 0.002 TRP C 101 HIS 0.007 0.001 HIS C 288 PHE 0.013 0.002 PHE D 42 TYR 0.025 0.002 TYR C 61 ARG 0.012 0.001 ARG C 73 Details of bonding type rmsd hydrogen bonds : bond 0.11616 ( 585) hydrogen bonds : angle 5.99572 ( 1557) SS BOND : bond 0.19946 ( 19) SS BOND : angle 15.89517 ( 38) covalent geometry : bond 0.00832 (17006) covalent geometry : angle 0.89538 (23046) Misc. bond : bond 0.03760 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 363 time to evaluate : 1.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 468 ILE cc_start: 0.8620 (OUTLIER) cc_final: 0.8309 (tt) REVERT: D 31 ARG cc_start: 0.8096 (ttp-170) cc_final: 0.7793 (ttm170) REVERT: B 386 TYR cc_start: 0.8065 (m-80) cc_final: 0.7782 (m-80) REVERT: B 477 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6875 (mp) REVERT: E 69 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.7910 (mp) REVERT: l 34 SER cc_start: 0.8724 (m) cc_final: 0.8500 (t) REVERT: C 151 MET cc_start: 0.6865 (mmm) cc_final: 0.6526 (mmm) outliers start: 49 outliers final: 19 residues processed: 397 average time/residue: 0.3029 time to fit residues: 177.4174 Evaluate side-chains 261 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 384 ASP Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain E residue 69 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 494 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 HIS A 399 HIS D 7 HIS D 13 GLN L 38 GLN L 39 HIS B 77 GLN B 85 GLN B 103 ASN B 266 HIS B 350 GLN B 446 HIS B 447 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 ASN l 38 GLN l 39 HIS C 134 ASN C 148 HIS C 163 ASN C 249 HIS ** C 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 465 GLN ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.159870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.128920 restraints weight = 19850.993| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.95 r_work: 0.3217 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 17026 Z= 0.143 Angle : 0.651 17.471 23084 Z= 0.340 Chirality : 0.044 0.226 2579 Planarity : 0.005 0.060 2912 Dihedral : 6.570 58.848 2357 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.10 % Favored : 90.76 % Rotamer: Outliers : 3.58 % Allowed : 14.43 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.17), residues: 2154 helix: -0.21 (0.24), residues: 439 sheet: 0.21 (0.20), residues: 694 loop : -2.62 (0.16), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 400 HIS 0.006 0.001 HIS D 7 PHE 0.015 0.001 PHE h 63 TYR 0.018 0.001 TYR A 61 ARG 0.005 0.000 ARG B 73 Details of bonding type rmsd hydrogen bonds : bond 0.04455 ( 585) hydrogen bonds : angle 5.31661 ( 1557) SS BOND : bond 0.00507 ( 19) SS BOND : angle 1.43354 ( 38) covalent geometry : bond 0.00325 (17006) covalent geometry : angle 0.64856 (23046) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 262 time to evaluate : 1.954 Fit side-chains REVERT: A 249 HIS cc_start: 0.7258 (OUTLIER) cc_final: 0.5583 (p90) REVERT: A 296 ASP cc_start: 0.7747 (p0) cc_final: 0.7463 (p0) REVERT: A 468 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8525 (tt) REVERT: A 473 MET cc_start: 0.8288 (mmm) cc_final: 0.7964 (mmt) REVERT: A 487 MET cc_start: 0.6783 (mmt) cc_final: 0.6524 (mmp) REVERT: D 31 ARG cc_start: 0.8651 (ttp-170) cc_final: 0.8374 (ttm170) REVERT: L 27 SER cc_start: 0.8971 (m) cc_final: 0.8646 (p) REVERT: L 27 ASP cc_start: 0.8157 (OUTLIER) cc_final: 0.7660 (p0) REVERT: B 81 TYR cc_start: 0.8744 (t80) cc_final: 0.8367 (t80) REVERT: B 204 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8684 (tp) REVERT: B 473 MET cc_start: 0.7130 (tmm) cc_final: 0.6627 (tpp) REVERT: B 477 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7643 (mp) REVERT: C 66 SER cc_start: 0.8380 (t) cc_final: 0.8045 (m) REVERT: C 151 MET cc_start: 0.8647 (mmm) cc_final: 0.8146 (mmm) outliers start: 64 outliers final: 38 residues processed: 310 average time/residue: 0.2598 time to fit residues: 124.8848 Evaluate side-chains 267 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 224 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 168 optimal weight: 0.0070 chunk 148 optimal weight: 30.0000 chunk 193 optimal weight: 7.9990 chunk 71 optimal weight: 10.0000 chunk 186 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 104 optimal weight: 20.0000 chunk 198 optimal weight: 10.0000 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 163 ASN B 85 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 249 HIS C 362 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.154442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123341 restraints weight = 19842.429| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.07 r_work: 0.3027 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17026 Z= 0.234 Angle : 0.693 19.829 23084 Z= 0.361 Chirality : 0.046 0.209 2579 Planarity : 0.005 0.134 2912 Dihedral : 6.413 57.884 2343 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.91 % Favored : 90.99 % Rotamer: Outliers : 4.25 % Allowed : 16.55 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.17), residues: 2154 helix: 0.06 (0.24), residues: 435 sheet: 0.18 (0.19), residues: 737 loop : -2.53 (0.17), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 400 HIS 0.015 0.001 HIS C 249 PHE 0.015 0.001 PHE C 431 TYR 0.018 0.002 TYR h 100J ARG 0.022 0.001 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04848 ( 585) hydrogen bonds : angle 5.27079 ( 1557) SS BOND : bond 0.00525 ( 19) SS BOND : angle 1.23179 ( 38) covalent geometry : bond 0.00552 (17006) covalent geometry : angle 0.69155 (23046) Misc. bond : bond 0.00430 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 225 time to evaluate : 1.934 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 197 ASP cc_start: 0.8195 (t70) cc_final: 0.7870 (p0) REVERT: A 244 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 249 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.5477 (p90) REVERT: A 296 ASP cc_start: 0.7619 (p0) cc_final: 0.7271 (p0) REVERT: A 468 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8460 (tt) REVERT: A 473 MET cc_start: 0.8404 (mmm) cc_final: 0.8039 (mmt) REVERT: D 31 ARG cc_start: 0.8714 (ttp-170) cc_final: 0.8421 (ttm170) REVERT: L 27 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7489 (p0) REVERT: B 81 TYR cc_start: 0.8687 (t80) cc_final: 0.8307 (t80) REVERT: B 204 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8633 (tp) REVERT: B 473 MET cc_start: 0.7017 (tmm) cc_final: 0.6441 (tpp) REVERT: C 151 MET cc_start: 0.8623 (mmm) cc_final: 0.8049 (mmm) outliers start: 76 outliers final: 52 residues processed: 282 average time/residue: 0.2522 time to fit residues: 111.7015 Evaluate side-chains 271 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 214 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain h residue 17 SER Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 184 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 151 optimal weight: 0.0070 chunk 76 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 70 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 208 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 GLN C 103 ASN ** C 447 GLN ** 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 = 0.3707 r_free = 0.3707 target = 0.155637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.124350 restraints weight = 19689.774| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.15 r_work: 0.3132 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17026 Z= 0.174 Angle : 0.625 17.999 23084 Z= 0.327 Chirality : 0.044 0.206 2579 Planarity : 0.005 0.112 2912 Dihedral : 6.010 58.350 2339 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.73 % Favored : 91.18 % Rotamer: Outliers : 4.87 % Allowed : 17.51 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.17), residues: 2154 helix: 0.20 (0.25), residues: 439 sheet: 0.37 (0.20), residues: 691 loop : -2.40 (0.16), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 400 HIS 0.013 0.001 HIS B 148 PHE 0.015 0.001 PHE E 42 TYR 0.016 0.001 TYR h 100J ARG 0.014 0.000 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 585) hydrogen bonds : angle 5.15412 ( 1557) SS BOND : bond 0.00368 ( 19) SS BOND : angle 0.92919 ( 38) covalent geometry : bond 0.00403 (17006) covalent geometry : angle 0.62472 (23046) Misc. bond : bond 0.00427 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 223 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8081 (tm-30) REVERT: A 249 HIS cc_start: 0.7311 (OUTLIER) cc_final: 0.5560 (p90) REVERT: A 296 ASP cc_start: 0.7764 (p0) cc_final: 0.7357 (p0) REVERT: A 468 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 473 MET cc_start: 0.8431 (mmm) cc_final: 0.8012 (mmt) REVERT: A 487 MET cc_start: 0.6790 (mmt) cc_final: 0.6527 (mmp) REVERT: D 31 ARG cc_start: 0.8691 (ttp-170) cc_final: 0.8418 (ttm170) REVERT: L 27 ASP cc_start: 0.8214 (OUTLIER) cc_final: 0.7720 (p0) REVERT: B 81 TYR cc_start: 0.8758 (t80) cc_final: 0.8425 (t80) REVERT: B 204 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8748 (tp) REVERT: B 473 MET cc_start: 0.7156 (tmm) cc_final: 0.6750 (mtt) REVERT: h 71 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7636 (pmt170) REVERT: C 151 MET cc_start: 0.8544 (mmm) cc_final: 0.7998 (mmm) REVERT: C 197 ASP cc_start: 0.8283 (t0) cc_final: 0.8001 (t0) outliers start: 87 outliers final: 61 residues processed: 287 average time/residue: 0.2619 time to fit residues: 117.0909 Evaluate side-chains 279 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 213 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 52 optimal weight: 10.0000 chunk 112 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 42 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 176 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 211 optimal weight: 10.0000 chunk 64 optimal weight: 40.0000 chunk 23 optimal weight: 0.0010 overall best weight: 3.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN ** C 447 GLN ** 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 = 0.3688 r_free = 0.3688 target = 0.153912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.122690 restraints weight = 19854.751| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.31 r_work: 0.3040 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2909 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 17026 Z= 0.216 Angle : 0.660 19.126 23084 Z= 0.343 Chirality : 0.045 0.213 2579 Planarity : 0.006 0.198 2912 Dihedral : 6.054 57.051 2339 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.15 % Favored : 90.76 % Rotamer: Outliers : 5.43 % Allowed : 17.62 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.17), residues: 2154 helix: 0.31 (0.25), residues: 431 sheet: 0.28 (0.20), residues: 721 loop : -2.38 (0.17), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP h 100D HIS 0.006 0.001 HIS C 249 PHE 0.014 0.001 PHE E 42 TYR 0.017 0.001 TYR h 100J ARG 0.023 0.001 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04671 ( 585) hydrogen bonds : angle 5.14825 ( 1557) SS BOND : bond 0.00425 ( 19) SS BOND : angle 0.95981 ( 38) covalent geometry : bond 0.00510 (17006) covalent geometry : angle 0.65894 (23046) Misc. bond : bond 0.00695 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8089 (tm-30) REVERT: A 249 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.5594 (p90) REVERT: A 296 ASP cc_start: 0.7812 (p0) cc_final: 0.7387 (p0) REVERT: A 468 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8616 (tt) REVERT: A 473 MET cc_start: 0.8493 (mmm) cc_final: 0.8139 (mmt) REVERT: D 25 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6210 (p90) REVERT: D 31 ARG cc_start: 0.8739 (ttp-170) cc_final: 0.8463 (ttm170) REVERT: H 100 THR cc_start: 0.8848 (OUTLIER) cc_final: 0.8530 (p) REVERT: L 27 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8633 (p) REVERT: L 27 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7704 (p0) REVERT: B 79 GLU cc_start: 0.3759 (OUTLIER) cc_final: 0.2266 (mp0) REVERT: B 81 TYR cc_start: 0.8770 (t80) cc_final: 0.8453 (t80) REVERT: B 204 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8773 (tp) REVERT: B 274 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8137 (mt-10) REVERT: B 386 TYR cc_start: 0.8634 (m-80) cc_final: 0.8406 (m-80) REVERT: B 448 ILE cc_start: 0.9246 (OUTLIER) cc_final: 0.8975 (mm) REVERT: h 71 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7614 (pmt170) REVERT: C 151 MET cc_start: 0.8579 (mmm) cc_final: 0.7986 (mmm) outliers start: 97 outliers final: 72 residues processed: 287 average time/residue: 0.2501 time to fit residues: 114.3255 Evaluate side-chains 284 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 202 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 60 SER Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 75 optimal weight: 40.0000 chunk 94 optimal weight: 0.2980 chunk 174 optimal weight: 9.9990 chunk 202 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 170 optimal weight: 4.9990 chunk 146 optimal weight: 20.0000 chunk 194 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 447 GLN ** 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 = 0.3696 r_free = 0.3696 target = 0.154620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123419 restraints weight = 19844.304| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.25 r_work: 0.3059 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17026 Z= 0.181 Angle : 0.622 17.958 23084 Z= 0.325 Chirality : 0.044 0.183 2579 Planarity : 0.005 0.165 2912 Dihedral : 5.887 57.521 2337 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.45 % Favored : 91.46 % Rotamer: Outliers : 5.09 % Allowed : 17.90 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.17), residues: 2154 helix: 0.30 (0.25), residues: 437 sheet: 0.35 (0.20), residues: 717 loop : -2.31 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 400 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE E 42 TYR 0.017 0.001 TYR A 61 ARG 0.022 0.000 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 585) hydrogen bonds : angle 5.11335 ( 1557) SS BOND : bond 0.00376 ( 19) SS BOND : angle 0.83870 ( 38) covalent geometry : bond 0.00425 (17006) covalent geometry : angle 0.62204 (23046) Misc. bond : bond 0.00542 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 212 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8084 (tm-30) REVERT: A 244 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: A 249 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.5388 (p90) REVERT: A 454 LYS cc_start: 0.8725 (tttt) cc_final: 0.8468 (tttp) REVERT: A 468 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8608 (tt) REVERT: A 473 MET cc_start: 0.8429 (mmm) cc_final: 0.8055 (mmt) REVERT: A 487 MET cc_start: 0.6858 (mmt) cc_final: 0.6586 (mmp) REVERT: D 25 TYR cc_start: 0.6828 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 31 ARG cc_start: 0.8721 (ttp-170) cc_final: 0.8465 (ttm170) REVERT: H 100 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8538 (p) REVERT: L 27 SER cc_start: 0.9001 (OUTLIER) cc_final: 0.8653 (p) REVERT: L 27 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7710 (p0) REVERT: B 79 GLU cc_start: 0.4000 (OUTLIER) cc_final: 0.3156 (mp0) REVERT: B 81 TYR cc_start: 0.8756 (t80) cc_final: 0.8443 (t80) REVERT: B 204 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8795 (tp) REVERT: B 386 TYR cc_start: 0.8585 (m-80) cc_final: 0.8370 (m-80) REVERT: B 448 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8955 (mm) REVERT: h 71 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7608 (pmt170) REVERT: h 94 ARG cc_start: 0.8577 (ptt180) cc_final: 0.8263 (ttp-170) REVERT: C 151 MET cc_start: 0.8599 (mmm) cc_final: 0.8028 (mmm) REVERT: C 197 ASP cc_start: 0.8348 (t0) cc_final: 0.7930 (t0) outliers start: 91 outliers final: 68 residues processed: 281 average time/residue: 0.2532 time to fit residues: 111.9941 Evaluate side-chains 286 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 207 time to evaluate : 1.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 448 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 12 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 49 optimal weight: 0.0770 chunk 184 optimal weight: 9.9990 chunk 25 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 3.7944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.153600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.122397 restraints weight = 19701.623| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.27 r_work: 0.3086 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17026 Z= 0.203 Angle : 0.638 18.689 23084 Z= 0.333 Chirality : 0.045 0.185 2579 Planarity : 0.005 0.149 2912 Dihedral : 5.853 57.307 2335 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.24 % Favored : 90.67 % Rotamer: Outliers : 5.48 % Allowed : 18.12 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 2154 helix: 0.29 (0.25), residues: 438 sheet: 0.31 (0.20), residues: 717 loop : -2.30 (0.17), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 101 HIS 0.005 0.001 HIS A 288 PHE 0.014 0.001 PHE D 42 TYR 0.016 0.001 TYR h 100J ARG 0.020 0.000 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04524 ( 585) hydrogen bonds : angle 5.15826 ( 1557) SS BOND : bond 0.00411 ( 19) SS BOND : angle 0.88255 ( 38) covalent geometry : bond 0.00479 (17006) covalent geometry : angle 0.63708 (23046) Misc. bond : bond 0.00487 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 212 time to evaluate : 1.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 GLU cc_start: 0.8590 (tm-30) cc_final: 0.8053 (tm-30) REVERT: A 244 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7443 (tp30) REVERT: A 249 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.5343 (p90) REVERT: A 296 ASP cc_start: 0.7767 (p0) cc_final: 0.7360 (p0) REVERT: A 454 LYS cc_start: 0.8739 (tttt) cc_final: 0.8480 (tttp) REVERT: A 468 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8643 (tt) REVERT: A 473 MET cc_start: 0.8465 (mmm) cc_final: 0.8141 (mmt) REVERT: A 487 MET cc_start: 0.6857 (mmt) cc_final: 0.6597 (mmp) REVERT: D 25 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.5959 (p90) REVERT: D 31 ARG cc_start: 0.8751 (ttp-170) cc_final: 0.8488 (ttm170) REVERT: H 100 THR cc_start: 0.8793 (OUTLIER) cc_final: 0.8593 (p) REVERT: L 27 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8649 (p) REVERT: L 27 ASP cc_start: 0.8263 (OUTLIER) cc_final: 0.7752 (p0) REVERT: B 79 GLU cc_start: 0.4150 (OUTLIER) cc_final: 0.3279 (mp0) REVERT: B 81 TYR cc_start: 0.8767 (t80) cc_final: 0.8458 (t80) REVERT: B 204 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8826 (tp) REVERT: B 386 TYR cc_start: 0.8603 (m-80) cc_final: 0.8382 (m-80) REVERT: h 71 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7596 (pmt170) REVERT: h 94 ARG cc_start: 0.8537 (ptt180) cc_final: 0.8206 (ttp-170) REVERT: C 151 MET cc_start: 0.8598 (mmm) cc_final: 0.8214 (mmm) REVERT: C 197 ASP cc_start: 0.8339 (t0) cc_final: 0.7875 (t0) REVERT: C 477 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8075 (mp) outliers start: 98 outliers final: 73 residues processed: 284 average time/residue: 0.2438 time to fit residues: 109.5086 Evaluate side-chains 291 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 207 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 4 optimal weight: 5.9990 chunk 121 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 132 optimal weight: 9.9990 chunk 203 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.150433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.118978 restraints weight = 19782.424| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 2.18 r_work: 0.3012 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 17026 Z= 0.286 Angle : 0.715 21.047 23084 Z= 0.373 Chirality : 0.047 0.201 2579 Planarity : 0.006 0.154 2912 Dihedral : 6.176 56.012 2335 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.33 % Favored : 90.53 % Rotamer: Outliers : 5.65 % Allowed : 18.29 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.17), residues: 2154 helix: 0.19 (0.25), residues: 434 sheet: 0.17 (0.20), residues: 711 loop : -2.40 (0.17), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 101 HIS 0.006 0.001 HIS A 288 PHE 0.013 0.002 PHE E 42 TYR 0.020 0.002 TYR h 100J ARG 0.019 0.001 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.05069 ( 585) hydrogen bonds : angle 5.30846 ( 1557) SS BOND : bond 0.00536 ( 19) SS BOND : angle 1.14797 ( 38) covalent geometry : bond 0.00683 (17006) covalent geometry : angle 0.71364 (23046) Misc. bond : bond 0.00515 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 203 time to evaluate : 1.745 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7455 (tp30) REVERT: A 249 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.5411 (p90) REVERT: A 276 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: A 468 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8655 (tt) REVERT: D 25 TYR cc_start: 0.7390 (OUTLIER) cc_final: 0.5873 (p90) REVERT: D 31 ARG cc_start: 0.8760 (ttp-170) cc_final: 0.8508 (ttm170) REVERT: H 100 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8527 (p) REVERT: L 27 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8668 (p) REVERT: L 27 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7776 (p0) REVERT: B 79 GLU cc_start: 0.4248 (OUTLIER) cc_final: 0.3125 (mp0) REVERT: B 204 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8786 (tp) REVERT: B 251 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7720 (ptmm) REVERT: B 386 TYR cc_start: 0.8623 (m-80) cc_final: 0.8414 (m-80) REVERT: B 491 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7362 (tp) REVERT: h 71 ARG cc_start: 0.8747 (OUTLIER) cc_final: 0.7599 (pmt170) REVERT: h 94 ARG cc_start: 0.8548 (ptt180) cc_final: 0.8178 (ttp-170) REVERT: C 151 MET cc_start: 0.8586 (mmm) cc_final: 0.8153 (mmm) REVERT: C 197 ASP cc_start: 0.8406 (t0) cc_final: 0.8149 (t0) outliers start: 101 outliers final: 76 residues processed: 283 average time/residue: 0.2549 time to fit residues: 113.6032 Evaluate side-chains 284 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 196 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 189 ASP Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 89 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 86 SER Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 307 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain h residue 21 SER Chi-restraints excluded: chain h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 SER Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 52 THR Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 207 optimal weight: 4.9990 chunk 110 optimal weight: 0.0970 chunk 1 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 163 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN B 371 ASN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 7 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.128254 restraints weight = 19709.318| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.12 r_work: 0.3184 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 17026 Z= 0.114 Angle : 0.569 11.066 23084 Z= 0.302 Chirality : 0.042 0.203 2579 Planarity : 0.005 0.197 2912 Dihedral : 5.573 59.342 2335 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.57 % Favored : 92.34 % Rotamer: Outliers : 3.52 % Allowed : 20.58 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.18), residues: 2154 helix: 0.51 (0.25), residues: 437 sheet: 0.61 (0.21), residues: 668 loop : -2.26 (0.17), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 19 HIS 0.004 0.001 HIS B 144 PHE 0.018 0.001 PHE D 42 TYR 0.017 0.001 TYR A 61 ARG 0.033 0.001 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 585) hydrogen bonds : angle 5.07050 ( 1557) SS BOND : bond 0.00275 ( 19) SS BOND : angle 0.59821 ( 38) covalent geometry : bond 0.00241 (17006) covalent geometry : angle 0.56884 (23046) Misc. bond : bond 0.00252 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7414 (tp30) REVERT: A 249 HIS cc_start: 0.7159 (OUTLIER) cc_final: 0.5519 (p90) REVERT: A 454 LYS cc_start: 0.8689 (tttt) cc_final: 0.8469 (tttp) REVERT: A 468 ILE cc_start: 0.8708 (OUTLIER) cc_final: 0.8445 (tt) REVERT: A 473 MET cc_start: 0.8249 (mmm) cc_final: 0.7935 (mmt) REVERT: D 25 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5696 (p90) REVERT: D 31 ARG cc_start: 0.8636 (ttp-170) cc_final: 0.8342 (ttm170) REVERT: L 27 SER cc_start: 0.9009 (OUTLIER) cc_final: 0.8643 (p) REVERT: L 27 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7793 (p0) REVERT: B 204 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8879 (tp) REVERT: B 251 LYS cc_start: 0.8026 (ptmm) cc_final: 0.7717 (ptmm) REVERT: B 473 MET cc_start: 0.7117 (tmm) cc_final: 0.6761 (mtt) REVERT: h 80 MET cc_start: 0.7904 (tmm) cc_final: 0.7603 (tmm) REVERT: h 94 ARG cc_start: 0.8499 (ptt180) cc_final: 0.8228 (ttp-170) REVERT: C 151 MET cc_start: 0.8543 (mmm) cc_final: 0.7981 (mmm) REVERT: C 197 ASP cc_start: 0.8367 (t0) cc_final: 0.8119 (t0) outliers start: 63 outliers final: 45 residues processed: 270 average time/residue: 0.2668 time to fit residues: 111.2663 Evaluate side-chains 255 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 434 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 194 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 65 optimal weight: 30.0000 chunk 79 optimal weight: 0.3980 chunk 209 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 150 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.123652 restraints weight = 19773.699| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.15 r_work: 0.3067 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17026 Z= 0.176 Angle : 0.613 13.790 23084 Z= 0.323 Chirality : 0.044 0.193 2579 Planarity : 0.006 0.229 2912 Dihedral : 5.684 57.507 2335 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.54 % Favored : 91.36 % Rotamer: Outliers : 3.64 % Allowed : 20.92 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2154 helix: 0.53 (0.25), residues: 436 sheet: 0.55 (0.20), residues: 680 loop : -2.28 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 474 HIS 0.004 0.001 HIS A 288 PHE 0.014 0.001 PHE D 42 TYR 0.016 0.001 TYR A 61 ARG 0.031 0.000 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 585) hydrogen bonds : angle 5.07155 ( 1557) SS BOND : bond 0.00351 ( 19) SS BOND : angle 0.78792 ( 38) covalent geometry : bond 0.00413 (17006) covalent geometry : angle 0.61266 (23046) Misc. bond : bond 0.00655 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4308 Ramachandran restraints generated. 2154 Oldfield, 0 Emsley, 2154 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 209 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: A 249 HIS cc_start: 0.7184 (OUTLIER) cc_final: 0.5372 (p90) REVERT: A 454 LYS cc_start: 0.8709 (tttt) cc_final: 0.8458 (tttp) REVERT: A 468 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8488 (tt) REVERT: D 25 TYR cc_start: 0.7007 (OUTLIER) cc_final: 0.5656 (p90) REVERT: D 31 ARG cc_start: 0.8686 (ttp-170) cc_final: 0.8436 (ttm170) REVERT: L 27 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8619 (p) REVERT: L 27 ASP cc_start: 0.8297 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 204 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8847 (tp) REVERT: B 251 LYS cc_start: 0.8010 (ptmm) cc_final: 0.7711 (ptmm) REVERT: B 460 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8285 (mtp) REVERT: B 473 MET cc_start: 0.7169 (tmm) cc_final: 0.6789 (mtt) REVERT: h 80 MET cc_start: 0.7927 (tmm) cc_final: 0.7510 (tmm) REVERT: h 94 ARG cc_start: 0.8522 (ptt180) cc_final: 0.8248 (ttp-170) REVERT: C 151 MET cc_start: 0.8595 (mmm) cc_final: 0.7991 (mmm) REVERT: C 197 ASP cc_start: 0.8368 (t0) cc_final: 0.8108 (t0) outliers start: 65 outliers final: 53 residues processed: 255 average time/residue: 0.2487 time to fit residues: 100.0331 Evaluate side-chains 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 203 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 246 LYS Chi-restraints excluded: chain A residue 249 HIS Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 366 THR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain D residue 25 TYR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 56 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 27 HIS Chi-restraints excluded: chain B residue 37 ASP Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 91 VAL Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 240 GLU Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 256 VAL Chi-restraints excluded: chain B residue 295 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 491 LEU Chi-restraints excluded: chain h residue 100 LEU Chi-restraints excluded: chain h residue 100 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 22 ASP Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 249 HIS Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 288 HIS Chi-restraints excluded: chain C residue 365 ILE Chi-restraints excluded: chain C residue 391 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 466 ILE Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 477 LEU Chi-restraints excluded: chain C residue 479 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 0.9980 chunk 102 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 58 optimal weight: 20.0000 chunk 105 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 143 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.154488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.123287 restraints weight = 19735.774| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.19 r_work: 0.3099 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17026 Z= 0.187 Angle : 0.629 13.140 23084 Z= 0.330 Chirality : 0.044 0.189 2579 Planarity : 0.006 0.224 2912 Dihedral : 5.750 57.373 2335 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.31 % Favored : 91.60 % Rotamer: Outliers : 3.75 % Allowed : 20.64 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.18), residues: 2154 helix: 0.52 (0.25), residues: 436 sheet: 0.53 (0.21), residues: 680 loop : -2.28 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 474 HIS 0.010 0.001 HIS B 148 PHE 0.018 0.001 PHE E 42 TYR 0.017 0.001 TYR A 61 ARG 0.029 0.000 ARG B 2 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 585) hydrogen bonds : angle 5.08987 ( 1557) SS BOND : bond 0.00376 ( 19) SS BOND : angle 0.79586 ( 38) covalent geometry : bond 0.00438 (17006) covalent geometry : angle 0.62869 (23046) Misc. bond : bond 0.00649 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9809.98 seconds wall clock time: 168 minutes 15.50 seconds (10095.50 seconds total)