Starting phenix.real_space_refine on Mon Nov 18 11:45:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_27056.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_27056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_27056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_27056.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cxh_27056/11_2024/8cxh_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 9.46, per 1000 atoms: 0.57 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=0, symmetry=0 Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 2.5 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: 2.08 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: 5.84 Time building geometry restraints manager: 5.03 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: 9 1.73 - 2.52: 196 2.52 - 3.32: 18691 3.32 - 4.11: 39612 4.11 - 4.90: 74479 Warning: very small nonbonded interaction distances. Nonbonded interactions: 132987 Sorted by model distance: nonbonded pdb=" CD1 LEU A 358 " pdb=" CD2 LEU A 378 " model vdw 0.938 3.880 nonbonded pdb=" NH1 ARG B 2 " pdb=" CB MET B 140 " model vdw 1.468 3.520 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 ... (remaining 132982 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: 0.690 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: 0.730 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.680 Find NCS groups from input model: 0.590 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.120 ------------------------------------------------------------------------------- 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 : 0.008 0.148 17006 Z= 0.558 Angle : 0.895 17.085 23046 Z= 0.532 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 *********************** 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 : 1.880 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: 0.3302 time to fit residues: 194.8162 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 : 1.964 ------------------------------------------------------------------------------- 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 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: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 17006 Z= 0.209 Angle : 0.648 17.876 23046 Z= 0.339 Chirality : 0.044 0.229 2579 Planarity : 0.005 0.060 2912 Dihedral : 6.582 58.896 2357 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.05 % Favored : 90.81 % Rotamer: Outliers : 3.80 % Allowed : 14.26 % Favored : 81.94 % 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: -0.22 (0.24), residues: 439 sheet: 0.20 (0.20), residues: 694 loop : -2.61 (0.16), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 400 HIS 0.006 0.001 HIS D 7 PHE 0.016 0.001 PHE h 63 TYR 0.018 0.001 TYR A 61 ARG 0.007 0.000 ARG B 2 *********************** 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 329 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 261 time to evaluate : 1.986 Fit side-chains REVERT: A 52 ASN cc_start: 0.8707 (p0) cc_final: 0.8438 (p0) REVERT: A 249 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.4894 (p90) REVERT: A 296 ASP cc_start: 0.6848 (p0) cc_final: 0.6455 (p0) REVERT: A 468 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8102 (tt) REVERT: A 473 MET cc_start: 0.6805 (mmm) cc_final: 0.6299 (mmt) REVERT: A 487 MET cc_start: 0.5348 (mmt) cc_final: 0.4983 (mmp) REVERT: H 34 MET cc_start: 0.8211 (tpp) cc_final: 0.8010 (tpp) REVERT: L 27 SER cc_start: 0.9008 (m) cc_final: 0.8737 (p) REVERT: L 27 ASP cc_start: 0.8383 (OUTLIER) cc_final: 0.7908 (p0) REVERT: B 81 TYR cc_start: 0.8330 (t80) cc_final: 0.8099 (t80) REVERT: B 204 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8233 (tp) REVERT: h 94 ARG cc_start: 0.8957 (ptt180) cc_final: 0.8757 (ptt180) outliers start: 68 outliers final: 39 residues processed: 311 average time/residue: 0.2726 time to fit residues: 130.7773 Evaluate side-chains 268 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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 1 ILE 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 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 107 optimal weight: 0.0470 chunk 60 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 193 optimal weight: 10.0000 chunk 209 optimal weight: 6.9990 chunk 172 optimal weight: 8.9990 chunk 192 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 155 optimal weight: 0.4980 overall best weight: 1.3084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 ASN C 362 ASN ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17006 Z= 0.174 Angle : 0.592 14.747 23046 Z= 0.311 Chirality : 0.042 0.209 2579 Planarity : 0.004 0.056 2912 Dihedral : 5.924 59.301 2341 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.22 % Favored : 91.69 % Rotamer: Outliers : 3.64 % Allowed : 16.00 % Favored : 80.37 % 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: -1.31 (0.17), residues: 2154 helix: 0.24 (0.25), residues: 437 sheet: 0.48 (0.20), residues: 683 loop : -2.42 (0.16), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 400 HIS 0.015 0.001 HIS C 249 PHE 0.015 0.001 PHE E 42 TYR 0.014 0.001 TYR A 61 ARG 0.004 0.000 ARG A 357 *********************** 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 305 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 240 time to evaluate : 1.942 Fit side-chains revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7028 (OUTLIER) cc_final: 0.6548 (tp30) REVERT: A 249 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.4809 (p90) REVERT: A 473 MET cc_start: 0.6690 (mmm) cc_final: 0.6141 (mmt) REVERT: A 487 MET cc_start: 0.5170 (mmt) cc_final: 0.4818 (mmp) REVERT: L 27 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7913 (p0) REVERT: B 2 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7265 (ptm-80) REVERT: B 81 TYR cc_start: 0.8344 (t80) cc_final: 0.8128 (t80) REVERT: B 204 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8255 (tp) outliers start: 65 outliers final: 46 residues processed: 292 average time/residue: 0.2656 time to fit residues: 120.7553 Evaluate side-chains 273 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 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 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 2 ARG 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 317 ILE Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 466 ILE 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 ASP Chi-restraints excluded: chain l residue 72 SER Chi-restraints excluded: chain l residue 89 SER 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 477 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 9.9990 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 92 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 205 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 163 ASN B 85 GLN B 447 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17006 Z= 0.443 Angle : 0.729 21.334 23046 Z= 0.377 Chirality : 0.048 0.221 2579 Planarity : 0.005 0.058 2912 Dihedral : 6.203 58.583 2337 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.30 % Rotamer: Outliers : 4.75 % Allowed : 17.28 % Favored : 77.96 % 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: -1.40 (0.17), residues: 2154 helix: 0.14 (0.25), residues: 437 sheet: 0.28 (0.20), residues: 724 loop : -2.45 (0.17), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 101 HIS 0.007 0.001 HIS B 266 PHE 0.015 0.002 PHE C 431 TYR 0.021 0.002 TYR h 100J ARG 0.005 0.001 ARG C 94 *********************** 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 303 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 218 time to evaluate : 1.840 Fit side-chains REVERT: A 140 MET cc_start: 0.7977 (mmm) cc_final: 0.7487 (mtp) REVERT: A 249 HIS cc_start: 0.6726 (OUTLIER) cc_final: 0.4878 (p90) REVERT: A 468 ILE cc_start: 0.8510 (OUTLIER) cc_final: 0.8223 (tt) REVERT: A 473 MET cc_start: 0.6949 (mmm) cc_final: 0.6467 (mmt) REVERT: H 100 THR cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (p) REVERT: L 27 SER cc_start: 0.9077 (OUTLIER) cc_final: 0.8776 (p) REVERT: L 27 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7929 (p0) REVERT: B 204 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8216 (tp) REVERT: h 71 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7617 (pmt170) outliers start: 85 outliers final: 55 residues processed: 283 average time/residue: 0.2763 time to fit residues: 120.3832 Evaluate side-chains 268 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 206 time to evaluate : 1.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL 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 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 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 2 ARG 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 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 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 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 180 LEU Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 288 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 20.0000 chunk 116 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 142 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 184 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17006 Z= 0.371 Angle : 0.679 19.736 23046 Z= 0.353 Chirality : 0.046 0.180 2579 Planarity : 0.005 0.059 2912 Dihedral : 6.090 57.020 2335 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.19 % Favored : 90.71 % Rotamer: Outliers : 5.09 % Allowed : 18.06 % Favored : 76.85 % 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: -1.40 (0.17), residues: 2154 helix: 0.13 (0.25), residues: 437 sheet: 0.26 (0.20), residues: 717 loop : -2.40 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP h 100D HIS 0.006 0.001 HIS A 288 PHE 0.014 0.001 PHE C 431 TYR 0.017 0.002 TYR h 100J ARG 0.005 0.000 ARG A 357 *********************** 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 312 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 221 time to evaluate : 1.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6710 (tp30) REVERT: A 249 HIS cc_start: 0.6626 (OUTLIER) cc_final: 0.4839 (p90) REVERT: A 296 ASP cc_start: 0.6744 (p0) cc_final: 0.6374 (p0) REVERT: A 473 MET cc_start: 0.6987 (mmm) cc_final: 0.6604 (mmt) REVERT: D 25 TYR cc_start: 0.6258 (OUTLIER) cc_final: 0.5518 (p90) REVERT: L 27 SER cc_start: 0.9072 (OUTLIER) cc_final: 0.8789 (p) REVERT: L 27 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.7946 (p0) REVERT: B 79 GLU cc_start: 0.4077 (OUTLIER) cc_final: 0.2176 (mp0) REVERT: B 204 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8265 (tp) REVERT: C 197 ASP cc_start: 0.7103 (t0) cc_final: 0.6880 (t0) outliers start: 91 outliers final: 69 residues processed: 286 average time/residue: 0.2623 time to fit residues: 117.0453 Evaluate side-chains 278 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 202 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 276 GLU 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 366 THR Chi-restraints excluded: chain A residue 434 VAL 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 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 2 ARG 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 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 456 LEU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain E residue 25 TYR Chi-restraints excluded: chain h residue 25 SER 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 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 65 ILE Chi-restraints excluded: chain C residue 95 THR 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 249 HIS 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 20.0000 chunk 185 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 206 optimal weight: 0.9980 chunk 171 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 68 optimal weight: 4.9990 chunk 108 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 17006 Z= 0.411 Angle : 0.705 20.658 23046 Z= 0.367 Chirality : 0.047 0.188 2579 Planarity : 0.005 0.062 2912 Dihedral : 6.174 57.171 2335 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.61 % Favored : 90.30 % Rotamer: Outliers : 5.43 % Allowed : 18.12 % Favored : 76.45 % 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: -1.49 (0.17), residues: 2154 helix: 0.10 (0.24), residues: 437 sheet: 0.13 (0.20), residues: 721 loop : -2.42 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP h 100D HIS 0.006 0.001 HIS A 288 PHE 0.014 0.001 PHE E 42 TYR 0.019 0.002 TYR h 100J ARG 0.004 0.000 ARG h 94 *********************** 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 305 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 208 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7961 (mmm) cc_final: 0.7511 (mtp) REVERT: A 244 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6721 (tp30) REVERT: A 249 HIS cc_start: 0.6742 (OUTLIER) cc_final: 0.4950 (p90) REVERT: A 296 ASP cc_start: 0.6788 (p0) cc_final: 0.6418 (p0) REVERT: A 468 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8185 (tt) REVERT: D 25 TYR cc_start: 0.6626 (OUTLIER) cc_final: 0.5345 (p90) REVERT: H 100 THR cc_start: 0.8755 (OUTLIER) cc_final: 0.8468 (p) REVERT: L 27 SER cc_start: 0.9078 (OUTLIER) cc_final: 0.8784 (p) REVERT: L 27 ASP cc_start: 0.8430 (OUTLIER) cc_final: 0.7912 (p0) REVERT: B 79 GLU cc_start: 0.4482 (OUTLIER) cc_final: 0.3454 (mp0) REVERT: B 204 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8254 (tp) REVERT: h 71 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7610 (pmt170) REVERT: C 197 ASP cc_start: 0.7186 (t0) cc_final: 0.6854 (t0) REVERT: C 473 MET cc_start: 0.7308 (tpp) cc_final: 0.6875 (mmt) outliers start: 97 outliers final: 71 residues processed: 283 average time/residue: 0.2838 time to fit residues: 126.4752 Evaluate side-chains 282 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 201 time to evaluate : 1.972 ------------------------------------------------------------------------------- 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 434 VAL 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 2 ARG 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 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 456 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 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 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 249 HIS 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 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 Chi-restraints excluded: chain C residue 491 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 150 optimal weight: 20.0000 chunk 116 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 125 optimal weight: 20.0000 chunk 94 optimal weight: 0.1980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17006 Z= 0.179 Angle : 0.568 15.067 23046 Z= 0.301 Chirality : 0.042 0.225 2579 Planarity : 0.004 0.056 2912 Dihedral : 5.633 59.362 2335 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.85 % Favored : 92.06 % Rotamer: Outliers : 4.08 % Allowed : 20.02 % 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: -1.14 (0.18), residues: 2154 helix: 0.47 (0.25), residues: 437 sheet: 0.48 (0.20), residues: 699 loop : -2.30 (0.17), residues: 1018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 400 HIS 0.004 0.001 HIS A 288 PHE 0.016 0.001 PHE D 42 TYR 0.017 0.001 TYR A 61 ARG 0.004 0.000 ARG h 94 *********************** 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 296 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 223 time to evaluate : 1.945 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7878 (mmm) cc_final: 0.7552 (mtp) REVERT: A 244 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6656 (tp30) REVERT: A 249 HIS cc_start: 0.6871 (OUTLIER) cc_final: 0.5197 (p90) REVERT: A 473 MET cc_start: 0.6785 (mmm) cc_final: 0.6248 (mmt) REVERT: A 487 MET cc_start: 0.5158 (mmt) cc_final: 0.4830 (mmp) REVERT: D 25 TYR cc_start: 0.6185 (OUTLIER) cc_final: 0.5290 (p90) REVERT: L 27 SER cc_start: 0.9035 (OUTLIER) cc_final: 0.8770 (p) REVERT: L 27 ASP cc_start: 0.8408 (OUTLIER) cc_final: 0.7930 (p0) REVERT: B 2 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7901 (ptm-80) REVERT: B 204 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 460 MET cc_start: 0.7743 (mtp) cc_final: 0.7442 (mtp) REVERT: h 71 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7521 (pmt170) REVERT: C 197 ASP cc_start: 0.7189 (t0) cc_final: 0.6881 (t0) REVERT: C 473 MET cc_start: 0.7119 (tpp) cc_final: 0.6741 (mmt) outliers start: 73 outliers final: 51 residues processed: 276 average time/residue: 0.2718 time to fit residues: 115.3371 Evaluate side-chains 264 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 112 SER 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 376 LEU 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 L residue 89 SER Chi-restraints excluded: chain B residue 2 ARG 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 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 180 LEU Chi-restraints excluded: chain B residue 204 LEU 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 h residue 25 SER Chi-restraints excluded: chain h residue 71 ARG 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 95 THR Chi-restraints excluded: chain C residue 122 SER 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 477 LEU Chi-restraints excluded: chain C residue 479 THR Chi-restraints excluded: chain C residue 491 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 0.0470 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 161 optimal weight: 4.9990 overall best weight: 3.5884 ------------------------------------------------------------------------------- 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 478 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17006 Z= 0.298 Angle : 0.619 18.066 23046 Z= 0.325 Chirality : 0.044 0.278 2579 Planarity : 0.004 0.055 2912 Dihedral : 5.691 57.430 2333 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.10 % Favored : 90.81 % Rotamer: Outliers : 4.31 % Allowed : 20.36 % Favored : 75.34 % 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: -1.17 (0.18), residues: 2154 helix: 0.47 (0.25), residues: 439 sheet: 0.42 (0.20), residues: 701 loop : -2.32 (0.17), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 474 HIS 0.004 0.001 HIS A 288 PHE 0.017 0.001 PHE E 42 TYR 0.015 0.001 TYR A 61 ARG 0.004 0.000 ARG h 94 *********************** 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 289 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 212 time to evaluate : 1.937 Fit side-chains REVERT: A 140 MET cc_start: 0.7947 (mmm) cc_final: 0.7478 (mtp) REVERT: A 244 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6685 (tp30) REVERT: A 249 HIS cc_start: 0.6670 (OUTLIER) cc_final: 0.4815 (p90) REVERT: A 296 ASP cc_start: 0.6773 (p0) cc_final: 0.6280 (p0) REVERT: A 473 MET cc_start: 0.6811 (mmm) cc_final: 0.6339 (mmt) REVERT: A 487 MET cc_start: 0.5317 (mmt) cc_final: 0.4966 (mmp) REVERT: D 25 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.5193 (p90) REVERT: L 27 SER cc_start: 0.9042 (OUTLIER) cc_final: 0.8767 (p) REVERT: L 27 ASP cc_start: 0.8457 (OUTLIER) cc_final: 0.7973 (p0) REVERT: B 79 GLU cc_start: 0.4336 (OUTLIER) cc_final: 0.2960 (mp0) REVERT: B 204 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8326 (tp) REVERT: B 460 MET cc_start: 0.7854 (mtp) cc_final: 0.7580 (mtp) REVERT: h 71 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7540 (pmt170) REVERT: C 197 ASP cc_start: 0.7181 (t0) cc_final: 0.6875 (t0) REVERT: C 473 MET cc_start: 0.7133 (tpp) cc_final: 0.6701 (mmt) outliers start: 77 outliers final: 58 residues processed: 271 average time/residue: 0.2659 time to fit residues: 111.5820 Evaluate side-chains 270 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 204 time to evaluate : 1.829 ------------------------------------------------------------------------------- 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 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 317 ILE Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 376 LEU 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 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 2 ARG 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 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 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 TYR Chi-restraints excluded: chain l residue 11 VAL Chi-restraints excluded: chain l residue 27 ASP 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 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 164 ARG 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 491 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 9.9990 chunk 196 optimal weight: 20.0000 chunk 179 optimal weight: 6.9990 chunk 191 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 172 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17006 Z= 0.366 Angle : 0.666 19.970 23046 Z= 0.348 Chirality : 0.046 0.319 2579 Planarity : 0.005 0.058 2912 Dihedral : 5.898 56.528 2333 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.24 % Favored : 90.62 % Rotamer: Outliers : 4.47 % Allowed : 20.25 % Favored : 75.28 % 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: -1.30 (0.17), residues: 2154 helix: 0.36 (0.25), residues: 438 sheet: 0.27 (0.20), residues: 707 loop : -2.34 (0.17), residues: 1009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 474 HIS 0.005 0.001 HIS A 288 PHE 0.016 0.001 PHE E 42 TYR 0.018 0.002 TYR h 100J ARG 0.003 0.000 ARG h 94 *********************** 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 284 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 204 time to evaluate : 1.884 Fit side-chains REVERT: A 244 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6705 (tp30) REVERT: A 249 HIS cc_start: 0.6738 (OUTLIER) cc_final: 0.4917 (p90) REVERT: A 296 ASP cc_start: 0.6787 (p0) cc_final: 0.6291 (p0) REVERT: A 468 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8159 (tt) REVERT: A 473 MET cc_start: 0.6862 (mmm) cc_final: 0.6430 (mmt) REVERT: D 25 TYR cc_start: 0.6742 (OUTLIER) cc_final: 0.5304 (p90) REVERT: L 27 SER cc_start: 0.9044 (OUTLIER) cc_final: 0.8777 (p) REVERT: L 27 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7961 (p0) REVERT: B 79 GLU cc_start: 0.4430 (OUTLIER) cc_final: 0.3142 (mp0) REVERT: B 204 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8346 (tp) REVERT: h 71 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7562 (pmt170) REVERT: h 99 ASP cc_start: 0.8585 (m-30) cc_final: 0.8314 (m-30) REVERT: C 473 MET cc_start: 0.7084 (tpp) cc_final: 0.6762 (mmt) REVERT: C 477 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7330 (mp) outliers start: 80 outliers final: 64 residues processed: 268 average time/residue: 0.2836 time to fit residues: 117.8333 Evaluate side-chains 275 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 201 time to evaluate : 1.933 ------------------------------------------------------------------------------- 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 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 317 ILE Chi-restraints excluded: chain A residue 330 VAL 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 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 2 ARG 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 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 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 89 SER Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 16 SER 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 164 ARG Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 213 VAL 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 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 195 optimal weight: 3.9990 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN B 85 GLN ** B 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 HIS ** C 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17006 Z= 0.156 Angle : 0.558 13.670 23046 Z= 0.295 Chirality : 0.042 0.238 2579 Planarity : 0.004 0.056 2912 Dihedral : 5.414 59.147 2333 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.88 % Rotamer: Outliers : 3.24 % Allowed : 21.53 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 2154 helix: 0.71 (0.25), residues: 434 sheet: 0.68 (0.21), residues: 665 loop : -2.26 (0.17), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 19 HIS 0.003 0.001 HIS A 288 PHE 0.017 0.001 PHE E 42 TYR 0.015 0.001 TYR A 61 ARG 0.004 0.000 ARG h 94 ********************** 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 273 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 215 time to evaluate : 1.768 Fit side-chains revert: symmetry clash REVERT: A 140 MET cc_start: 0.7796 (mmm) cc_final: 0.7551 (mtp) REVERT: A 244 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: A 249 HIS cc_start: 0.6577 (OUTLIER) cc_final: 0.4899 (p90) REVERT: A 473 MET cc_start: 0.6676 (mmm) cc_final: 0.6148 (mmt) REVERT: A 487 MET cc_start: 0.4932 (mmt) cc_final: 0.4627 (mmp) REVERT: D 25 TYR cc_start: 0.6230 (OUTLIER) cc_final: 0.5155 (p90) REVERT: L 27 SER cc_start: 0.8991 (OUTLIER) cc_final: 0.8716 (p) REVERT: L 27 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.7985 (p0) REVERT: B 2 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7889 (ptm-80) REVERT: B 204 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8361 (tp) REVERT: h 71 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7595 (pmt170) REVERT: h 80 MET cc_start: 0.8047 (tmm) cc_final: 0.7708 (tmm) REVERT: h 99 ASP cc_start: 0.8629 (m-30) cc_final: 0.8400 (m-30) outliers start: 58 outliers final: 42 residues processed: 260 average time/residue: 0.2795 time to fit residues: 111.6971 Evaluate side-chains 256 residues out of total 1788 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 VAL 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 376 LEU 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 60 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain B residue 2 ARG 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 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 254 THR Chi-restraints excluded: chain B residue 256 VAL 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 h residue 71 ARG Chi-restraints excluded: chain h residue 100 TYR 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 23 VAL Chi-restraints excluded: chain C residue 65 ILE Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 158 HIS Chi-restraints excluded: chain C residue 213 VAL 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 491 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 50.0000 chunk 180 optimal weight: 8.9990 chunk 51 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 169 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 173 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.155447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.124470 restraints weight = 19791.157| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.28 r_work: 0.3120 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17006 Z= 0.255 Angle : 0.606 16.409 23046 Z= 0.316 Chirality : 0.044 0.265 2579 Planarity : 0.004 0.055 2912 Dihedral : 5.470 57.631 2332 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.59 % Favored : 91.32 % Rotamer: Outliers : 3.19 % Allowed : 21.92 % Favored : 74.89 % 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: -1.06 (0.18), residues: 2154 helix: 0.62 (0.25), residues: 436 sheet: 0.59 (0.21), residues: 679 loop : -2.29 (0.17), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 474 HIS 0.004 0.001 HIS A 288 PHE 0.016 0.001 PHE E 42 TYR 0.015 0.001 TYR A 61 ARG 0.004 0.000 ARG h 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3706.48 seconds wall clock time: 68 minutes 38.69 seconds (4118.69 seconds total)