Starting phenix.real_space_refine on Fri Mar 15 14:46:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lic_23372/03_2024/7lic_23372.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 120 5.16 5 C 7888 2.51 5 N 1920 2.21 5 O 2052 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A GLU 400": "OE1" <-> "OE2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 43": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 118": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "B GLU 232": "OE1" <-> "OE2" Residue "B GLU 336": "OE1" <-> "OE2" Residue "B TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 397": "OE1" <-> "OE2" Residue "B GLU 400": "OE1" <-> "OE2" Residue "B ARG 422": "NH1" <-> "NH2" Residue "B PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 37": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 118": "OE1" <-> "OE2" Residue "C TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 185": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 397": "OE1" <-> "OE2" Residue "C GLU 400": "OE1" <-> "OE2" Residue "C ARG 422": "NH1" <-> "NH2" Residue "C PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 118": "OE1" <-> "OE2" Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 232": "OE1" <-> "OE2" Residue "D GLU 336": "OE1" <-> "OE2" Residue "D TYR 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 397": "OE1" <-> "OE2" Residue "D GLU 400": "OE1" <-> "OE2" Residue "D ARG 422": "NH1" <-> "NH2" Residue "D PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11980 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2995 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 9, 'TRANS': 367} Chain breaks: 3 Chain: "B" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2995 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 9, 'TRANS': 367} Chain breaks: 3 Chain: "C" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2995 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 9, 'TRANS': 367} Chain breaks: 3 Chain: "D" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 2995 Classifications: {'peptide': 377} Link IDs: {'PTRANS': 9, 'TRANS': 367} Chain breaks: 3 Time building chain proxies: 6.67, per 1000 atoms: 0.56 Number of scatterers: 11980 At special positions: 0 Unit cell: (111.24, 110.21, 89.61, 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 120 16.00 O 2052 8.00 N 1920 7.00 C 7888 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 4.86 Conformation dependent library (CDL) restraints added in 2.5 seconds 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2896 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 83.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.633A pdb=" N HIS A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.760A pdb=" N LYS A 47 " --> pdb=" O ASN A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 48 through 75 Processing helix chain 'A' and resid 78 through 105 removed outlier: 3.646A pdb=" N LEU A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL A 88 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.606A pdb=" N LEU A 166 " --> pdb=" O PRO A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 215 " --> pdb=" O PHE A 211 " (cutoff:3.500A) Proline residue: A 216 - end of helix Processing helix chain 'A' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY A 376 " --> pdb=" O THR A 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS A 407 " --> pdb=" O LEU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 418 through 433 removed outlier: 3.682A pdb=" N GLN A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 468 Processing helix chain 'B' and resid 13 through 31 Processing helix chain 'B' and resid 44 through 47 removed outlier: 3.760A pdb=" N LYS B 47 " --> pdb=" O ASN B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 44 through 47' Processing helix chain 'B' and resid 48 through 75 Processing helix chain 'B' and resid 78 through 105 removed outlier: 3.645A pdb=" N LEU B 83 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ASN B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N THR B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 118 removed outlier: 3.852A pdb=" N GLU B 118 " --> pdb=" O ASN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU B 161 " --> pdb=" O MET B 157 " (cutoff:3.500A) Proline residue: B 162 - end of helix removed outlier: 3.605A pdb=" N LEU B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 247 removed outlier: 3.765A pdb=" N GLU B 199 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA B 215 " --> pdb=" O PHE B 211 " (cutoff:3.500A) Proline residue: B 216 - end of helix Processing helix chain 'B' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER B 343 " --> pdb=" O GLN B 339 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N SER B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 387 " --> pdb=" O TYR B 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 398 " --> pdb=" O LEU B 394 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 399 " --> pdb=" O ALA B 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN B 426 " --> pdb=" O ARG B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 468 Processing helix chain 'C' and resid 13 through 31 Processing helix chain 'C' and resid 44 through 47 removed outlier: 3.761A pdb=" N LYS C 47 " --> pdb=" O ASN C 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 48 through 75 Processing helix chain 'C' and resid 78 through 105 removed outlier: 3.645A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR C 87 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL C 88 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU C 118 " --> pdb=" O ASN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 167 removed outlier: 3.815A pdb=" N SER C 131 " --> pdb=" O GLY C 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU C 161 " --> pdb=" O MET C 157 " (cutoff:3.500A) Proline residue: C 162 - end of helix removed outlier: 3.606A pdb=" N LEU C 166 " --> pdb=" O PRO C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU C 199 " --> pdb=" O SER C 195 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ALA C 215 " --> pdb=" O PHE C 211 " (cutoff:3.500A) Proline residue: C 216 - end of helix Processing helix chain 'C' and resid 318 through 366 removed outlier: 3.841A pdb=" N SER C 343 " --> pdb=" O GLN C 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR C 345 " --> pdb=" O VAL C 341 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 407 removed outlier: 4.265A pdb=" N GLY C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG C 387 " --> pdb=" O TYR C 383 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL C 398 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA C 399 " --> pdb=" O ALA C 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS C 407 " --> pdb=" O LEU C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN C 426 " --> pdb=" O ARG C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 468 Processing helix chain 'D' and resid 13 through 31 Processing helix chain 'D' and resid 44 through 47 removed outlier: 3.761A pdb=" N LYS D 47 " --> pdb=" O ASN D 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 44 through 47' Processing helix chain 'D' and resid 48 through 75 Processing helix chain 'D' and resid 78 through 105 removed outlier: 3.646A pdb=" N LEU D 83 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL D 88 " --> pdb=" O ASN D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 removed outlier: 3.851A pdb=" N GLU D 118 " --> pdb=" O ASN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 167 removed outlier: 3.816A pdb=" N SER D 131 " --> pdb=" O GLY D 127 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Proline residue: D 162 - end of helix removed outlier: 3.605A pdb=" N LEU D 166 " --> pdb=" O PRO D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 247 removed outlier: 3.767A pdb=" N GLU D 199 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA D 215 " --> pdb=" O PHE D 211 " (cutoff:3.500A) Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 318 through 366 removed outlier: 3.840A pdb=" N SER D 343 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N SER D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N TYR D 345 " --> pdb=" O VAL D 341 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N ALA D 366 " --> pdb=" O TYR D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 407 removed outlier: 4.264A pdb=" N GLY D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG D 387 " --> pdb=" O TYR D 383 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL D 398 " --> pdb=" O LEU D 394 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N HIS D 407 " --> pdb=" O LEU D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 418 through 433 removed outlier: 3.683A pdb=" N GLN D 426 " --> pdb=" O ARG D 422 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 972 hydrogen bonds defined for protein. 2892 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 5.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3558 1.34 - 1.46: 2825 1.46 - 1.58: 5697 1.58 - 1.69: 0 1.69 - 1.81: 172 Bond restraints: 12252 Sorted by residual: bond pdb=" C SER D 195 " pdb=" N PRO D 196 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 7.07e+00 bond pdb=" C SER C 195 " pdb=" N PRO C 196 " ideal model delta sigma weight residual 1.336 1.368 -0.032 1.20e-02 6.94e+03 6.96e+00 bond pdb=" C SER A 195 " pdb=" N PRO A 196 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.80e+00 bond pdb=" C SER B 195 " pdb=" N PRO B 196 " ideal model delta sigma weight residual 1.336 1.367 -0.031 1.20e-02 6.94e+03 6.67e+00 bond pdb=" C VAL D 374 " pdb=" N PRO D 375 " ideal model delta sigma weight residual 1.334 1.356 -0.022 1.51e-02 4.39e+03 2.13e+00 ... (remaining 12247 not shown) Histogram of bond angle deviations from ideal: 98.28 - 105.43: 169 105.43 - 112.58: 6565 112.58 - 119.73: 3787 119.73 - 126.87: 5959 126.87 - 134.02: 132 Bond angle restraints: 16612 Sorted by residual: angle pdb=" CA THR C 367 " pdb=" C THR C 367 " pdb=" N SER C 368 " ideal model delta sigma weight residual 115.55 120.52 -4.97 1.33e+00 5.65e-01 1.40e+01 angle pdb=" CA THR A 367 " pdb=" C THR A 367 " pdb=" N SER A 368 " ideal model delta sigma weight residual 115.55 120.51 -4.96 1.33e+00 5.65e-01 1.39e+01 angle pdb=" C THR A 367 " pdb=" CA THR A 367 " pdb=" CB THR A 367 " ideal model delta sigma weight residual 109.50 115.79 -6.29 1.69e+00 3.50e-01 1.39e+01 angle pdb=" CA THR B 367 " pdb=" C THR B 367 " pdb=" N SER B 368 " ideal model delta sigma weight residual 115.55 120.50 -4.95 1.33e+00 5.65e-01 1.39e+01 angle pdb=" C THR C 367 " pdb=" CA THR C 367 " pdb=" CB THR C 367 " ideal model delta sigma weight residual 109.50 115.75 -6.25 1.69e+00 3.50e-01 1.37e+01 ... (remaining 16607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 6414 17.55 - 35.10: 598 35.10 - 52.65: 152 52.65 - 70.20: 24 70.20 - 87.75: 8 Dihedral angle restraints: 7196 sinusoidal: 2740 harmonic: 4456 Sorted by residual: dihedral pdb=" CA ASN A 85 " pdb=" C ASN A 85 " pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta harmonic sigma weight residual -180.00 -159.17 -20.83 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ASN C 85 " pdb=" C ASN C 85 " pdb=" N ILE C 86 " pdb=" CA ILE C 86 " ideal model delta harmonic sigma weight residual -180.00 -159.18 -20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ASN D 85 " pdb=" C ASN D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual -180.00 -159.21 -20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 7193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1275 0.037 - 0.074: 522 0.074 - 0.111: 151 0.111 - 0.148: 32 0.148 - 0.185: 12 Chirality restraints: 1992 Sorted by residual: chirality pdb=" CG LEU D 83 " pdb=" CB LEU D 83 " pdb=" CD1 LEU D 83 " pdb=" CD2 LEU D 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CG LEU B 83 " pdb=" CB LEU B 83 " pdb=" CD1 LEU B 83 " pdb=" CD2 LEU B 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CG LEU A 83 " pdb=" CB LEU A 83 " pdb=" CD1 LEU A 83 " pdb=" CD2 LEU A 83 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 8.44e-01 ... (remaining 1989 not shown) Planarity restraints: 1988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 96 " -0.013 2.00e-02 2.50e+03 2.63e-02 6.92e+00 pdb=" C CYS B 96 " 0.046 2.00e-02 2.50e+03 pdb=" O CYS B 96 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL B 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 96 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.79e+00 pdb=" C CYS A 96 " 0.045 2.00e-02 2.50e+03 pdb=" O CYS A 96 " -0.017 2.00e-02 2.50e+03 pdb=" N VAL A 97 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS C 96 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C CYS C 96 " -0.045 2.00e-02 2.50e+03 pdb=" O CYS C 96 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL C 97 " 0.015 2.00e-02 2.50e+03 ... (remaining 1985 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3052 2.79 - 3.32: 12148 3.32 - 3.84: 19802 3.84 - 4.37: 21248 4.37 - 4.90: 37126 Nonbonded interactions: 93376 Sorted by model distance: nonbonded pdb=" OE1 GLU C 397 " pdb=" NH1 ARG D 442 " model vdw 2.261 2.520 nonbonded pdb=" OG SER A 78 " pdb=" OE1 GLN A 81 " model vdw 2.281 2.440 nonbonded pdb=" OG SER D 78 " pdb=" OE1 GLN D 81 " model vdw 2.281 2.440 nonbonded pdb=" OG SER B 78 " pdb=" OE1 GLN B 81 " model vdw 2.281 2.440 nonbonded pdb=" OG SER C 78 " pdb=" OE1 GLN C 81 " model vdw 2.282 2.440 ... (remaining 93371 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.010 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 6.360 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 35.340 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 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 : 0.004 0.033 12252 Z= 0.254 Angle : 0.808 7.888 16612 Z= 0.482 Chirality : 0.045 0.185 1992 Planarity : 0.007 0.057 1988 Dihedral : 15.151 87.752 4300 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.90 % Allowed : 5.00 % Favored : 94.10 % 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: -0.82 (0.20), residues: 1476 helix: -0.08 (0.14), residues: 1188 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 155 HIS 0.004 0.001 HIS B 420 PHE 0.011 0.001 PHE D 450 TYR 0.017 0.002 TYR D 204 ARG 0.002 0.000 ARG B 422 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 406 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8279 (t0) cc_final: 0.7652 (t0) REVERT: A 110 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7839 (tp30) REVERT: A 128 TYR cc_start: 0.8299 (t80) cc_final: 0.8029 (t80) REVERT: A 158 TRP cc_start: 0.7992 (t-100) cc_final: 0.7602 (m-10) REVERT: A 205 GLU cc_start: 0.8332 (tm-30) cc_final: 0.7843 (tm-30) REVERT: A 214 THR cc_start: 0.8884 (p) cc_final: 0.8682 (m) REVERT: A 419 ASP cc_start: 0.7632 (p0) cc_final: 0.7397 (p0) REVERT: B 54 TYR cc_start: 0.8497 (t80) cc_final: 0.8273 (t80) REVERT: B 84 ASN cc_start: 0.8203 (t0) cc_final: 0.7849 (t0) REVERT: B 110 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7930 (tp30) REVERT: B 128 TYR cc_start: 0.8213 (t80) cc_final: 0.7962 (t80) REVERT: B 158 TRP cc_start: 0.8032 (t-100) cc_final: 0.7764 (m-10) REVERT: B 198 ASN cc_start: 0.7890 (t0) cc_final: 0.7617 (t0) REVERT: B 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.8107 (tm-30) REVERT: B 397 GLU cc_start: 0.7850 (tp30) cc_final: 0.7641 (tp30) REVERT: B 419 ASP cc_start: 0.7689 (p0) cc_final: 0.7422 (p0) REVERT: C 45 GLN cc_start: 0.7268 (pm20) cc_final: 0.6914 (pm20) REVERT: C 54 TYR cc_start: 0.8194 (t80) cc_final: 0.7895 (t80) REVERT: C 84 ASN cc_start: 0.8204 (t0) cc_final: 0.7682 (t0) REVERT: C 128 TYR cc_start: 0.8203 (t80) cc_final: 0.7939 (t80) REVERT: C 158 TRP cc_start: 0.8054 (t-100) cc_final: 0.7668 (m-10) REVERT: C 184 VAL cc_start: 0.7336 (p) cc_final: 0.6906 (p) REVERT: C 198 ASN cc_start: 0.7887 (t0) cc_final: 0.7342 (t0) REVERT: C 205 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7795 (tm-30) REVERT: C 214 THR cc_start: 0.9045 (p) cc_final: 0.8786 (p) REVERT: C 351 PHE cc_start: 0.8671 (t80) cc_final: 0.8414 (m-80) REVERT: C 419 ASP cc_start: 0.7718 (p0) cc_final: 0.7486 (p0) REVERT: D 84 ASN cc_start: 0.8322 (t0) cc_final: 0.7644 (t0) REVERT: D 110 GLU cc_start: 0.8250 (tm-30) cc_final: 0.7888 (tp30) REVERT: D 128 TYR cc_start: 0.8325 (t80) cc_final: 0.7980 (t80) REVERT: D 158 TRP cc_start: 0.7974 (t-100) cc_final: 0.7643 (m-10) REVERT: D 205 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7998 (tm-30) outliers start: 12 outliers final: 4 residues processed: 418 average time/residue: 0.2264 time to fit residues: 134.9772 Evaluate side-chains 233 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 229 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 100 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 38 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 116 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS B 433 GLN C 33 HIS C 420 HIS C 433 GLN D 233 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12252 Z= 0.191 Angle : 0.599 6.801 16612 Z= 0.311 Chirality : 0.037 0.132 1992 Planarity : 0.004 0.046 1988 Dihedral : 3.937 14.058 1628 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.54 % Allowed : 15.82 % Favored : 81.64 % 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 (0.22), residues: 1476 helix: 1.72 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -1.53 (0.38), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 155 HIS 0.004 0.001 HIS B 233 PHE 0.011 0.001 PHE B 450 TYR 0.020 0.002 TYR A 362 ARG 0.007 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 288 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.9285 (tp) cc_final: 0.9025 (tp) REVERT: A 110 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7824 (tp30) REVERT: A 158 TRP cc_start: 0.7943 (t-100) cc_final: 0.7603 (m-10) REVERT: A 205 GLU cc_start: 0.8409 (tm-30) cc_final: 0.7855 (tm-30) REVERT: A 214 THR cc_start: 0.8640 (p) cc_final: 0.8349 (t) REVERT: A 233 HIS cc_start: 0.8144 (t-90) cc_final: 0.7907 (t70) REVERT: A 377 MET cc_start: 0.8443 (mpp) cc_final: 0.8033 (mpp) REVERT: A 394 LEU cc_start: 0.9245 (mt) cc_final: 0.9031 (mt) REVERT: A 419 ASP cc_start: 0.7721 (p0) cc_final: 0.7496 (p0) REVERT: A 465 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8430 (tt) REVERT: B 110 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7842 (tp30) REVERT: B 198 ASN cc_start: 0.8191 (t0) cc_final: 0.7672 (t0) REVERT: B 205 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8041 (tm-30) REVERT: B 397 GLU cc_start: 0.7792 (tp30) cc_final: 0.7555 (tp30) REVERT: B 419 ASP cc_start: 0.7799 (p0) cc_final: 0.7550 (p0) REVERT: B 465 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8482 (tt) REVERT: C 17 LEU cc_start: 0.9436 (tt) cc_final: 0.9171 (pp) REVERT: C 54 TYR cc_start: 0.8231 (t80) cc_final: 0.7984 (t80) REVERT: C 95 SER cc_start: 0.9360 (p) cc_final: 0.9074 (p) REVERT: C 128 TYR cc_start: 0.8406 (t80) cc_final: 0.8151 (t80) REVERT: C 198 ASN cc_start: 0.8135 (t0) cc_final: 0.7476 (t0) REVERT: C 205 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7682 (tm-30) REVERT: C 214 THR cc_start: 0.8829 (p) cc_final: 0.8485 (t) REVERT: C 239 MET cc_start: 0.8400 (tpp) cc_final: 0.8139 (tpp) REVERT: C 419 ASP cc_start: 0.7806 (p0) cc_final: 0.7566 (p0) REVERT: C 465 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8729 (mm) REVERT: D 110 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7807 (tp30) REVERT: D 136 THR cc_start: 0.9489 (p) cc_final: 0.9274 (p) REVERT: D 158 TRP cc_start: 0.7961 (t-100) cc_final: 0.7733 (m-10) REVERT: D 205 GLU cc_start: 0.8432 (tm-30) cc_final: 0.7906 (tm-30) REVERT: D 377 MET cc_start: 0.8484 (mpp) cc_final: 0.8178 (mpp) REVERT: D 465 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8463 (tt) outliers start: 34 outliers final: 16 residues processed: 305 average time/residue: 0.1856 time to fit residues: 86.2148 Evaluate side-chains 258 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 238 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 111 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 HIS B 233 HIS B 407 HIS C 84 ASN ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 HIS ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12252 Z= 0.195 Angle : 0.588 8.234 16612 Z= 0.302 Chirality : 0.038 0.158 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.701 15.793 1624 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.51 % Allowed : 18.88 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.22), residues: 1476 helix: 2.29 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -1.13 (0.39), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 20 HIS 0.006 0.001 HIS B 233 PHE 0.011 0.001 PHE A 92 TYR 0.020 0.002 TYR C 204 ARG 0.005 0.000 ARG D 431 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 265 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7903 (tp30) REVERT: A 136 THR cc_start: 0.9475 (p) cc_final: 0.9247 (p) REVERT: A 205 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7781 (tm-30) REVERT: A 214 THR cc_start: 0.8522 (p) cc_final: 0.8203 (t) REVERT: A 377 MET cc_start: 0.8445 (mpp) cc_final: 0.8129 (mpp) REVERT: A 394 LEU cc_start: 0.9224 (mt) cc_final: 0.8988 (mt) REVERT: A 419 ASP cc_start: 0.7753 (p0) cc_final: 0.7532 (p0) REVERT: A 465 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8418 (tt) REVERT: B 110 GLU cc_start: 0.8465 (tm-30) cc_final: 0.7949 (tp30) REVERT: B 141 LYS cc_start: 0.8902 (mtmt) cc_final: 0.8580 (pttp) REVERT: B 197 MET cc_start: 0.6982 (tpp) cc_final: 0.6707 (tpp) REVERT: B 198 ASN cc_start: 0.8146 (t0) cc_final: 0.7530 (t0) REVERT: B 205 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8053 (tm-30) REVERT: B 214 THR cc_start: 0.8672 (m) cc_final: 0.8460 (t) REVERT: B 377 MET cc_start: 0.8695 (mmm) cc_final: 0.8257 (mpp) REVERT: B 419 ASP cc_start: 0.7831 (p0) cc_final: 0.7560 (p0) REVERT: B 465 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8469 (tt) REVERT: C 54 TYR cc_start: 0.8234 (t80) cc_final: 0.8017 (t80) REVERT: C 95 SER cc_start: 0.9365 (p) cc_final: 0.9098 (p) REVERT: C 128 TYR cc_start: 0.8491 (t80) cc_final: 0.8225 (t80) REVERT: C 205 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7729 (tm-30) REVERT: C 214 THR cc_start: 0.8701 (p) cc_final: 0.8363 (t) REVERT: C 222 MET cc_start: 0.8311 (tmm) cc_final: 0.7987 (tmm) REVERT: C 239 MET cc_start: 0.8433 (tpp) cc_final: 0.6224 (tpp) REVERT: C 242 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: C 383 TYR cc_start: 0.8511 (t80) cc_final: 0.8017 (t80) REVERT: C 419 ASP cc_start: 0.7857 (p0) cc_final: 0.7586 (p0) REVERT: C 465 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8709 (mm) REVERT: D 110 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7833 (tp30) REVERT: D 158 TRP cc_start: 0.7943 (t-100) cc_final: 0.7679 (m-10) REVERT: D 197 MET cc_start: 0.6500 (tpp) cc_final: 0.6234 (tpp) REVERT: D 205 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7868 (tm-30) REVERT: D 214 THR cc_start: 0.8713 (m) cc_final: 0.8482 (t) REVERT: D 377 MET cc_start: 0.8440 (mpp) cc_final: 0.8183 (mpp) REVERT: D 465 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 47 outliers final: 26 residues processed: 297 average time/residue: 0.1873 time to fit residues: 85.6285 Evaluate side-chains 256 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 225 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 151 SER Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 415 VAL Chi-restraints excluded: chain B residue 420 HIS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 21 ILE Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 166 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 133 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 chunk 38 optimal weight: 0.0570 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12252 Z= 0.173 Angle : 0.569 8.568 16612 Z= 0.291 Chirality : 0.038 0.143 1992 Planarity : 0.003 0.041 1988 Dihedral : 3.527 15.150 1624 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.58 % Allowed : 20.07 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.22), residues: 1476 helix: 2.55 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.97 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 20 HIS 0.005 0.000 HIS A 233 PHE 0.011 0.001 PHE A 92 TYR 0.023 0.002 TYR B 99 ARG 0.003 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 1.489 Fit side-chains revert: symmetry clash REVERT: A 110 GLU cc_start: 0.8440 (tm-30) cc_final: 0.7933 (tp30) REVERT: A 197 MET cc_start: 0.6995 (tpp) cc_final: 0.6457 (tpp) REVERT: A 205 GLU cc_start: 0.8320 (tm-30) cc_final: 0.7224 (tm-30) REVERT: A 214 THR cc_start: 0.8466 (p) cc_final: 0.8255 (t) REVERT: A 377 MET cc_start: 0.8406 (mpp) cc_final: 0.8181 (mpp) REVERT: A 382 MET cc_start: 0.8685 (tpp) cc_final: 0.8458 (tpt) REVERT: A 394 LEU cc_start: 0.9189 (mt) cc_final: 0.8961 (mt) REVERT: A 419 ASP cc_start: 0.7806 (p0) cc_final: 0.7597 (p0) REVERT: A 465 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8429 (tt) REVERT: B 110 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7932 (tp30) REVERT: B 141 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8462 (pttp) REVERT: B 158 TRP cc_start: 0.7893 (t-100) cc_final: 0.7685 (t60) REVERT: B 197 MET cc_start: 0.6918 (tpp) cc_final: 0.6616 (tpp) REVERT: B 198 ASN cc_start: 0.8198 (t0) cc_final: 0.7539 (t0) REVERT: B 205 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7470 (tm-30) REVERT: B 377 MET cc_start: 0.8753 (mmm) cc_final: 0.8297 (mpp) REVERT: B 419 ASP cc_start: 0.7778 (p0) cc_final: 0.7498 (p0) REVERT: B 465 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8442 (tt) REVERT: C 95 SER cc_start: 0.9310 (p) cc_final: 0.9063 (p) REVERT: C 128 TYR cc_start: 0.8457 (t80) cc_final: 0.8217 (t80) REVERT: C 198 ASN cc_start: 0.8218 (t0) cc_final: 0.7654 (t0) REVERT: C 205 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7776 (tm-30) REVERT: C 214 THR cc_start: 0.8600 (p) cc_final: 0.8362 (t) REVERT: C 239 MET cc_start: 0.8415 (tpp) cc_final: 0.6287 (tpp) REVERT: C 242 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7719 (pp20) REVERT: C 383 TYR cc_start: 0.8505 (t80) cc_final: 0.7845 (t80) REVERT: C 419 ASP cc_start: 0.7826 (p0) cc_final: 0.7552 (p0) REVERT: C 465 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8740 (mm) REVERT: D 20 TRP cc_start: 0.8562 (t-100) cc_final: 0.8173 (t-100) REVERT: D 110 GLU cc_start: 0.8443 (tm-30) cc_final: 0.7874 (tp30) REVERT: D 197 MET cc_start: 0.6645 (tpp) cc_final: 0.6260 (tpp) REVERT: D 205 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7267 (tm-30) REVERT: D 352 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8846 (t) REVERT: D 377 MET cc_start: 0.8391 (mpp) cc_final: 0.8163 (mpp) REVERT: D 382 MET cc_start: 0.8701 (tpp) cc_final: 0.8464 (tpt) REVERT: D 465 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8421 (tt) outliers start: 48 outliers final: 22 residues processed: 308 average time/residue: 0.1906 time to fit residues: 90.4890 Evaluate side-chains 272 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 244 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 355 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 151 SER Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 0.1980 chunk 106 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 128 optimal weight: 0.7980 chunk 36 optimal weight: 0.0050 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 HIS D 407 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12252 Z= 0.164 Angle : 0.594 10.187 16612 Z= 0.295 Chirality : 0.037 0.165 1992 Planarity : 0.003 0.040 1988 Dihedral : 3.450 15.737 1624 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.91 % Allowed : 22.39 % Favored : 74.70 % 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: 3.07 (0.22), residues: 1476 helix: 2.62 (0.15), residues: 1208 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 20 HIS 0.008 0.001 HIS D 233 PHE 0.010 0.001 PHE C 346 TYR 0.019 0.001 TYR D 99 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 278 time to evaluate : 1.326 Fit side-chains REVERT: A 141 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8475 (pttp) REVERT: A 160 LEU cc_start: 0.8580 (tt) cc_final: 0.8215 (mp) REVERT: A 205 GLU cc_start: 0.8223 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 214 THR cc_start: 0.8480 (p) cc_final: 0.8203 (t) REVERT: A 220 ASP cc_start: 0.8540 (t70) cc_final: 0.8229 (t70) REVERT: B 95 SER cc_start: 0.9310 (p) cc_final: 0.9056 (p) REVERT: B 110 GLU cc_start: 0.8523 (tm-30) cc_final: 0.7976 (tp30) REVERT: B 197 MET cc_start: 0.6873 (tpp) cc_final: 0.6563 (tpp) REVERT: B 198 ASN cc_start: 0.8216 (t0) cc_final: 0.7544 (t0) REVERT: B 205 GLU cc_start: 0.8425 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 377 MET cc_start: 0.8726 (mmm) cc_final: 0.8365 (mpp) REVERT: B 419 ASP cc_start: 0.7750 (p0) cc_final: 0.7476 (p0) REVERT: B 465 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 95 SER cc_start: 0.9268 (p) cc_final: 0.9037 (p) REVERT: C 128 TYR cc_start: 0.8416 (t80) cc_final: 0.8171 (t80) REVERT: C 198 ASN cc_start: 0.8356 (t0) cc_final: 0.7761 (t0) REVERT: C 205 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7768 (tm-30) REVERT: C 214 THR cc_start: 0.8610 (p) cc_final: 0.8302 (t) REVERT: C 239 MET cc_start: 0.8403 (tpp) cc_final: 0.6168 (tpp) REVERT: C 242 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7677 (pp20) REVERT: C 336 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8008 (pp20) REVERT: C 419 ASP cc_start: 0.7764 (p0) cc_final: 0.7482 (p0) REVERT: C 465 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (mm) REVERT: D 20 TRP cc_start: 0.8540 (t-100) cc_final: 0.8186 (t-100) REVERT: D 110 GLU cc_start: 0.8449 (tm-30) cc_final: 0.7800 (tp30) REVERT: D 220 ASP cc_start: 0.8522 (t70) cc_final: 0.8186 (t70) REVERT: D 352 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8922 (t) REVERT: D 382 MET cc_start: 0.8584 (tpp) cc_final: 0.8322 (tpt) REVERT: D 426 GLN cc_start: 0.8227 (tp-100) cc_final: 0.7990 (tp-100) REVERT: D 433 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8209 (tm-30) REVERT: D 465 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8426 (tt) outliers start: 39 outliers final: 16 residues processed: 305 average time/residue: 0.1990 time to fit residues: 92.3644 Evaluate side-chains 261 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 240 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 415 VAL Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 465 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.7980 chunk 128 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 143 optimal weight: 0.0040 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12252 Z= 0.185 Angle : 0.604 8.404 16612 Z= 0.303 Chirality : 0.038 0.167 1992 Planarity : 0.004 0.040 1988 Dihedral : 3.439 15.501 1624 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.84 % Allowed : 24.40 % Favored : 72.76 % 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: 3.11 (0.22), residues: 1476 helix: 2.67 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.92 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 20 HIS 0.003 0.000 HIS C 233 PHE 0.014 0.001 PHE B 92 TYR 0.022 0.002 TYR D 99 ARG 0.004 0.000 ARG D 373 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 262 time to evaluate : 1.459 Fit side-chains revert: symmetry clash REVERT: A 94 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8562 (mm-40) REVERT: A 160 LEU cc_start: 0.8567 (tt) cc_final: 0.8242 (mp) REVERT: A 214 THR cc_start: 0.8334 (p) cc_final: 0.8101 (t) REVERT: B 92 PHE cc_start: 0.8433 (m-80) cc_final: 0.8109 (m-80) REVERT: B 110 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8139 (tp30) REVERT: B 197 MET cc_start: 0.6936 (tpp) cc_final: 0.6602 (tpp) REVERT: B 377 MET cc_start: 0.8809 (mmm) cc_final: 0.8386 (mpp) REVERT: B 419 ASP cc_start: 0.7845 (p0) cc_final: 0.7563 (p0) REVERT: B 465 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8417 (tt) REVERT: C 94 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8519 (tp-100) REVERT: C 95 SER cc_start: 0.9292 (p) cc_final: 0.9055 (p) REVERT: C 128 TYR cc_start: 0.8454 (t80) cc_final: 0.8226 (t80) REVERT: C 198 ASN cc_start: 0.8399 (t0) cc_final: 0.7819 (t0) REVERT: C 205 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7278 (tm-30) REVERT: C 214 THR cc_start: 0.8596 (p) cc_final: 0.8285 (t) REVERT: C 239 MET cc_start: 0.8443 (tpp) cc_final: 0.6261 (tpp) REVERT: C 242 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7703 (pp20) REVERT: C 419 ASP cc_start: 0.7820 (p0) cc_final: 0.7533 (p0) REVERT: D 94 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8585 (mm-40) REVERT: D 157 MET cc_start: 0.8554 (tmm) cc_final: 0.8185 (ppp) REVERT: D 220 ASP cc_start: 0.8497 (t70) cc_final: 0.8292 (t70) REVERT: D 232 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7258 (tm-30) REVERT: D 352 THR cc_start: 0.9132 (OUTLIER) cc_final: 0.8878 (t) REVERT: D 426 GLN cc_start: 0.8298 (tp-100) cc_final: 0.8033 (tp-100) REVERT: D 433 GLN cc_start: 0.8602 (tm-30) cc_final: 0.8210 (tm-30) REVERT: D 465 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8436 (tt) outliers start: 38 outliers final: 21 residues processed: 292 average time/residue: 0.1802 time to fit residues: 82.8522 Evaluate side-chains 260 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 388 ILE Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 385 PHE Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 8.9990 chunk 16 optimal weight: 0.0370 chunk 81 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 86 optimal weight: 0.2980 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12252 Z= 0.179 Angle : 0.633 10.917 16612 Z= 0.310 Chirality : 0.038 0.168 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.433 14.862 1624 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.13 % Allowed : 25.52 % Favored : 71.34 % 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: 3.14 (0.22), residues: 1476 helix: 2.68 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.84 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 20 HIS 0.002 0.000 HIS A 33 PHE 0.014 0.001 PHE D 92 TYR 0.023 0.002 TYR A 99 ARG 0.003 0.000 ARG C 43 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 266 time to evaluate : 1.351 Fit side-chains REVERT: A 94 GLN cc_start: 0.8767 (mm-40) cc_final: 0.8561 (mm-40) REVERT: A 160 LEU cc_start: 0.8588 (tt) cc_final: 0.8238 (mp) REVERT: B 92 PHE cc_start: 0.8410 (m-80) cc_final: 0.8046 (m-80) REVERT: B 94 GLN cc_start: 0.8768 (mm-40) cc_final: 0.8542 (tp-100) REVERT: B 110 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 160 LEU cc_start: 0.8518 (tt) cc_final: 0.8169 (mp) REVERT: B 197 MET cc_start: 0.6902 (tpp) cc_final: 0.6574 (tpp) REVERT: B 377 MET cc_start: 0.8788 (mmm) cc_final: 0.8362 (mpp) REVERT: B 419 ASP cc_start: 0.7864 (p0) cc_final: 0.7562 (p0) REVERT: B 465 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8454 (tt) REVERT: C 92 PHE cc_start: 0.8257 (m-80) cc_final: 0.7859 (m-80) REVERT: C 95 SER cc_start: 0.9325 (p) cc_final: 0.9049 (p) REVERT: C 128 TYR cc_start: 0.8492 (t80) cc_final: 0.8177 (t80) REVERT: C 198 ASN cc_start: 0.8470 (t0) cc_final: 0.7989 (t0) REVERT: C 205 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7892 (tm-30) REVERT: C 214 THR cc_start: 0.8558 (p) cc_final: 0.8294 (t) REVERT: C 239 MET cc_start: 0.8462 (tpp) cc_final: 0.6103 (tpp) REVERT: C 242 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7263 (pp20) REVERT: C 419 ASP cc_start: 0.7796 (p0) cc_final: 0.7510 (p0) REVERT: D 92 PHE cc_start: 0.8333 (m-80) cc_final: 0.7992 (m-80) REVERT: D 94 GLN cc_start: 0.8815 (mm-40) cc_final: 0.8581 (mm-40) REVERT: D 110 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7905 (tp30) REVERT: D 157 MET cc_start: 0.8544 (tmm) cc_final: 0.8292 (ppp) REVERT: D 197 MET cc_start: 0.6848 (ttm) cc_final: 0.6563 (tpp) REVERT: D 232 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7271 (tm-30) REVERT: D 352 THR cc_start: 0.9134 (OUTLIER) cc_final: 0.8867 (t) REVERT: D 426 GLN cc_start: 0.8299 (tp-100) cc_final: 0.8021 (tp-100) REVERT: D 433 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8233 (tm-30) REVERT: D 465 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 42 outliers final: 24 residues processed: 296 average time/residue: 0.1899 time to fit residues: 86.7694 Evaluate side-chains 280 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 252 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 466 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12252 Z= 0.191 Angle : 0.628 9.780 16612 Z= 0.312 Chirality : 0.039 0.139 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.409 14.646 1624 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.06 % Allowed : 25.90 % Favored : 71.04 % 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: 3.19 (0.22), residues: 1476 helix: 2.71 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.83 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 20 HIS 0.002 0.000 HIS C 233 PHE 0.014 0.001 PHE D 92 TYR 0.028 0.002 TYR A 99 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 252 time to evaluate : 1.295 Fit side-chains REVERT: A 94 GLN cc_start: 0.8787 (mm-40) cc_final: 0.8560 (mm-40) REVERT: A 160 LEU cc_start: 0.8599 (tt) cc_final: 0.8244 (mp) REVERT: A 392 CYS cc_start: 0.8267 (m) cc_final: 0.7847 (m) REVERT: B 94 GLN cc_start: 0.8745 (mm-40) cc_final: 0.8533 (tp-100) REVERT: B 160 LEU cc_start: 0.8550 (tt) cc_final: 0.8174 (mp) REVERT: B 197 MET cc_start: 0.7028 (tpp) cc_final: 0.6716 (tpp) REVERT: B 377 MET cc_start: 0.8797 (mmm) cc_final: 0.8351 (mpp) REVERT: B 419 ASP cc_start: 0.7878 (p0) cc_final: 0.7574 (p0) REVERT: B 465 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 92 PHE cc_start: 0.8219 (m-80) cc_final: 0.7882 (m-80) REVERT: C 95 SER cc_start: 0.9339 (p) cc_final: 0.9044 (p) REVERT: C 198 ASN cc_start: 0.8457 (t0) cc_final: 0.8032 (t0) REVERT: C 205 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8054 (tm-30) REVERT: C 214 THR cc_start: 0.8523 (p) cc_final: 0.8253 (t) REVERT: C 239 MET cc_start: 0.8474 (tpp) cc_final: 0.8268 (tpp) REVERT: C 419 ASP cc_start: 0.7838 (p0) cc_final: 0.7543 (p0) REVERT: D 92 PHE cc_start: 0.8409 (m-80) cc_final: 0.8084 (m-80) REVERT: D 94 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8578 (mm-40) REVERT: D 110 GLU cc_start: 0.8528 (tm-30) cc_final: 0.7893 (tp30) REVERT: D 197 MET cc_start: 0.6910 (ttm) cc_final: 0.6702 (ttm) REVERT: D 232 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7362 (tm-30) REVERT: D 352 THR cc_start: 0.9121 (OUTLIER) cc_final: 0.8855 (t) REVERT: D 433 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8249 (tm-30) REVERT: D 465 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8438 (tt) outliers start: 41 outliers final: 23 residues processed: 281 average time/residue: 0.1903 time to fit residues: 82.6619 Evaluate side-chains 268 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 242 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12252 Z= 0.198 Angle : 0.661 9.836 16612 Z= 0.326 Chirality : 0.039 0.181 1992 Planarity : 0.004 0.041 1988 Dihedral : 3.419 15.527 1624 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.54 % Allowed : 26.64 % Favored : 70.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 3.24 (0.22), residues: 1476 helix: 2.75 (0.15), residues: 1204 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 20 HIS 0.002 0.000 HIS B 40 PHE 0.013 0.001 PHE D 92 TYR 0.027 0.002 TYR A 99 ARG 0.003 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 262 time to evaluate : 1.442 Fit side-chains REVERT: A 94 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8550 (mm-40) REVERT: A 160 LEU cc_start: 0.8592 (tt) cc_final: 0.8209 (mp) REVERT: A 392 CYS cc_start: 0.8258 (m) cc_final: 0.7884 (m) REVERT: B 94 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8510 (tp-100) REVERT: B 197 MET cc_start: 0.7121 (tpp) cc_final: 0.6810 (tpp) REVERT: B 232 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7235 (tm-30) REVERT: B 419 ASP cc_start: 0.7894 (p0) cc_final: 0.7587 (p0) REVERT: B 465 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 20 TRP cc_start: 0.8256 (t60) cc_final: 0.8028 (t60) REVERT: C 92 PHE cc_start: 0.8264 (m-80) cc_final: 0.7948 (m-80) REVERT: C 95 SER cc_start: 0.9373 (p) cc_final: 0.9094 (p) REVERT: C 198 ASN cc_start: 0.8421 (t0) cc_final: 0.8044 (t0) REVERT: C 214 THR cc_start: 0.8482 (p) cc_final: 0.8216 (t) REVERT: C 239 MET cc_start: 0.8464 (tpp) cc_final: 0.8132 (tpp) REVERT: C 419 ASP cc_start: 0.7849 (p0) cc_final: 0.7551 (p0) REVERT: D 92 PHE cc_start: 0.8456 (m-80) cc_final: 0.8128 (m-80) REVERT: D 94 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8542 (mm-40) REVERT: D 110 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8303 (tp30) REVERT: D 197 MET cc_start: 0.7034 (ttm) cc_final: 0.6811 (ttm) REVERT: D 232 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7413 (tm-30) REVERT: D 352 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8889 (t) REVERT: D 433 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8203 (tm-30) REVERT: D 465 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8468 (tt) outliers start: 34 outliers final: 24 residues processed: 289 average time/residue: 0.1763 time to fit residues: 79.5548 Evaluate side-chains 268 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 90 optimal weight: 0.2980 chunk 71 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 433 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12252 Z= 0.205 Angle : 0.682 9.110 16612 Z= 0.334 Chirality : 0.039 0.160 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.424 15.898 1624 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.31 % Allowed : 27.46 % Favored : 70.22 % 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: 3.22 (0.22), residues: 1476 helix: 2.74 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 20 HIS 0.002 0.000 HIS A 33 PHE 0.012 0.001 PHE D 92 TYR 0.027 0.002 TYR A 99 ARG 0.003 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2952 Ramachandran restraints generated. 1476 Oldfield, 0 Emsley, 1476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 250 time to evaluate : 1.596 Fit side-chains REVERT: A 94 GLN cc_start: 0.8772 (mm-40) cc_final: 0.8546 (mm-40) REVERT: A 160 LEU cc_start: 0.8609 (tt) cc_final: 0.8211 (mp) REVERT: A 214 THR cc_start: 0.8633 (t) cc_final: 0.8427 (t) REVERT: A 392 CYS cc_start: 0.8227 (m) cc_final: 0.7867 (m) REVERT: B 160 LEU cc_start: 0.8546 (tt) cc_final: 0.8142 (mp) REVERT: B 197 MET cc_start: 0.7106 (tpp) cc_final: 0.6800 (tpp) REVERT: B 419 ASP cc_start: 0.7907 (p0) cc_final: 0.7602 (p0) REVERT: B 465 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8467 (tt) REVERT: C 20 TRP cc_start: 0.8309 (t60) cc_final: 0.8060 (t60) REVERT: C 95 SER cc_start: 0.9357 (p) cc_final: 0.9069 (p) REVERT: C 110 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8478 (tp30) REVERT: C 198 ASN cc_start: 0.8364 (t0) cc_final: 0.8104 (t0) REVERT: C 214 THR cc_start: 0.8433 (p) cc_final: 0.8183 (t) REVERT: C 419 ASP cc_start: 0.7851 (p0) cc_final: 0.7554 (p0) REVERT: D 92 PHE cc_start: 0.8483 (m-80) cc_final: 0.8158 (m-80) REVERT: D 94 GLN cc_start: 0.8775 (mm-40) cc_final: 0.8540 (mm-40) REVERT: D 110 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7961 (tp30) REVERT: D 232 GLU cc_start: 0.7667 (tm-30) cc_final: 0.7406 (tm-30) REVERT: D 352 THR cc_start: 0.9124 (OUTLIER) cc_final: 0.8867 (t) REVERT: D 382 MET cc_start: 0.8467 (tpp) cc_final: 0.8204 (tpt) REVERT: D 433 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8230 (tm-30) REVERT: D 465 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8452 (tt) outliers start: 31 outliers final: 27 residues processed: 276 average time/residue: 0.1811 time to fit residues: 77.3273 Evaluate side-chains 273 residues out of total 1340 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 243 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 446 VAL Chi-restraints excluded: chain A residue 465 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 224 CYS Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 12 ASP Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 166 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 415 VAL Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 153 PHE Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 224 CYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 446 VAL Chi-restraints excluded: chain D residue 465 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.0770 chunk 108 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.107585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.088874 restraints weight = 29600.070| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 4.40 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12252 Z= 0.200 Angle : 0.698 13.550 16612 Z= 0.336 Chirality : 0.039 0.168 1992 Planarity : 0.004 0.042 1988 Dihedral : 3.414 16.276 1624 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.69 % Allowed : 27.46 % Favored : 69.85 % 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: 3.25 (0.22), residues: 1476 helix: 2.74 (0.14), residues: 1204 sheet: None (None), residues: 0 loop : -0.75 (0.41), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP D 158 HIS 0.002 0.000 HIS A 33 PHE 0.011 0.001 PHE D 92 TYR 0.027 0.002 TYR D 461 ARG 0.003 0.000 ARG C 43 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2547.51 seconds wall clock time: 47 minutes 0.13 seconds (2820.13 seconds total)