Starting phenix.real_space_refine on Sat Aug 10 12:06:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/08_2024/7ccr_30340.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 588 5.49 5 S 58 5.16 5 C 16892 2.51 5 N 5488 2.21 5 O 6696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "H ARG 33": "NH1" <-> "NH2" Residue "K ARG 236": "NH1" <-> "NH2" Residue "K ARG 281": "NH1" <-> "NH2" Residue "K TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "Q ARG 45": "NH1" <-> "NH2" Residue "S ARG 33": "NH1" <-> "NH2" Residue "V ARG 236": "NH1" <-> "NH2" Residue "V ARG 281": "NH1" <-> "NH2" Residue "V TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 29722 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2962 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "M" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "N" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 787 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "P" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "Q" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "R" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 789 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 4, 'TRANS': 97} Chain: "S" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "T" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "U" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "V" Number of atoms: 2962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2962 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 12, 'TRANS': 348} Chain breaks: 1 Time building chain proxies: 16.30, per 1000 atoms: 0.55 Number of scatterers: 29722 At special positions: 0 Unit cell: (158, 165, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 588 15.00 O 6696 8.00 N 5488 7.00 C 16892 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: 16.01 Conformation dependent library (CDL) restraints added in 3.5 seconds 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 66.6% alpha, 5.1% beta 286 base pairs and 510 stacking pairs defined. Time for finding SS restraints: 13.03 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.787A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.577A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.253A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.785A pdb=" N PHE K 203 " --> pdb=" O ASP K 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 200 through 204' Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS K 432 " --> pdb=" O HIS K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.844A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.807A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP K 520 " --> pdb=" O PRO K 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE L 78 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 120 through 132 Processing helix chain 'M' and resid 30 through 42 Processing helix chain 'M' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 94 removed outlier: 3.788A pdb=" N VAL M 86 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.182A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'O' and resid 37 through 49 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 103 through 123 Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 removed outlier: 3.578A pdb=" N ILE P 124 " --> pdb=" O MET P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 37 through 49 Processing helix chain 'S' and resid 55 through 85 Processing helix chain 'S' and resid 90 through 102 Processing helix chain 'S' and resid 103 through 124 Processing helix chain 'V' and resid 161 through 176 Processing helix chain 'V' and resid 178 through 198 removed outlier: 4.252A pdb=" N ALA V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY V 184 " --> pdb=" O SER V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 204 removed outlier: 3.784A pdb=" N PHE V 203 " --> pdb=" O ASP V 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 204 " --> pdb=" O SER V 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 200 through 204' Processing helix chain 'V' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN V 289 " --> pdb=" O LYS V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 335 Processing helix chain 'V' and resid 345 through 354 Processing helix chain 'V' and resid 379 through 389 Processing helix chain 'V' and resid 405 through 424 Processing helix chain 'V' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS V 432 " --> pdb=" O HIS V 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 434 through 449 removed outlier: 3.843A pdb=" N VAL V 438 " --> pdb=" O SER V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 452 through 458 removed outlier: 3.808A pdb=" N ASP V 456 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG V 457 " --> pdb=" O GLN V 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS V 458 " --> pdb=" O TRP V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 477 Processing helix chain 'V' and resid 497 through 513 Processing helix chain 'V' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP V 520 " --> pdb=" O PRO V 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.524A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG L 83 " --> pdb=" O VAL M 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'M' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR M 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR N 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'P' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG R 42 " --> pdb=" O ILE S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'V' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE V 230 " --> pdb=" O ALA V 323 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU V 325 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU V 232 " --> pdb=" O GLU V 325 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU V 322 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR V 358 " --> pdb=" O SER V 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE V 297 " --> pdb=" O LEU V 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU V 311 " --> pdb=" O ILE V 297 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 728 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 286 basepair parallelities 510 stacking parallelities Total time for adding SS restraints: 16.89 Time building geometry restraints manager: 17.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5214 1.33 - 1.45: 10194 1.45 - 1.57: 14790 1.57 - 1.69: 1172 1.69 - 1.81: 88 Bond restraints: 31458 Sorted by residual: bond pdb=" C3' DG T 20 " pdb=" O3' DG T 20 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" C3' DC U 6 " pdb=" O3' DC U 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.32e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.24e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.360 0.062 3.00e-02 1.11e+03 4.23e+00 bond pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 1.523 1.548 -0.025 1.30e-02 5.92e+03 3.59e+00 ... (remaining 31453 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.54: 3076 105.54 - 112.65: 17116 112.65 - 119.76: 10459 119.76 - 126.87: 12763 126.87 - 133.99: 1540 Bond angle restraints: 44954 Sorted by residual: angle pdb=" N LYS V 432 " pdb=" CA LYS V 432 " pdb=" C LYS V 432 " ideal model delta sigma weight residual 111.28 119.14 -7.86 1.09e+00 8.42e-01 5.19e+01 angle pdb=" N LYS K 432 " pdb=" CA LYS K 432 " pdb=" C LYS K 432 " ideal model delta sigma weight residual 111.28 119.12 -7.84 1.09e+00 8.42e-01 5.17e+01 angle pdb=" N LEU V 430 " pdb=" CA LEU V 430 " pdb=" C LEU V 430 " ideal model delta sigma weight residual 111.28 118.24 -6.96 1.09e+00 8.42e-01 4.08e+01 angle pdb=" N LYS K 427 " pdb=" CA LYS K 427 " pdb=" C LYS K 427 " ideal model delta sigma weight residual 110.35 119.03 -8.68 1.36e+00 5.41e-01 4.07e+01 angle pdb=" N LEU K 430 " pdb=" CA LEU K 430 " pdb=" C LEU K 430 " ideal model delta sigma weight residual 111.28 118.22 -6.94 1.09e+00 8.42e-01 4.06e+01 ... (remaining 44949 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 14566 32.34 - 64.68: 2832 64.68 - 97.02: 74 97.02 - 129.36: 2 129.36 - 161.70: 4 Dihedral angle restraints: 17478 sinusoidal: 11068 harmonic: 6410 Sorted by residual: dihedral pdb=" CA PRO O 103 " pdb=" C PRO O 103 " pdb=" N GLY O 104 " pdb=" CA GLY O 104 " ideal model delta harmonic sigma weight residual -180.00 -150.49 -29.51 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 -150.50 -29.50 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA PRO K 361 " pdb=" C PRO K 361 " pdb=" N LYS K 362 " pdb=" CA LYS K 362 " ideal model delta harmonic sigma weight residual 180.00 153.23 26.77 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 17475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 3815 0.061 - 0.123: 1041 0.123 - 0.184: 172 0.184 - 0.245: 26 0.245 - 0.307: 18 Chirality restraints: 5072 Sorted by residual: chirality pdb=" C1' DC T -27 " pdb=" O4' DC T -27 " pdb=" C2' DC T -27 " pdb=" N1 DC T -27 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1' DC I -27 " pdb=" O4' DC I -27 " pdb=" C2' DC I -27 " pdb=" N1 DC I -27 " both_signs ideal model delta sigma weight residual False 2.47 2.16 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C1' DT U 13 " pdb=" O4' DT U 13 " pdb=" C2' DT U 13 " pdb=" N1 DT U 13 " both_signs ideal model delta sigma weight residual False 2.47 2.17 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 5069 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC U 56 " 0.045 2.00e-02 2.50e+03 3.32e-02 2.48e+01 pdb=" N1 DC U 56 " -0.076 2.00e-02 2.50e+03 pdb=" C2 DC U 56 " 0.040 2.00e-02 2.50e+03 pdb=" O2 DC U 56 " -0.019 2.00e-02 2.50e+03 pdb=" N3 DC U 56 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC U 56 " 0.005 2.00e-02 2.50e+03 pdb=" N4 DC U 56 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DC U 56 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DC U 56 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 56 " -0.045 2.00e-02 2.50e+03 3.31e-02 2.47e+01 pdb=" N1 DC J 56 " 0.075 2.00e-02 2.50e+03 pdb=" C2 DC J 56 " -0.040 2.00e-02 2.50e+03 pdb=" O2 DC J 56 " 0.019 2.00e-02 2.50e+03 pdb=" N3 DC J 56 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 56 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 56 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC J 56 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC J 56 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS V 425 " 0.025 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C LYS V 425 " -0.085 2.00e-02 2.50e+03 pdb=" O LYS V 425 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP V 426 " 0.029 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.25: 4 2.25 - 2.92: 10890 2.92 - 3.58: 46988 3.58 - 4.24: 80363 4.24 - 4.90: 118794 Nonbonded interactions: 257039 Sorted by model distance: nonbonded pdb=" OP1 DA U 57 " pdb=" NZ LYS V 350 " model vdw 1.593 3.120 nonbonded pdb=" OP1 DA J 57 " pdb=" NZ LYS K 350 " model vdw 1.593 3.120 nonbonded pdb=" N2 DG T 21 " pdb=" O2 DC U -21 " model vdw 2.244 2.496 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.244 2.496 nonbonded pdb=" O LYS K 362 " pdb=" OG1 THR K 374 " model vdw 2.269 3.040 ... (remaining 257034 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 40 through 134) selection = chain 'L' selection = (chain 'P' and resid 40 through 134) } ncs_group { reference = (chain 'B' and resid 24 through 101) selection = (chain 'F' and resid 24 through 101) selection = (chain 'M' and resid 24 through 101) selection = (chain 'Q' and resid 24 through 101) } ncs_group { reference = (chain 'C' and resid 16 through 116) selection = (chain 'G' and resid 16 through 116) selection = (chain 'N' and resid 16 through 116) selection = (chain 'R' and resid 16 through 116) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 123) selection = chain 'O' selection = (chain 'S' and resid 32 through 123) } ncs_group { reference = chain 'I' selection = chain 'T' } ncs_group { reference = chain 'J' selection = chain 'U' } ncs_group { reference = chain 'K' selection = chain 'V' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 17.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 93.850 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.170 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 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 : 0.007 0.066 31458 Z= 0.410 Angle : 0.963 10.085 44954 Z= 0.579 Chirality : 0.058 0.307 5072 Planarity : 0.009 0.065 3660 Dihedral : 24.746 161.695 13330 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.11 % Allowed : 1.37 % Favored : 98.52 % 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: -2.64 (0.14), residues: 2162 helix: -1.31 (0.11), residues: 1342 sheet: -2.27 (0.44), residues: 90 loop : -2.26 (0.19), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP V 343 HIS 0.021 0.003 HIS G 82 PHE 0.027 0.003 PHE V 280 TYR 0.035 0.004 TYR M 88 ARG 0.009 0.001 ARG A 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 2.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 64 ASN cc_start: 0.9457 (m-40) cc_final: 0.9256 (m110) REVERT: B 68 ASP cc_start: 0.8061 (m-30) cc_final: 0.7701 (m-30) REVERT: C 64 GLU cc_start: 0.8473 (tt0) cc_final: 0.8148 (tm-30) REVERT: D 62 MET cc_start: 0.9410 (mmm) cc_final: 0.8870 (mmm) REVERT: D 73 ILE cc_start: 0.9427 (mt) cc_final: 0.9192 (tp) REVERT: D 95 GLN cc_start: 0.9651 (tt0) cc_final: 0.9110 (tm-30) REVERT: D 106 LEU cc_start: 0.8517 (tt) cc_final: 0.8154 (pp) REVERT: E 51 ILE cc_start: 0.8845 (mt) cc_final: 0.8465 (mm) REVERT: E 54 TYR cc_start: 0.8511 (m-80) cc_final: 0.8245 (m-10) REVERT: E 94 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8037 (mm-30) REVERT: F 37 LEU cc_start: 0.9678 (mt) cc_final: 0.9451 (mt) REVERT: F 72 TYR cc_start: 0.8160 (m-80) cc_final: 0.7547 (m-80) REVERT: G 38 ASN cc_start: 0.7870 (m110) cc_final: 0.7604 (p0) REVERT: G 56 GLU cc_start: 0.8464 (tt0) cc_final: 0.7864 (mt-10) REVERT: G 95 LYS cc_start: 0.9326 (tttt) cc_final: 0.8797 (pttm) REVERT: G 97 LEU cc_start: 0.9091 (mt) cc_final: 0.8667 (mt) REVERT: H 68 ASP cc_start: 0.9276 (t0) cc_final: 0.8218 (t0) REVERT: H 72 ARG cc_start: 0.8782 (mtt180) cc_final: 0.8290 (mtt180) REVERT: H 73 ILE cc_start: 0.9388 (mt) cc_final: 0.9144 (tt) REVERT: H 76 GLU cc_start: 0.8555 (tp30) cc_final: 0.8291 (tp30) REVERT: H 78 SER cc_start: 0.9467 (t) cc_final: 0.9200 (p) REVERT: H 80 LEU cc_start: 0.9256 (mt) cc_final: 0.8338 (mt) REVERT: H 100 LEU cc_start: 0.9028 (mt) cc_final: 0.7525 (mt) REVERT: H 101 LEU cc_start: 0.8558 (mt) cc_final: 0.8317 (mt) REVERT: K 276 MET cc_start: 0.9482 (mmm) cc_final: 0.9084 (tmm) REVERT: K 456 ASP cc_start: 0.8381 (t0) cc_final: 0.8108 (p0) REVERT: L 54 TYR cc_start: 0.9145 (m-80) cc_final: 0.8402 (m-10) REVERT: M 63 GLU cc_start: 0.9281 (mt-10) cc_final: 0.9059 (tp30) REVERT: M 68 ASP cc_start: 0.8266 (m-30) cc_final: 0.7848 (m-30) REVERT: N 64 GLU cc_start: 0.8545 (tt0) cc_final: 0.8261 (tm-30) REVERT: O 51 ASP cc_start: 0.8111 (m-30) cc_final: 0.7832 (t0) REVERT: O 62 MET cc_start: 0.9440 (mmm) cc_final: 0.8941 (mmm) REVERT: O 95 GLN cc_start: 0.9636 (tt0) cc_final: 0.9016 (tm-30) REVERT: O 106 LEU cc_start: 0.8467 (tt) cc_final: 0.8122 (pp) REVERT: P 51 ILE cc_start: 0.8721 (mt) cc_final: 0.8237 (mm) REVERT: P 54 TYR cc_start: 0.8461 (m-80) cc_final: 0.8221 (m-80) REVERT: P 94 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8189 (mm-30) REVERT: P 99 TYR cc_start: 0.8764 (t80) cc_final: 0.8392 (t80) REVERT: Q 37 LEU cc_start: 0.9666 (mt) cc_final: 0.9436 (mt) REVERT: Q 72 TYR cc_start: 0.8200 (m-80) cc_final: 0.7272 (m-80) REVERT: R 38 ASN cc_start: 0.7608 (m110) cc_final: 0.7382 (p0) REVERT: R 56 GLU cc_start: 0.8526 (tt0) cc_final: 0.8014 (mt-10) REVERT: R 95 LYS cc_start: 0.9303 (tttt) cc_final: 0.8723 (pttm) REVERT: R 97 LEU cc_start: 0.9072 (mt) cc_final: 0.8487 (mt) REVERT: S 72 ARG cc_start: 0.8787 (mtt180) cc_final: 0.8480 (mtt180) REVERT: S 73 ILE cc_start: 0.9380 (mt) cc_final: 0.9097 (tt) REVERT: S 76 GLU cc_start: 0.8583 (tp30) cc_final: 0.8017 (tp30) REVERT: S 78 SER cc_start: 0.9437 (t) cc_final: 0.9213 (p) REVERT: S 80 LEU cc_start: 0.9243 (mt) cc_final: 0.8858 (mt) REVERT: S 98 VAL cc_start: 0.9454 (t) cc_final: 0.9165 (p) REVERT: S 100 LEU cc_start: 0.8985 (mt) cc_final: 0.6871 (mt) REVERT: V 276 MET cc_start: 0.9531 (mmm) cc_final: 0.9148 (tmm) REVERT: V 456 ASP cc_start: 0.8318 (t0) cc_final: 0.8058 (p0) outliers start: 2 outliers final: 0 residues processed: 555 average time/residue: 0.4611 time to fit residues: 384.4571 Evaluate side-chains 278 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 10.0000 chunk 203 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 20.0000 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN E 68 GLN E 93 GLN ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS K 192 HIS K 260 ASN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN L 68 GLN ** L 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN P 68 GLN ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 109 HIS V 192 HIS ** V 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 437 HIS V 449 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6954 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 31458 Z= 0.292 Angle : 0.705 8.713 44954 Z= 0.409 Chirality : 0.040 0.196 5072 Planarity : 0.006 0.067 3660 Dihedral : 30.407 166.258 8852 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % 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: -0.62 (0.16), residues: 2162 helix: 0.35 (0.12), residues: 1406 sheet: -2.28 (0.45), residues: 88 loop : -1.64 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP K 375 HIS 0.013 0.003 HIS M 75 PHE 0.022 0.002 PHE V 280 TYR 0.025 0.002 TYR C 39 ARG 0.013 0.001 ARG M 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 2.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 TYR cc_start: 0.8193 (t80) cc_final: 0.7965 (t80) REVERT: B 85 ASP cc_start: 0.8456 (m-30) cc_final: 0.8023 (m-30) REVERT: B 93 GLN cc_start: 0.9420 (pt0) cc_final: 0.8549 (tm-30) REVERT: C 64 GLU cc_start: 0.8544 (tt0) cc_final: 0.8221 (tm-30) REVERT: C 73 ASN cc_start: 0.9513 (t0) cc_final: 0.9272 (t0) REVERT: D 51 ASP cc_start: 0.8200 (t0) cc_final: 0.7434 (t70) REVERT: D 62 MET cc_start: 0.9146 (mmm) cc_final: 0.8713 (mmm) REVERT: D 71 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8546 (mm-30) REVERT: D 73 ILE cc_start: 0.9514 (mt) cc_final: 0.9196 (tp) REVERT: D 95 GLN cc_start: 0.9662 (tt0) cc_final: 0.9352 (tm-30) REVERT: D 106 LEU cc_start: 0.8639 (tt) cc_final: 0.8387 (pp) REVERT: D 111 VAL cc_start: 0.9027 (t) cc_final: 0.8752 (t) REVERT: E 54 TYR cc_start: 0.8994 (m-80) cc_final: 0.8754 (m-10) REVERT: E 99 TYR cc_start: 0.8743 (t80) cc_final: 0.7376 (t80) REVERT: E 105 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8540 (tm-30) REVERT: F 61 PHE cc_start: 0.8838 (t80) cc_final: 0.8112 (t80) REVERT: F 63 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8562 (mm-30) REVERT: F 72 TYR cc_start: 0.8354 (m-80) cc_final: 0.7265 (m-80) REVERT: G 38 ASN cc_start: 0.8053 (m110) cc_final: 0.7458 (t0) REVERT: G 56 GLU cc_start: 0.8825 (tt0) cc_final: 0.8333 (mt-10) REVERT: G 90 ASP cc_start: 0.8588 (t70) cc_final: 0.8178 (t0) REVERT: G 93 LEU cc_start: 0.9324 (mt) cc_final: 0.9056 (mt) REVERT: G 97 LEU cc_start: 0.8912 (mt) cc_final: 0.8628 (mt) REVERT: H 80 LEU cc_start: 0.9510 (mt) cc_final: 0.8570 (mt) REVERT: H 100 LEU cc_start: 0.8948 (mt) cc_final: 0.8680 (mt) REVERT: K 276 MET cc_start: 0.9492 (mmm) cc_final: 0.9210 (mmm) REVERT: K 413 MET cc_start: 0.1313 (ptm) cc_final: 0.1034 (ttp) REVERT: K 456 ASP cc_start: 0.8314 (t0) cc_final: 0.8035 (p0) REVERT: M 50 ILE cc_start: 0.9052 (mm) cc_final: 0.8820 (mm) REVERT: M 85 ASP cc_start: 0.8456 (m-30) cc_final: 0.8144 (m-30) REVERT: N 64 GLU cc_start: 0.8739 (tt0) cc_final: 0.8386 (tm-30) REVERT: O 51 ASP cc_start: 0.8629 (m-30) cc_final: 0.8091 (t70) REVERT: O 62 MET cc_start: 0.9196 (mmm) cc_final: 0.8788 (mmm) REVERT: O 71 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8501 (mm-30) REVERT: O 95 GLN cc_start: 0.9657 (tt0) cc_final: 0.9432 (tm-30) REVERT: O 106 LEU cc_start: 0.8614 (tt) cc_final: 0.8287 (pp) REVERT: O 111 VAL cc_start: 0.9023 (t) cc_final: 0.8720 (t) REVERT: P 54 TYR cc_start: 0.8939 (m-80) cc_final: 0.8704 (m-10) REVERT: P 99 TYR cc_start: 0.8434 (t80) cc_final: 0.7923 (t80) REVERT: P 104 PHE cc_start: 0.9688 (m-10) cc_final: 0.9476 (m-10) REVERT: Q 63 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8542 (mm-30) REVERT: Q 68 ASP cc_start: 0.9187 (m-30) cc_final: 0.8918 (m-30) REVERT: Q 72 TYR cc_start: 0.8400 (m-80) cc_final: 0.7665 (m-80) REVERT: Q 93 GLN cc_start: 0.8839 (tp40) cc_final: 0.8216 (tm-30) REVERT: Q 95 ARG cc_start: 0.8500 (mmp80) cc_final: 0.8287 (mmp80) REVERT: R 38 ASN cc_start: 0.8052 (m110) cc_final: 0.7356 (t0) REVERT: R 51 LEU cc_start: 0.9866 (tp) cc_final: 0.9651 (tp) REVERT: R 56 GLU cc_start: 0.8870 (tt0) cc_final: 0.8477 (mt-10) REVERT: R 90 ASP cc_start: 0.8431 (t70) cc_final: 0.8062 (t0) REVERT: R 93 LEU cc_start: 0.9323 (mt) cc_final: 0.8887 (mt) REVERT: S 80 LEU cc_start: 0.9482 (mt) cc_final: 0.8742 (mt) REVERT: S 100 LEU cc_start: 0.9202 (mt) cc_final: 0.8940 (mt) REVERT: S 116 LYS cc_start: 0.9604 (ttmt) cc_final: 0.9392 (ttpp) REVERT: V 276 MET cc_start: 0.9597 (mmm) cc_final: 0.9117 (ppp) REVERT: V 413 MET cc_start: 0.1323 (ptm) cc_final: 0.0815 (ptm) REVERT: V 456 ASP cc_start: 0.8263 (t0) cc_final: 0.7949 (p0) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.4290 time to fit residues: 218.2178 Evaluate side-chains 218 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 218 time to evaluate : 2.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 0.0020 chunk 75 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 165 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 243 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 217 optimal weight: 10.0000 chunk 241 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 overall best weight: 3.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 95 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 437 HIS K 466 ASN ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 95 GLN ** V 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31458 Z= 0.212 Angle : 0.601 7.802 44954 Z= 0.353 Chirality : 0.036 0.172 5072 Planarity : 0.005 0.054 3660 Dihedral : 30.280 174.982 8852 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.11 % Allowed : 1.95 % Favored : 97.95 % 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: 0.27 (0.17), residues: 2162 helix: 1.13 (0.13), residues: 1376 sheet: -2.23 (0.52), residues: 68 loop : -1.41 (0.22), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP V 330 HIS 0.005 0.001 HIS A 113 PHE 0.017 0.002 PHE K 280 TYR 0.020 0.002 TYR F 88 ARG 0.008 0.001 ARG Q 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 308 time to evaluate : 2.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.9323 (tmt170) cc_final: 0.9009 (mtm110) REVERT: A 54 TYR cc_start: 0.9331 (m-10) cc_final: 0.9094 (m-80) REVERT: A 92 LEU cc_start: 0.8536 (tt) cc_final: 0.8196 (tt) REVERT: B 68 ASP cc_start: 0.8904 (m-30) cc_final: 0.8475 (m-30) REVERT: B 85 ASP cc_start: 0.8485 (m-30) cc_final: 0.8238 (m-30) REVERT: B 93 GLN cc_start: 0.9484 (pt0) cc_final: 0.8791 (tm-30) REVERT: C 64 GLU cc_start: 0.8446 (tt0) cc_final: 0.8138 (tm-30) REVERT: C 73 ASN cc_start: 0.9545 (t0) cc_final: 0.9287 (t0) REVERT: C 111 ILE cc_start: 0.7947 (mm) cc_final: 0.7665 (mm) REVERT: D 51 ASP cc_start: 0.8130 (t0) cc_final: 0.7348 (t0) REVERT: D 62 MET cc_start: 0.9026 (mmm) cc_final: 0.8529 (mmm) REVERT: D 71 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8472 (mm-30) REVERT: D 73 ILE cc_start: 0.9487 (mt) cc_final: 0.9222 (tp) REVERT: D 95 GLN cc_start: 0.9734 (tt0) cc_final: 0.9134 (tm-30) REVERT: D 106 LEU cc_start: 0.8612 (tt) cc_final: 0.8410 (pp) REVERT: E 51 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8641 (mm) REVERT: E 54 TYR cc_start: 0.8941 (m-80) cc_final: 0.8705 (m-10) REVERT: E 90 MET cc_start: 0.9074 (mmp) cc_final: 0.8817 (mmm) REVERT: E 105 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8712 (tm-30) REVERT: F 63 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8503 (mm-30) REVERT: F 72 TYR cc_start: 0.8376 (m-80) cc_final: 0.7534 (m-80) REVERT: G 38 ASN cc_start: 0.7981 (m110) cc_final: 0.7233 (t0) REVERT: G 51 LEU cc_start: 0.9857 (tp) cc_final: 0.9587 (tp) REVERT: G 56 GLU cc_start: 0.8821 (tt0) cc_final: 0.8207 (mt-10) REVERT: G 90 ASP cc_start: 0.8547 (t70) cc_final: 0.8038 (p0) REVERT: G 93 LEU cc_start: 0.9326 (mt) cc_final: 0.8879 (mt) REVERT: G 95 LYS cc_start: 0.9227 (tttt) cc_final: 0.8637 (ptmm) REVERT: G 97 LEU cc_start: 0.8816 (mt) cc_final: 0.8570 (mt) REVERT: G 99 ARG cc_start: 0.7460 (pmt170) cc_final: 0.6710 (mmt180) REVERT: H 98 VAL cc_start: 0.9543 (t) cc_final: 0.9057 (p) REVERT: K 276 MET cc_start: 0.9513 (mmm) cc_final: 0.9036 (ppp) REVERT: K 456 ASP cc_start: 0.8227 (t0) cc_final: 0.7922 (p0) REVERT: M 68 ASP cc_start: 0.9056 (m-30) cc_final: 0.8597 (m-30) REVERT: M 85 ASP cc_start: 0.8476 (m-30) cc_final: 0.8091 (m-30) REVERT: N 64 GLU cc_start: 0.8602 (tt0) cc_final: 0.8266 (tm-30) REVERT: O 51 ASP cc_start: 0.8792 (m-30) cc_final: 0.8152 (t0) REVERT: O 62 MET cc_start: 0.9142 (mmm) cc_final: 0.8770 (mmm) REVERT: O 71 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8456 (mm-30) REVERT: O 95 GLN cc_start: 0.9624 (tt0) cc_final: 0.9018 (tm-30) REVERT: O 106 LEU cc_start: 0.8717 (tt) cc_final: 0.8453 (pp) REVERT: P 94 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8657 (mt-10) REVERT: P 104 PHE cc_start: 0.9625 (m-10) cc_final: 0.9415 (m-10) REVERT: P 105 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8654 (tm-30) REVERT: Q 62 LEU cc_start: 0.9803 (tp) cc_final: 0.9530 (tt) REVERT: Q 63 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8421 (mm-30) REVERT: Q 68 ASP cc_start: 0.8900 (m-30) cc_final: 0.8575 (m-30) REVERT: Q 93 GLN cc_start: 0.8710 (tp40) cc_final: 0.8207 (tm-30) REVERT: R 38 ASN cc_start: 0.8086 (m110) cc_final: 0.7381 (t0) REVERT: R 50 TYR cc_start: 0.8561 (t80) cc_final: 0.8313 (t80) REVERT: R 51 LEU cc_start: 0.9860 (tp) cc_final: 0.9632 (tp) REVERT: R 55 LEU cc_start: 0.9638 (mt) cc_final: 0.9423 (mt) REVERT: R 56 GLU cc_start: 0.8855 (tt0) cc_final: 0.8424 (mt-10) REVERT: R 90 ASP cc_start: 0.8415 (t70) cc_final: 0.7965 (p0) REVERT: R 93 LEU cc_start: 0.9274 (mt) cc_final: 0.8838 (mt) REVERT: R 95 LYS cc_start: 0.9240 (tttt) cc_final: 0.8603 (ptmm) REVERT: R 97 LEU cc_start: 0.8720 (mt) cc_final: 0.8423 (mt) REVERT: S 73 ILE cc_start: 0.9267 (tt) cc_final: 0.8201 (tt) REVERT: S 98 VAL cc_start: 0.9451 (t) cc_final: 0.8915 (p) REVERT: S 101 LEU cc_start: 0.8885 (mt) cc_final: 0.8605 (mt) REVERT: V 276 MET cc_start: 0.9601 (mmm) cc_final: 0.9103 (ppp) REVERT: V 413 MET cc_start: 0.1295 (ptm) cc_final: 0.0862 (ptm) REVERT: V 456 ASP cc_start: 0.8141 (t0) cc_final: 0.7815 (p0) outliers start: 2 outliers final: 0 residues processed: 309 average time/residue: 0.3630 time to fit residues: 176.5498 Evaluate side-chains 222 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 221 time to evaluate : 1.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 240 optimal weight: 0.0270 chunk 183 optimal weight: 20.0000 chunk 126 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 116 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 259 optimal weight: 0.3980 chunk 127 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 overall best weight: 3.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31458 Z= 0.196 Angle : 0.587 9.851 44954 Z= 0.344 Chirality : 0.035 0.150 5072 Planarity : 0.005 0.053 3660 Dihedral : 30.215 178.439 8852 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.05 % Allowed : 1.48 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.17), residues: 2162 helix: 1.43 (0.13), residues: 1376 sheet: -2.36 (0.56), residues: 64 loop : -1.30 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP V 330 HIS 0.006 0.001 HIS E 113 PHE 0.024 0.002 PHE L 67 TYR 0.023 0.002 TYR F 88 ARG 0.013 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4324 Ramachandran restraints generated. 2162 Oldfield, 0 Emsley, 2162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 301 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.9319 (tmt170) cc_final: 0.8865 (mtp-110) REVERT: A 99 TYR cc_start: 0.8098 (t80) cc_final: 0.7831 (t80) REVERT: B 68 ASP cc_start: 0.9062 (m-30) cc_final: 0.8618 (m-30) REVERT: B 85 ASP cc_start: 0.8442 (m-30) cc_final: 0.8237 (m-30) REVERT: C 64 GLU cc_start: 0.8466 (tt0) cc_final: 0.8146 (tm-30) REVERT: C 73 ASN cc_start: 0.9558 (t0) cc_final: 0.9328 (t0) REVERT: C 111 ILE cc_start: 0.7956 (mm) cc_final: 0.7649 (mm) REVERT: D 51 ASP cc_start: 0.8020 (t0) cc_final: 0.7228 (t0) REVERT: D 62 MET cc_start: 0.9095 (mmm) cc_final: 0.8639 (mmm) REVERT: D 73 ILE cc_start: 0.9417 (mt) cc_final: 0.9175 (tp) REVERT: D 95 GLN cc_start: 0.9704 (tt0) cc_final: 0.9117 (tm-30) REVERT: D 106 LEU cc_start: 0.8694 (tt) cc_final: 0.8489 (pp) REVERT: E 51 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8696 (mm) REVERT: E 54 TYR cc_start: 0.8939 (m-80) cc_final: 0.8727 (m-10) REVERT: E 99 TYR cc_start: 0.8525 (t80) cc_final: 0.8276 (t80) REVERT: E 104 PHE cc_start: 0.9583 (m-10) cc_final: 0.9362 (m-10) REVERT: E 105 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8758 (tm-30) REVERT: F 63 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8491 (mm-30) REVERT: F 72 TYR cc_start: 0.8319 (m-80) cc_final: 0.7468 (m-80) REVERT: G 38 ASN cc_start: 0.8049 (m110) cc_final: 0.7265 (t0) REVERT: G 51 LEU cc_start: 0.9846 (tp) cc_final: 0.9633 (tp) REVERT: G 90 ASP cc_start: 0.8655 (t70) cc_final: 0.8235 (p0) REVERT: G 93 LEU cc_start: 0.9300 (mt) cc_final: 0.8864 (mt) REVERT: G 95 LYS cc_start: 0.9147 (tttt) cc_final: 0.8542 (ttpp) REVERT: G 99 ARG cc_start: 0.7669 (pmt170) cc_final: 0.6920 (mmt180) REVERT: H 59 MET cc_start: 0.5492 (tpp) cc_final: 0.4633 (tpp) REVERT: H 101 LEU cc_start: 0.8754 (mt) cc_final: 0.8432 (mt) REVERT: K 276 MET cc_start: 0.9516 (mmm) cc_final: 0.9040 (ppp) REVERT: K 456 ASP cc_start: 0.7970 (t0) cc_final: 0.7606 (p0) REVERT: K 498 LYS cc_start: 0.8993 (pttm) cc_final: 0.8759 (tppt) REVERT: M 68 ASP cc_start: 0.8969 (m-30) cc_final: 0.8494 (m-30) REVERT: M 85 ASP cc_start: 0.8503 (m-30) cc_final: 0.8032 (m-30) REVERT: N 64 GLU cc_start: 0.8658 (tt0) cc_final: 0.8285 (tm-30) REVERT: N 76 THR cc_start: 0.8473 (t) cc_final: 0.8181 (t) REVERT: O 51 ASP cc_start: 0.8734 (m-30) cc_final: 0.8106 (t70) REVERT: O 62 MET cc_start: 0.9126 (mmm) cc_final: 0.8727 (mmm) REVERT: O 71 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8395 (mm-30) REVERT: O 95 GLN cc_start: 0.9650 (tt0) cc_final: 0.9326 (tm-30) REVERT: O 106 LEU cc_start: 0.8769 (tt) cc_final: 0.8502 (pp) REVERT: P 94 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8529 (mt-10) REVERT: P 104 PHE cc_start: 0.9616 (m-10) cc_final: 0.9407 (m-10) REVERT: P 105 GLU cc_start: 0.9104 (tm-30) cc_final: 0.8697 (tm-30) REVERT: Q 62 LEU cc_start: 0.9758 (tp) cc_final: 0.9557 (tp) REVERT: Q 63 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8462 (mm-30) REVERT: R 38 ASN cc_start: 0.8089 (m110) cc_final: 0.7446 (t0) REVERT: R 51 LEU cc_start: 0.9855 (tp) cc_final: 0.9638 (tp) REVERT: R 90 ASP cc_start: 0.8462 (t70) cc_final: 0.8095 (p0) REVERT: R 93 LEU cc_start: 0.9258 (mt) cc_final: 0.8979 (mt) REVERT: R 95 LYS cc_start: 0.9160 (tttt) cc_final: 0.8483 (ptmm) REVERT: S 59 MET cc_start: 0.4951 (tpp) cc_final: 0.4062 (tpp) REVERT: S 80 LEU cc_start: 0.9543 (mt) cc_final: 0.9219 (pp) REVERT: S 98 VAL cc_start: 0.9480 (t) cc_final: 0.9062 (p) REVERT: V 276 MET cc_start: 0.9501 (mmm) cc_final: 0.9084 (ppp) REVERT: V 413 MET cc_start: 0.1274 (ptm) cc_final: 0.0832 (ptm) REVERT: V 456 ASP cc_start: 0.8091 (t0) cc_final: 0.7711 (p0) REVERT: V 498 LYS cc_start: 0.8978 (pttm) cc_final: 0.8715 (tppt) outliers start: 1 outliers final: 0 residues processed: 302 average time/residue: 0.3765 time to fit residues: 179.1614 Evaluate side-chains 216 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 215 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 215 optimal weight: 10.0000 chunk 147 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 192 optimal weight: 8.9990 chunk 106 optimal weight: 0.0770 chunk 221 optimal weight: 10.0000 chunk 179 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 30.0000 chunk 232 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 overall best weight: 5.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -build -allalt -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: