Starting phenix.real_space_refine on Thu Mar 21 08:15:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/03_2024/7ccr_30340.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/03_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_30340/03_2024/7ccr_30340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/03_2024/7ccr_30340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/03_2024/7ccr_30340.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/03_2024/7ccr_30340.pdb" } 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-5265/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: 15.96, per 1000 atoms: 0.54 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: 14.57 Conformation dependent library (CDL) restraints added in 3.3 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: 13.32 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: 15.46 Time building geometry restraints manager: 15.55 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 2.520 nonbonded pdb=" OP1 DA J 57 " pdb=" NZ LYS K 350 " model vdw 1.593 2.520 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 2.440 ... (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 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: 1.620 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: 0.030 Extract box with map and model: 7.570 Check model and map are aligned: 0.470 Set scattering table: 0.260 Process input model: 91.740 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.000 ------------------------------------------------------------------------------- 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 : 2.378 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: 0.4444 time to fit residues: 372.7777 Evaluate side-chains 278 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 278 time to evaluate : 2.663 ------------------------------------------------------------------------------- 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: 0.9980 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 108 optimal weight: 30.0000 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 40.0000 chunk 156 optimal weight: 9.9990 chunk 243 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN D 95 GLN E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 192 HIS K 260 ASN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 466 ASN L 68 GLN ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 ASN O 95 GLN P 68 GLN ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 192 HIS ** V 381 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 449 ASN V 473 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 31458 Z= 0.260 Angle : 0.667 8.258 44954 Z= 0.390 Chirality : 0.038 0.175 5072 Planarity : 0.006 0.060 3660 Dihedral : 30.171 165.565 8852 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: -0.47 (0.17), residues: 2162 helix: 0.53 (0.12), residues: 1394 sheet: -2.69 (0.40), residues: 106 loop : -1.59 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 343 HIS 0.012 0.002 HIS M 75 PHE 0.024 0.002 PHE V 280 TYR 0.026 0.002 TYR C 39 ARG 0.009 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 329 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.553 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: A 99 TYR cc_start: 0.8172 (t80) cc_final: 0.7958 (t80) REVERT: B 54 THR cc_start: 0.9565 (m) cc_final: 0.9036 (m) REVERT: B 68 ASP cc_start: 0.8348 (m-30) cc_final: 0.7966 (m-30) REVERT: B 85 ASP cc_start: 0.8201 (m-30) cc_final: 0.7817 (m-30) REVERT: B 93 GLN cc_start: 0.9460 (pt0) cc_final: 0.8623 (tm-30) REVERT: C 64 GLU cc_start: 0.8459 (tt0) cc_final: 0.8155 (tm-30) REVERT: C 73 ASN cc_start: 0.9536 (t0) cc_final: 0.9321 (t0) REVERT: D 51 ASP cc_start: 0.8057 (t0) cc_final: 0.7168 (t70) REVERT: D 62 MET cc_start: 0.9177 (mmm) cc_final: 0.8664 (mmm) REVERT: D 71 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8401 (mm-30) REVERT: D 73 ILE cc_start: 0.9501 (mt) cc_final: 0.9192 (tp) REVERT: D 95 GLN cc_start: 0.9653 (tt0) cc_final: 0.9143 (tm-30) REVERT: D 106 LEU cc_start: 0.8585 (tt) cc_final: 0.8237 (pp) REVERT: E 54 TYR cc_start: 0.8907 (m-80) cc_final: 0.8663 (m-10) REVERT: E 99 TYR cc_start: 0.8702 (t80) cc_final: 0.7251 (t80) REVERT: E 105 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8597 (tm-30) REVERT: F 37 LEU cc_start: 0.9695 (mt) cc_final: 0.9485 (mt) REVERT: F 61 PHE cc_start: 0.8808 (t80) cc_final: 0.7995 (t80) REVERT: F 63 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8594 (mm-30) REVERT: F 72 TYR cc_start: 0.8410 (m-80) cc_final: 0.7303 (m-80) REVERT: G 38 ASN cc_start: 0.8053 (m110) cc_final: 0.7365 (t0) REVERT: G 90 ASP cc_start: 0.8596 (t70) cc_final: 0.8271 (t0) REVERT: G 93 LEU cc_start: 0.9263 (mt) cc_final: 0.8985 (mt) REVERT: G 95 LYS cc_start: 0.9283 (tttt) cc_final: 0.8671 (ptmm) REVERT: H 80 LEU cc_start: 0.9465 (mt) cc_final: 0.8593 (mt) REVERT: H 100 LEU cc_start: 0.8893 (mt) cc_final: 0.8581 (mt) REVERT: K 276 MET cc_start: 0.9521 (mmm) cc_final: 0.9117 (ppp) REVERT: K 413 MET cc_start: 0.1355 (ptm) cc_final: 0.1079 (ptm) REVERT: K 456 ASP cc_start: 0.8364 (t0) cc_final: 0.8090 (p0) REVERT: M 85 ASP cc_start: 0.8307 (m-30) cc_final: 0.7913 (m-30) REVERT: N 64 GLU cc_start: 0.8672 (tt0) cc_final: 0.8340 (tm-30) REVERT: O 51 ASP cc_start: 0.8591 (m-30) cc_final: 0.7997 (t70) REVERT: O 62 MET cc_start: 0.9210 (mmm) cc_final: 0.8809 (mmm) REVERT: O 71 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8441 (mm-30) REVERT: O 95 GLN cc_start: 0.9659 (tt0) cc_final: 0.9330 (tm-30) REVERT: O 106 LEU cc_start: 0.8577 (tt) cc_final: 0.8190 (pp) REVERT: P 54 TYR cc_start: 0.8861 (m-80) cc_final: 0.8650 (m-10) REVERT: P 94 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8217 (mm-30) REVERT: P 97 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8856 (mt-10) REVERT: P 104 PHE cc_start: 0.9677 (m-10) cc_final: 0.9464 (m-10) REVERT: Q 63 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8549 (mm-30) REVERT: Q 68 ASP cc_start: 0.9247 (m-30) cc_final: 0.8833 (m-30) REVERT: Q 72 TYR cc_start: 0.8387 (m-80) cc_final: 0.7126 (m-80) REVERT: R 38 ASN cc_start: 0.8072 (m110) cc_final: 0.7351 (t0) REVERT: R 56 GLU cc_start: 0.8839 (tt0) cc_final: 0.8472 (mt-10) REVERT: R 90 ASP cc_start: 0.8472 (t70) cc_final: 0.8239 (t70) REVERT: R 95 LYS cc_start: 0.9255 (tttt) cc_final: 0.8662 (ptmm) REVERT: S 73 ILE cc_start: 0.9495 (mt) cc_final: 0.9290 (tt) REVERT: V 276 MET cc_start: 0.9598 (mmm) cc_final: 0.9183 (ppp) REVERT: V 413 MET cc_start: 0.1290 (ptm) cc_final: 0.0851 (ptm) REVERT: V 456 ASP cc_start: 0.8279 (t0) cc_final: 0.7970 (p0) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4247 time to fit residues: 217.9632 Evaluate side-chains 225 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 2.599 ------------------------------------------------------------------------------- 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: 8.9990 chunk 75 optimal weight: 10.0000 chunk 202 optimal weight: 0.8980 chunk 165 optimal weight: 0.0870 chunk 67 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 263 optimal weight: 8.9990 chunk 217 optimal weight: 20.0000 chunk 241 optimal weight: 8.9990 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 0.0970 overall best weight: 2.1758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** 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** O 95 GLN ** P 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 67 ASN V 437 HIS ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN ** V 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31458 Z= 0.184 Angle : 0.575 7.541 44954 Z= 0.339 Chirality : 0.035 0.252 5072 Planarity : 0.004 0.057 3660 Dihedral : 29.891 167.948 8852 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.16 % Allowed : 2.16 % Favored : 97.68 % 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: 0.32 (0.17), residues: 2162 helix: 1.19 (0.13), residues: 1386 sheet: -2.48 (0.42), residues: 102 loop : -1.35 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 343 HIS 0.007 0.001 HIS B 75 PHE 0.016 0.001 PHE K 280 TYR 0.018 0.002 TYR Q 88 ARG 0.004 0.000 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 314 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 311 time to evaluate : 2.522 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: 0.8198 (t80) cc_final: 0.7978 (t80) REVERT: B 63 GLU cc_start: 0.9079 (tp30) cc_final: 0.8275 (tp30) REVERT: B 68 ASP cc_start: 0.8470 (m-30) cc_final: 0.8176 (m-30) REVERT: B 85 ASP cc_start: 0.8024 (m-30) cc_final: 0.7607 (m-30) REVERT: B 93 GLN cc_start: 0.9347 (pt0) cc_final: 0.8663 (tm-30) REVERT: C 64 GLU cc_start: 0.8410 (tt0) cc_final: 0.8088 (tm-30) REVERT: C 111 ILE cc_start: 0.7887 (mm) cc_final: 0.7636 (mm) REVERT: D 51 ASP cc_start: 0.7991 (t0) cc_final: 0.7064 (t0) REVERT: D 62 MET cc_start: 0.8990 (mmm) cc_final: 0.8604 (mmm) REVERT: D 73 ILE cc_start: 0.9424 (mt) cc_final: 0.9208 (tp) REVERT: D 106 LEU cc_start: 0.8633 (tt) cc_final: 0.8306 (pp) REVERT: E 51 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8638 (mm) REVERT: E 54 TYR cc_start: 0.8827 (m-80) cc_final: 0.8588 (m-10) REVERT: E 90 MET cc_start: 0.9034 (mmp) cc_final: 0.8783 (mmm) REVERT: E 99 TYR cc_start: 0.8519 (t80) cc_final: 0.8193 (t80) REVERT: E 105 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8742 (tm-30) REVERT: F 63 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8564 (mm-30) REVERT: F 72 TYR cc_start: 0.8447 (m-80) cc_final: 0.7161 (m-80) REVERT: G 38 ASN cc_start: 0.7959 (m110) cc_final: 0.7069 (t0) REVERT: G 51 LEU cc_start: 0.9868 (tp) cc_final: 0.9652 (tp) REVERT: G 90 ASP cc_start: 0.8466 (t70) cc_final: 0.7984 (p0) REVERT: G 93 LEU cc_start: 0.9281 (mt) cc_final: 0.8901 (mt) REVERT: G 95 LYS cc_start: 0.9229 (tttt) cc_final: 0.8601 (ptmm) REVERT: H 65 PHE cc_start: 0.9018 (t80) cc_final: 0.8758 (t80) REVERT: H 98 VAL cc_start: 0.9530 (t) cc_final: 0.9212 (p) REVERT: K 276 MET cc_start: 0.9545 (mmm) cc_final: 0.9116 (ppp) REVERT: K 413 MET cc_start: 0.1455 (ptm) cc_final: 0.1184 (ttp) REVERT: K 456 ASP cc_start: 0.8327 (t0) cc_final: 0.8015 (p0) REVERT: M 68 ASP cc_start: 0.9224 (m-30) cc_final: 0.8976 (m-30) REVERT: M 85 ASP cc_start: 0.8184 (m-30) cc_final: 0.7564 (m-30) REVERT: N 64 GLU cc_start: 0.8553 (tt0) cc_final: 0.8238 (tm-30) REVERT: N 111 ILE cc_start: 0.7960 (mm) cc_final: 0.7648 (mm) REVERT: O 51 ASP cc_start: 0.8634 (m-30) cc_final: 0.8044 (t70) REVERT: O 62 MET cc_start: 0.9131 (mmm) cc_final: 0.8753 (mmm) REVERT: O 71 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8462 (mm-30) REVERT: O 95 GLN cc_start: 0.9602 (tt0) cc_final: 0.9084 (tm-30) REVERT: O 106 LEU cc_start: 0.8638 (tt) cc_final: 0.8293 (pp) REVERT: P 51 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8557 (mm) REVERT: P 94 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8209 (mm-30) REVERT: P 104 PHE cc_start: 0.9615 (m-10) cc_final: 0.9403 (m-10) REVERT: P 105 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8635 (tm-30) REVERT: Q 63 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8525 (mm-30) REVERT: Q 72 TYR cc_start: 0.8171 (m-80) cc_final: 0.7190 (m-80) REVERT: R 38 ASN cc_start: 0.8000 (m110) cc_final: 0.7197 (t0) REVERT: R 51 LEU cc_start: 0.9871 (tp) cc_final: 0.9660 (tp) REVERT: R 56 GLU cc_start: 0.8801 (tt0) cc_final: 0.8270 (mt-10) REVERT: R 90 ASP cc_start: 0.8353 (t70) cc_final: 0.7828 (p0) REVERT: R 93 LEU cc_start: 0.9244 (mt) cc_final: 0.8771 (mt) REVERT: R 95 LYS cc_start: 0.9224 (tttt) cc_final: 0.8607 (ptmm) REVERT: S 69 ILE cc_start: 0.9514 (mm) cc_final: 0.9134 (pt) REVERT: S 73 ILE cc_start: 0.9450 (mt) cc_final: 0.8507 (tt) REVERT: V 276 MET cc_start: 0.9565 (mmm) cc_final: 0.9189 (ppp) REVERT: V 413 MET cc_start: 0.1377 (ptm) cc_final: 0.0944 (ptm) REVERT: V 456 ASP cc_start: 0.8270 (t0) cc_final: 0.7963 (p0) outliers start: 3 outliers final: 0 residues processed: 313 average time/residue: 0.4147 time to fit residues: 203.3898 Evaluate side-chains 224 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 222 time to evaluate : 2.578 ------------------------------------------------------------------------------- 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: 1.9990 chunk 183 optimal weight: 9.9990 chunk 126 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 163 optimal weight: 0.6980 chunk 244 optimal weight: 7.9990 chunk 259 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 69 optimal weight: 8.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- 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 89 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 ASN O 95 GLN ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 31458 Z= 0.277 Angle : 0.672 15.006 44954 Z= 0.390 Chirality : 0.038 0.344 5072 Planarity : 0.006 0.073 3660 Dihedral : 30.576 178.893 8852 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 22.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.21 % Allowed : 1.84 % 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: 0.12 (0.17), residues: 2162 helix: 0.97 (0.13), residues: 1372 sheet: -2.76 (0.47), residues: 84 loop : -1.25 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 343 HIS 0.009 0.002 HIS B 75 PHE 0.026 0.002 PHE L 67 TYR 0.020 0.002 TYR F 88 ARG 0.008 0.001 ARG A 49 *********************** 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 289 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 285 time to evaluate : 2.437 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: B 68 ASP cc_start: 0.8575 (m-30) cc_final: 0.8270 (m-30) REVERT: B 93 GLN cc_start: 0.9539 (pt0) cc_final: 0.8981 (tm-30) REVERT: C 64 GLU cc_start: 0.8604 (tt0) cc_final: 0.8226 (tm-30) REVERT: C 111 ILE cc_start: 0.8105 (mm) cc_final: 0.7733 (mm) REVERT: D 51 ASP cc_start: 0.8179 (t0) cc_final: 0.7370 (t0) REVERT: D 62 MET cc_start: 0.9146 (mmm) cc_final: 0.8679 (mmm) REVERT: D 71 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8263 (mm-30) REVERT: D 73 ILE cc_start: 0.9496 (mt) cc_final: 0.9228 (tp) REVERT: D 95 GLN cc_start: 0.9571 (tt0) cc_final: 0.9087 (tm-30) REVERT: D 106 LEU cc_start: 0.8818 (tt) cc_final: 0.8519 (pp) REVERT: E 51 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8775 (mm) REVERT: E 54 TYR cc_start: 0.8960 (m-80) cc_final: 0.8760 (m-10) REVERT: E 94 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8481 (mt-10) REVERT: E 99 TYR cc_start: 0.8570 (t80) cc_final: 0.7144 (t80) REVERT: E 105 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8941 (tm-30) REVERT: F 61 PHE cc_start: 0.8852 (t80) cc_final: 0.8207 (t80) REVERT: F 62 LEU cc_start: 0.9792 (tp) cc_final: 0.9586 (tt) REVERT: F 63 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8519 (mm-30) REVERT: F 68 ASP cc_start: 0.8856 (m-30) cc_final: 0.8575 (m-30) REVERT: F 72 TYR cc_start: 0.8306 (m-80) cc_final: 0.7875 (m-80) REVERT: F 84 MET cc_start: 0.9330 (pmm) cc_final: 0.9003 (pmm) REVERT: G 38 ASN cc_start: 0.8098 (m110) cc_final: 0.7752 (t0) REVERT: G 90 ASP cc_start: 0.8820 (t70) cc_final: 0.8399 (p0) REVERT: G 93 LEU cc_start: 0.9246 (mt) cc_final: 0.9003 (mt) REVERT: G 97 LEU cc_start: 0.9017 (mt) cc_final: 0.8622 (mp) REVERT: K 276 MET cc_start: 0.9549 (mmm) cc_final: 0.9074 (ppp) REVERT: K 413 MET cc_start: 0.1429 (ptm) cc_final: 0.1178 (ttp) REVERT: K 456 ASP cc_start: 0.7980 (t0) cc_final: 0.7572 (p0) REVERT: K 498 LYS cc_start: 0.8980 (pttm) cc_final: 0.8729 (tppt) REVERT: L 54 TYR cc_start: 0.9195 (m-10) cc_final: 0.8974 (m-10) REVERT: L 97 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7402 (mm-30) REVERT: M 68 ASP cc_start: 0.9406 (m-30) cc_final: 0.9206 (m-30) REVERT: N 64 GLU cc_start: 0.8725 (tt0) cc_final: 0.8383 (tm-30) REVERT: N 96 LEU cc_start: 0.9660 (tp) cc_final: 0.9418 (tp) REVERT: O 62 MET cc_start: 0.9171 (mmm) cc_final: 0.8788 (mmm) REVERT: O 106 LEU cc_start: 0.8807 (tt) cc_final: 0.8477 (pp) REVERT: P 104 PHE cc_start: 0.9586 (m-10) cc_final: 0.9331 (m-10) REVERT: P 105 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8766 (tm-30) REVERT: Q 63 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8503 (mm-30) REVERT: R 50 TYR cc_start: 0.8664 (t80) cc_final: 0.8305 (t80) REVERT: R 51 LEU cc_start: 0.9830 (tp) cc_final: 0.9504 (tp) REVERT: R 90 ASP cc_start: 0.8965 (t70) cc_final: 0.8521 (p0) REVERT: R 93 LEU cc_start: 0.9235 (mt) cc_final: 0.8991 (mt) REVERT: R 97 LEU cc_start: 0.8675 (mt) cc_final: 0.8442 (mt) REVERT: V 276 MET cc_start: 0.9564 (mmm) cc_final: 0.9256 (mmm) REVERT: V 413 MET cc_start: 0.1485 (ptm) cc_final: 0.1113 (ptm) REVERT: V 456 ASP cc_start: 0.7956 (t0) cc_final: 0.7550 (p0) REVERT: V 498 LYS cc_start: 0.8926 (pttm) cc_final: 0.8643 (tppt) outliers start: 4 outliers final: 1 residues processed: 288 average time/residue: 0.4401 time to fit residues: 201.0609 Evaluate side-chains 218 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 216 time to evaluate : 2.483 ------------------------------------------------------------------------------- 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: 4.9990 chunk 3 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 40.0000 chunk 221 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 chunk 232 optimal weight: 40.0000 chunk 65 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 31 HIS E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 342 ASN K 429 HIS ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 HIS ** R 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.5751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 31458 Z= 0.245 Angle : 0.634 7.470 44954 Z= 0.370 Chirality : 0.037 0.213 5072 Planarity : 0.005 0.070 3660 Dihedral : 30.768 177.444 8852 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.05 % Allowed : 2.00 % 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: 0.25 (0.17), residues: 2162 helix: 1.09 (0.13), residues: 1370 sheet: -2.60 (0.47), residues: 84 loop : -1.26 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 343 HIS 0.008 0.001 HIS E 113 PHE 0.017 0.002 PHE D 65 TYR 0.018 0.002 TYR O 121 ARG 0.018 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 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 284 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.722 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: B 68 ASP cc_start: 0.8634 (m-30) cc_final: 0.8382 (m-30) REVERT: B 93 GLN cc_start: 0.9508 (pt0) cc_final: 0.9281 (pt0) REVERT: C 64 GLU cc_start: 0.8546 (tt0) cc_final: 0.8178 (tm-30) REVERT: D 62 MET cc_start: 0.8974 (mmm) cc_final: 0.8562 (mmm) REVERT: D 73 ILE cc_start: 0.9512 (mt) cc_final: 0.9282 (tp) REVERT: D 106 LEU cc_start: 0.8943 (tt) cc_final: 0.8716 (tt) REVERT: E 54 TYR cc_start: 0.8992 (m-80) cc_final: 0.8756 (m-10) REVERT: E 99 TYR cc_start: 0.8480 (t80) cc_final: 0.7142 (t80) REVERT: E 105 GLU cc_start: 0.9147 (tm-30) cc_final: 0.8877 (tm-30) REVERT: F 61 PHE cc_start: 0.8842 (t80) cc_final: 0.8245 (t80) REVERT: F 62 LEU cc_start: 0.9772 (tp) cc_final: 0.9557 (tt) REVERT: F 63 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8573 (mm-30) REVERT: F 84 MET cc_start: 0.9443 (pmm) cc_final: 0.9156 (pmm) REVERT: G 90 ASP cc_start: 0.8894 (t70) cc_final: 0.8599 (p0) REVERT: G 97 LEU cc_start: 0.8676 (mt) cc_final: 0.8446 (mp) REVERT: H 59 MET cc_start: 0.5769 (tpp) cc_final: 0.4811 (tpp) REVERT: K 276 MET cc_start: 0.9557 (mmm) cc_final: 0.9003 (tmm) REVERT: K 456 ASP cc_start: 0.7930 (t0) cc_final: 0.7499 (p0) REVERT: K 498 LYS cc_start: 0.8997 (pttm) cc_final: 0.8759 (tppt) REVERT: M 68 ASP cc_start: 0.9190 (m-30) cc_final: 0.8767 (m-30) REVERT: N 64 GLU cc_start: 0.8655 (tt0) cc_final: 0.8345 (tm-30) REVERT: O 62 MET cc_start: 0.9128 (mmm) cc_final: 0.8703 (mmm) REVERT: O 95 GLN cc_start: 0.9616 (tt0) cc_final: 0.9031 (tm-30) REVERT: O 106 LEU cc_start: 0.8950 (tt) cc_final: 0.8729 (tt) REVERT: P 54 TYR cc_start: 0.8998 (m-10) cc_final: 0.8693 (m-10) REVERT: P 105 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8696 (tm-30) REVERT: Q 63 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8525 (mm-30) REVERT: Q 68 ASP cc_start: 0.9214 (m-30) cc_final: 0.8899 (m-30) REVERT: R 38 ASN cc_start: 0.7325 (t0) cc_final: 0.6892 (t0) REVERT: R 50 TYR cc_start: 0.8703 (t80) cc_final: 0.8393 (t80) REVERT: R 51 LEU cc_start: 0.9820 (tp) cc_final: 0.9549 (tp) REVERT: R 90 ASP cc_start: 0.9004 (t70) cc_final: 0.8721 (t0) REVERT: R 93 LEU cc_start: 0.9198 (mt) cc_final: 0.8908 (mt) REVERT: S 59 MET cc_start: 0.5271 (tpp) cc_final: 0.4507 (tpp) REVERT: S 65 PHE cc_start: 0.9321 (t80) cc_final: 0.8954 (t80) REVERT: S 120 LYS cc_start: 0.9238 (pptt) cc_final: 0.8750 (pptt) REVERT: V 276 MET cc_start: 0.9563 (mmm) cc_final: 0.9243 (mmm) REVERT: V 413 MET cc_start: 0.1533 (ptm) cc_final: 0.1260 (ptm) REVERT: V 456 ASP cc_start: 0.7707 (t0) cc_final: 0.7212 (p0) REVERT: V 498 LYS cc_start: 0.8936 (pttm) cc_final: 0.8677 (tppt) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.4130 time to fit residues: 185.6481 Evaluate side-chains 213 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 87 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 259 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 136 optimal weight: 0.0000 overall best weight: 6.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 95 GLN Q 64 ASN R 38 ASN R 68 ASN V 217 HIS V 342 ASN ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 31458 Z= 0.306 Angle : 0.706 10.785 44954 Z= 0.409 Chirality : 0.040 0.215 5072 Planarity : 0.006 0.119 3660 Dihedral : 31.256 176.292 8852 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 30.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.05 % Allowed : 1.74 % Favored : 98.21 % 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: -0.18 (0.17), residues: 2162 helix: 0.68 (0.13), residues: 1356 sheet: -2.61 (0.50), residues: 84 loop : -1.22 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP V 343 HIS 0.009 0.001 HIS M 75 PHE 0.031 0.002 PHE A 67 TYR 0.024 0.003 TYR O 121 ARG 0.011 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 6 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 270 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 269 time to evaluate : 2.351 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: A 90 MET cc_start: 0.5133 (mmp) cc_final: 0.4922 (mmt) REVERT: B 93 GLN cc_start: 0.9521 (pt0) cc_final: 0.9252 (pt0) REVERT: C 64 GLU cc_start: 0.8637 (tt0) cc_final: 0.8253 (tm-30) REVERT: D 62 MET cc_start: 0.8942 (mmm) cc_final: 0.8554 (mmm) REVERT: D 73 ILE cc_start: 0.9527 (mt) cc_final: 0.9264 (tp) REVERT: D 106 LEU cc_start: 0.9079 (tt) cc_final: 0.8803 (pp) REVERT: E 54 TYR cc_start: 0.9109 (m-80) cc_final: 0.8803 (m-10) REVERT: E 104 PHE cc_start: 0.9584 (m-10) cc_final: 0.9355 (m-10) REVERT: E 105 GLU cc_start: 0.9168 (tm-30) cc_final: 0.8895 (tm-30) REVERT: F 63 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8560 (mm-30) REVERT: F 72 TYR cc_start: 0.8347 (m-80) cc_final: 0.8032 (m-80) REVERT: G 15 LYS cc_start: 0.9283 (tptt) cc_final: 0.8825 (mtmm) REVERT: G 50 TYR cc_start: 0.8836 (t80) cc_final: 0.8557 (t80) REVERT: G 51 LEU cc_start: 0.9849 (mt) cc_final: 0.9648 (mt) REVERT: G 90 ASP cc_start: 0.9022 (t70) cc_final: 0.8694 (p0) REVERT: G 93 LEU cc_start: 0.9214 (mt) cc_final: 0.8973 (mp) REVERT: G 95 LYS cc_start: 0.9234 (tttt) cc_final: 0.8659 (pttt) REVERT: G 97 LEU cc_start: 0.8877 (mt) cc_final: 0.8574 (mp) REVERT: K 276 MET cc_start: 0.9502 (mmm) cc_final: 0.9163 (mmm) REVERT: K 456 ASP cc_start: 0.7645 (t0) cc_final: 0.7102 (p0) REVERT: K 498 LYS cc_start: 0.8966 (pttm) cc_final: 0.8694 (tppt) REVERT: O 62 MET cc_start: 0.9113 (mmm) cc_final: 0.8683 (mmm) REVERT: O 106 LEU cc_start: 0.8891 (tt) cc_final: 0.8627 (pp) REVERT: P 104 PHE cc_start: 0.9547 (m-10) cc_final: 0.9331 (m-10) REVERT: P 105 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8662 (tm-30) REVERT: Q 63 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8501 (mm-30) REVERT: R 15 LYS cc_start: 0.9120 (tptt) cc_final: 0.8683 (mtmm) REVERT: R 38 ASN cc_start: 0.7960 (t0) cc_final: 0.7502 (t0) REVERT: R 50 TYR cc_start: 0.8851 (t80) cc_final: 0.8517 (t80) REVERT: R 90 ASP cc_start: 0.9071 (t70) cc_final: 0.8605 (p0) REVERT: R 93 LEU cc_start: 0.9205 (mt) cc_final: 0.8623 (mp) REVERT: V 276 MET cc_start: 0.9579 (mmm) cc_final: 0.9274 (mmm) REVERT: V 456 ASP cc_start: 0.7514 (t0) cc_final: 0.6944 (p0) REVERT: V 498 LYS cc_start: 0.8840 (pttm) cc_final: 0.8575 (tppt) outliers start: 1 outliers final: 0 residues processed: 270 average time/residue: 0.3874 time to fit residues: 168.9589 Evaluate side-chains 201 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 249 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 3.9990 chunk 189 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 218 optimal weight: 20.0000 chunk 144 optimal weight: 30.0000 chunk 258 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 157 optimal weight: 4.9990 chunk 119 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS R 89 ASN ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 31458 Z= 0.219 Angle : 0.627 10.996 44954 Z= 0.365 Chirality : 0.037 0.186 5072 Planarity : 0.005 0.081 3660 Dihedral : 31.106 179.817 8852 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 21.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % 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: 1.09 (0.13), residues: 1356 sheet: -2.52 (0.50), residues: 84 loop : -1.17 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 343 HIS 0.005 0.001 HIS B 75 PHE 0.019 0.002 PHE A 67 TYR 0.018 0.002 TYR O 121 ARG 0.004 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 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 279 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 278 time to evaluate : 2.663 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: C 39 TYR cc_start: 0.7671 (m-80) cc_final: 0.7234 (m-80) REVERT: C 64 GLU cc_start: 0.8502 (tt0) cc_final: 0.8185 (tm-30) REVERT: D 62 MET cc_start: 0.8868 (mmm) cc_final: 0.8643 (mmp) REVERT: D 106 LEU cc_start: 0.9055 (tt) cc_final: 0.8746 (tt) REVERT: E 54 TYR cc_start: 0.9028 (m-80) cc_final: 0.8746 (m-10) REVERT: E 94 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8626 (mt-10) REVERT: E 105 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8873 (tm-30) REVERT: F 63 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8547 (mm-30) REVERT: F 68 ASP cc_start: 0.9203 (m-30) cc_final: 0.8932 (m-30) REVERT: F 72 TYR cc_start: 0.7989 (m-80) cc_final: 0.7611 (m-80) REVERT: G 15 LYS cc_start: 0.9157 (tptt) cc_final: 0.8647 (mtmm) REVERT: G 51 LEU cc_start: 0.9816 (mt) cc_final: 0.9605 (mt) REVERT: K 276 MET cc_start: 0.9526 (mmm) cc_final: 0.9057 (ppp) REVERT: K 413 MET cc_start: -0.1506 (ptt) cc_final: -0.1740 (ptt) REVERT: K 498 LYS cc_start: 0.9016 (pttm) cc_final: 0.8779 (tppt) REVERT: M 68 ASP cc_start: 0.9000 (m-30) cc_final: 0.8684 (m-30) REVERT: N 64 GLU cc_start: 0.8533 (tt0) cc_final: 0.8253 (tm-30) REVERT: O 62 MET cc_start: 0.8991 (mmm) cc_final: 0.8569 (mmm) REVERT: O 95 GLN cc_start: 0.9738 (tt0) cc_final: 0.9479 (tm-30) REVERT: O 106 LEU cc_start: 0.8941 (tt) cc_final: 0.8625 (pp) REVERT: P 99 TYR cc_start: 0.8612 (t80) cc_final: 0.8229 (t80) REVERT: P 105 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8688 (tm-30) REVERT: Q 63 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8538 (mm-30) REVERT: R 15 LYS cc_start: 0.9078 (tptt) cc_final: 0.8627 (mtmm) REVERT: R 38 ASN cc_start: 0.7853 (t0) cc_final: 0.7542 (t0) REVERT: R 50 TYR cc_start: 0.8813 (t80) cc_final: 0.8356 (t80) REVERT: R 90 ASP cc_start: 0.8963 (t70) cc_final: 0.8561 (p0) REVERT: R 93 LEU cc_start: 0.9169 (mt) cc_final: 0.8728 (mp) REVERT: S 65 PHE cc_start: 0.9271 (t80) cc_final: 0.8862 (t80) REVERT: V 276 MET cc_start: 0.9566 (mmm) cc_final: 0.8980 (tmm) REVERT: V 498 LYS cc_start: 0.8803 (pttm) cc_final: 0.8574 (tppt) outliers start: 1 outliers final: 0 residues processed: 279 average time/residue: 0.3969 time to fit residues: 178.0450 Evaluate side-chains 210 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 159 optimal weight: 8.9990 chunk 103 optimal weight: 50.0000 chunk 154 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 164 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 chunk 127 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 chunk 203 optimal weight: 6.9990 chunk 234 optimal weight: 0.7980 overall best weight: 4.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.7385 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= 0.228 Angle : 0.629 8.024 44954 Z= 0.366 Chirality : 0.037 0.212 5072 Planarity : 0.005 0.081 3660 Dihedral : 31.057 179.619 8852 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.05 % Allowed : 1.05 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.17), residues: 2162 helix: 1.17 (0.13), residues: 1368 sheet: -2.47 (0.50), residues: 84 loop : -1.15 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 343 HIS 0.005 0.001 HIS B 75 PHE 0.025 0.002 PHE A 67 TYR 0.020 0.002 TYR D 121 ARG 0.005 0.001 ARG M 92 *********************** REFINEMENT MACRO_CYCLE 8 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 271 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 270 time to evaluate : 2.520 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: B 93 GLN cc_start: 0.9345 (pt0) cc_final: 0.9124 (pt0) REVERT: C 39 TYR cc_start: 0.7696 (m-80) cc_final: 0.7260 (m-80) REVERT: C 64 GLU cc_start: 0.8489 (tt0) cc_final: 0.8184 (tm-30) REVERT: D 62 MET cc_start: 0.8872 (mmm) cc_final: 0.8631 (mmp) REVERT: E 54 TYR cc_start: 0.9006 (m-80) cc_final: 0.8716 (m-10) REVERT: E 94 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8752 (mt-10) REVERT: E 104 PHE cc_start: 0.9594 (m-10) cc_final: 0.9324 (m-10) REVERT: E 105 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8904 (tm-30) REVERT: F 63 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8488 (mm-30) REVERT: F 72 TYR cc_start: 0.7949 (m-80) cc_final: 0.7493 (m-80) REVERT: G 15 LYS cc_start: 0.9102 (tptt) cc_final: 0.8595 (mtmm) REVERT: G 56 GLU cc_start: 0.8582 (pt0) cc_final: 0.7994 (mt-10) REVERT: G 97 LEU cc_start: 0.8774 (mt) cc_final: 0.8507 (mp) REVERT: K 276 MET cc_start: 0.9510 (mmm) cc_final: 0.9030 (ppp) REVERT: K 498 LYS cc_start: 0.8935 (pttm) cc_final: 0.8712 (tppt) REVERT: M 40 ARG cc_start: 0.7177 (mtt-85) cc_final: 0.6825 (mmt180) REVERT: N 64 GLU cc_start: 0.8523 (tt0) cc_final: 0.8266 (tm-30) REVERT: O 62 MET cc_start: 0.9020 (mmm) cc_final: 0.8614 (mmm) REVERT: O 71 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8675 (tt0) REVERT: O 106 LEU cc_start: 0.9020 (tt) cc_final: 0.8764 (pp) REVERT: P 54 TYR cc_start: 0.8781 (m-10) cc_final: 0.8445 (m-10) REVERT: P 99 TYR cc_start: 0.8523 (t80) cc_final: 0.8145 (t80) REVERT: P 103 LEU cc_start: 0.9724 (mt) cc_final: 0.9337 (mt) REVERT: P 104 PHE cc_start: 0.9578 (m-10) cc_final: 0.9299 (m-10) REVERT: P 105 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8719 (tm-30) REVERT: Q 63 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8451 (mm-30) REVERT: Q 68 ASP cc_start: 0.9224 (m-30) cc_final: 0.8975 (m-30) REVERT: R 15 LYS cc_start: 0.9089 (tptt) cc_final: 0.8677 (mtmm) REVERT: R 38 ASN cc_start: 0.7948 (t0) cc_final: 0.7615 (t0) REVERT: R 50 TYR cc_start: 0.8729 (t80) cc_final: 0.8454 (t80) REVERT: R 65 LEU cc_start: 0.9450 (mt) cc_final: 0.9239 (mt) REVERT: R 90 ASP cc_start: 0.8969 (t70) cc_final: 0.8554 (p0) REVERT: R 93 LEU cc_start: 0.9187 (mt) cc_final: 0.8496 (mp) REVERT: S 65 PHE cc_start: 0.9260 (t80) cc_final: 0.8884 (t80) REVERT: V 276 MET cc_start: 0.9562 (mmm) cc_final: 0.8971 (tmm) REVERT: V 498 LYS cc_start: 0.8798 (pttm) cc_final: 0.8566 (tppt) outliers start: 1 outliers final: 0 residues processed: 271 average time/residue: 0.3790 time to fit residues: 166.6424 Evaluate side-chains 211 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 211 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 247 optimal weight: 20.0000 chunk 225 optimal weight: 10.0000 chunk 240 optimal weight: 30.0000 chunk 144 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 189 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 239 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 5.2790 ------------------------------------------------------------------------------- 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** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.7873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 31458 Z= 0.256 Angle : 0.657 8.192 44954 Z= 0.382 Chirality : 0.038 0.206 5072 Planarity : 0.005 0.067 3660 Dihedral : 31.274 178.918 8852 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 24.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.05 % Allowed : 0.53 % Favored : 99.42 % 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: 0.24 (0.17), residues: 2162 helix: 1.02 (0.13), residues: 1368 sheet: -2.50 (0.51), residues: 84 loop : -1.12 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 343 HIS 0.005 0.001 HIS F 75 PHE 0.020 0.002 PHE A 67 TYR 0.032 0.002 TYR E 99 ARG 0.008 0.001 ARG O 99 *********************** REFINEMENT MACRO_CYCLE 9 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 265 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 264 time to evaluate : 2.353 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: B 93 GLN cc_start: 0.9488 (pt0) cc_final: 0.9264 (pt0) REVERT: C 64 GLU cc_start: 0.8486 (tt0) cc_final: 0.8211 (tm-30) REVERT: D 51 ASP cc_start: 0.7962 (t0) cc_final: 0.7206 (t0) REVERT: D 62 MET cc_start: 0.8886 (mmm) cc_final: 0.8622 (mmm) REVERT: E 54 TYR cc_start: 0.9010 (m-80) cc_final: 0.8670 (m-10) REVERT: E 94 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8568 (pt0) REVERT: E 104 PHE cc_start: 0.9607 (m-10) cc_final: 0.9322 (m-10) REVERT: E 105 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8910 (tm-30) REVERT: F 63 GLU cc_start: 0.9221 (mt-10) cc_final: 0.8575 (mm-30) REVERT: F 72 TYR cc_start: 0.8008 (m-80) cc_final: 0.7689 (m-80) REVERT: G 15 LYS cc_start: 0.9164 (tptt) cc_final: 0.8684 (mtmm) REVERT: H 54 ILE cc_start: 0.5835 (tt) cc_final: 0.5519 (tp) REVERT: H 59 MET cc_start: 0.8952 (mtt) cc_final: 0.8260 (mmt) REVERT: K 276 MET cc_start: 0.9507 (mmm) cc_final: 0.9022 (ppp) REVERT: K 413 MET cc_start: -0.1295 (ptt) cc_final: -0.1540 (ptt) REVERT: K 498 LYS cc_start: 0.8915 (pttm) cc_final: 0.8673 (tppt) REVERT: O 62 MET cc_start: 0.9050 (mmm) cc_final: 0.8647 (mmm) REVERT: O 106 LEU cc_start: 0.9048 (tt) cc_final: 0.8811 (pp) REVERT: P 54 TYR cc_start: 0.8909 (m-10) cc_final: 0.8672 (m-10) REVERT: P 99 TYR cc_start: 0.8411 (t80) cc_final: 0.8068 (t80) REVERT: P 103 LEU cc_start: 0.9649 (mt) cc_final: 0.9204 (mt) REVERT: P 104 PHE cc_start: 0.9571 (m-10) cc_final: 0.9303 (m-10) REVERT: P 105 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8739 (tm-30) REVERT: Q 63 GLU cc_start: 0.9208 (mt-10) cc_final: 0.8580 (mm-30) REVERT: Q 68 ASP cc_start: 0.9285 (m-30) cc_final: 0.9053 (m-30) REVERT: Q 72 TYR cc_start: 0.8253 (m-80) cc_final: 0.7986 (m-80) REVERT: R 15 LYS cc_start: 0.9255 (tptt) cc_final: 0.8849 (mtmm) REVERT: R 38 ASN cc_start: 0.8131 (t0) cc_final: 0.7625 (t0) REVERT: R 50 TYR cc_start: 0.8790 (t80) cc_final: 0.8413 (t80) REVERT: R 65 LEU cc_start: 0.9521 (mt) cc_final: 0.9318 (mt) REVERT: R 90 ASP cc_start: 0.9005 (t70) cc_final: 0.8590 (p0) REVERT: R 93 LEU cc_start: 0.9111 (mt) cc_final: 0.8339 (mp) REVERT: S 59 MET cc_start: 0.8630 (mtt) cc_final: 0.8168 (mmm) REVERT: S 65 PHE cc_start: 0.9324 (t80) cc_final: 0.8949 (t80) REVERT: V 276 MET cc_start: 0.9572 (mmm) cc_final: 0.9104 (ppp) REVERT: V 498 LYS cc_start: 0.8823 (pttm) cc_final: 0.8590 (tppt) outliers start: 1 outliers final: 0 residues processed: 265 average time/residue: 0.4100 time to fit residues: 175.6926 Evaluate side-chains 207 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 207 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 254 optimal weight: 30.0000 chunk 155 optimal weight: 7.9990 chunk 120 optimal weight: 30.0000 chunk 176 optimal weight: 7.9990 chunk 266 optimal weight: 6.9990 chunk 245 optimal weight: 30.0000 chunk 212 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 164 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 168 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 ASN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.8920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 31458 Z= 0.342 Angle : 0.752 9.853 44954 Z= 0.434 Chirality : 0.042 0.210 5072 Planarity : 0.006 0.089 3660 Dihedral : 32.015 177.120 8852 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 33.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.18 % Favored : 94.77 % Rotamer: Outliers : 0.05 % Allowed : 0.26 % Favored : 99.68 % 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: -0.37 (0.17), residues: 2162 helix: 0.48 (0.13), residues: 1352 sheet: -2.65 (0.57), residues: 68 loop : -1.25 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP V 343 HIS 0.010 0.002 HIS B 75 PHE 0.023 0.003 PHE R 25 TYR 0.027 0.003 TYR O 121 ARG 0.012 0.001 ARG O 99 ********************** REFINEMENT MACRO_CYCLE 10 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 249 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 248 time to evaluate : 2.451 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: B 93 GLN cc_start: 0.9466 (pt0) cc_final: 0.9102 (pt0) REVERT: D 62 MET cc_start: 0.8911 (mmm) cc_final: 0.8668 (mmm) REVERT: E 104 PHE cc_start: 0.9618 (m-10) cc_final: 0.9302 (m-10) REVERT: E 105 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8901 (tm-30) REVERT: F 63 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8454 (mm-30) REVERT: F 72 TYR cc_start: 0.8065 (m-80) cc_final: 0.7791 (m-80) REVERT: G 15 LYS cc_start: 0.9316 (tptt) cc_final: 0.8859 (mtmm) REVERT: G 56 GLU cc_start: 0.8660 (pt0) cc_final: 0.8229 (pt0) REVERT: G 93 LEU cc_start: 0.9173 (mt) cc_final: 0.8850 (mp) REVERT: H 59 MET cc_start: 0.8975 (mtt) cc_final: 0.8459 (mmt) REVERT: K 276 MET cc_start: 0.9496 (mmm) cc_final: 0.9034 (ppp) REVERT: K 413 MET cc_start: -0.1010 (ptt) cc_final: -0.1346 (ptt) REVERT: K 498 LYS cc_start: 0.8828 (pttm) cc_final: 0.8579 (tppt) REVERT: O 62 MET cc_start: 0.9086 (mmm) cc_final: 0.8676 (mmm) REVERT: O 106 LEU cc_start: 0.9055 (tt) cc_final: 0.8818 (pp) REVERT: P 54 TYR cc_start: 0.8939 (m-10) cc_final: 0.8659 (m-10) REVERT: P 94 GLU cc_start: 0.8835 (pt0) cc_final: 0.8382 (tt0) REVERT: P 99 TYR cc_start: 0.8551 (t80) cc_final: 0.8304 (t80) REVERT: P 104 PHE cc_start: 0.9576 (m-10) cc_final: 0.9291 (m-10) REVERT: P 105 GLU cc_start: 0.9001 (tm-30) cc_final: 0.8763 (tm-30) REVERT: Q 63 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8581 (mm-30) REVERT: R 15 LYS cc_start: 0.9307 (tptt) cc_final: 0.9009 (mtmm) REVERT: R 38 ASN cc_start: 0.8467 (t0) cc_final: 0.8034 (t0) REVERT: R 50 TYR cc_start: 0.8896 (t80) cc_final: 0.8565 (t80) REVERT: S 59 MET cc_start: 0.9195 (mtt) cc_final: 0.8766 (mmm) REVERT: S 65 PHE cc_start: 0.9402 (t80) cc_final: 0.9008 (t80) REVERT: V 276 MET cc_start: 0.9561 (mmm) cc_final: 0.9276 (mmm) REVERT: V 498 LYS cc_start: 0.8772 (pttm) cc_final: 0.8536 (tppt) outliers start: 1 outliers final: 0 residues processed: 249 average time/residue: 0.3905 time to fit residues: 157.0652 Evaluate side-chains 180 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 196 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 59 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 186 optimal weight: 0.9980 overall best weight: 3.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 68 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 ASN ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 449 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 473 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.076021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.054058 restraints weight = 311706.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.054218 restraints weight = 228419.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.054759 restraints weight = 175798.757| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 31458 Z= 0.228 Angle : 0.655 8.361 44954 Z= 0.380 Chirality : 0.039 0.205 5072 Planarity : 0.005 0.081 3660 Dihedral : 31.628 178.740 8852 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 23.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % 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: 0.04 (0.17), residues: 2162 helix: 0.85 (0.13), residues: 1372 sheet: -2.56 (0.58), residues: 68 loop : -1.22 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP V 343 HIS 0.005 0.001 HIS B 75 PHE 0.025 0.002 PHE A 67 TYR 0.020 0.002 TYR O 121 ARG 0.008 0.001 ARG O 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4940.52 seconds wall clock time: 91 minutes 0.59 seconds (5460.59 seconds total)