Starting phenix.real_space_refine (version: dev) on Fri Dec 16 08:47:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/12_2022/7ccr_30340.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/12_2022/7ccr_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_30340/12_2022/7ccr_30340.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/12_2022/7ccr_30340.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/12_2022/7ccr_30340.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ccr_30340/12_2022/7ccr_30340.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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-4807/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: 15.65, per 1000 atoms: 0.53 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: 17.20 Conformation dependent library (CDL) restraints added in 2.4 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: 13.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.787A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.181A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.577A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 161 through 176 Processing helix chain 'K' and resid 178 through 198 removed outlier: 4.253A pdb=" N ALA K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.785A pdb=" N PHE K 203 " --> pdb=" O ASP K 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG K 204 " --> pdb=" O SER K 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 200 through 204' Processing helix chain 'K' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN K 289 " --> pdb=" O LYS K 285 " (cutoff:3.500A) Processing helix chain 'K' and resid 331 through 335 Processing helix chain 'K' and resid 345 through 354 Processing helix chain 'K' and resid 379 through 389 Processing helix chain 'K' and resid 405 through 424 Processing helix chain 'K' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS K 432 " --> pdb=" O HIS K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 449 removed outlier: 3.844A pdb=" N VAL K 438 " --> pdb=" O SER K 434 " (cutoff:3.500A) Processing helix chain 'K' and resid 452 through 458 removed outlier: 3.807A pdb=" N ASP K 456 " --> pdb=" O SER K 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG K 457 " --> pdb=" O GLN K 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS K 458 " --> pdb=" O TRP K 455 " (cutoff:3.500A) Processing helix chain 'K' and resid 459 through 477 Processing helix chain 'K' and resid 497 through 513 Processing helix chain 'K' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP K 520 " --> pdb=" O PRO K 517 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 57 removed outlier: 3.744A pdb=" N LYS L 56 " --> pdb=" O ARG L 52 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 79 removed outlier: 3.505A pdb=" N PHE L 78 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 120 through 132 Processing helix chain 'M' and resid 30 through 42 Processing helix chain 'M' and resid 49 through 76 removed outlier: 3.564A pdb=" N GLU M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 94 removed outlier: 3.788A pdb=" N VAL M 86 " --> pdb=" O THR M 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 22 Processing helix chain 'N' and resid 26 through 37 Processing helix chain 'N' and resid 45 through 73 removed outlier: 4.182A pdb=" N VAL N 49 " --> pdb=" O ALA N 45 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 90 removed outlier: 3.515A pdb=" N LEU N 83 " --> pdb=" O ILE N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 90 through 97 Processing helix chain 'O' and resid 37 through 49 Processing helix chain 'O' and resid 55 through 84 Processing helix chain 'O' and resid 90 through 102 Processing helix chain 'O' and resid 103 through 123 Processing helix chain 'P' and resid 44 through 57 Processing helix chain 'P' and resid 63 through 79 Processing helix chain 'P' and resid 85 through 114 Processing helix chain 'P' and resid 120 through 132 removed outlier: 3.578A pdb=" N ILE P 124 " --> pdb=" O MET P 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 30 through 41 Processing helix chain 'Q' and resid 49 through 76 removed outlier: 3.533A pdb=" N GLU Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL Q 86 " --> pdb=" O THR Q 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 22 Processing helix chain 'R' and resid 26 through 37 Processing helix chain 'R' and resid 45 through 73 removed outlier: 4.228A pdb=" N VAL R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) Processing helix chain 'R' and resid 79 through 90 Processing helix chain 'R' and resid 90 through 97 Processing helix chain 'S' and resid 37 through 49 Processing helix chain 'S' and resid 55 through 85 Processing helix chain 'S' and resid 90 through 102 Processing helix chain 'S' and resid 103 through 124 Processing helix chain 'V' and resid 161 through 176 Processing helix chain 'V' and resid 178 through 198 removed outlier: 4.252A pdb=" N ALA V 182 " --> pdb=" O ASP V 178 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY V 184 " --> pdb=" O SER V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 200 through 204 removed outlier: 3.784A pdb=" N PHE V 203 " --> pdb=" O ASP V 200 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG V 204 " --> pdb=" O SER V 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 200 through 204' Processing helix chain 'V' and resid 260 through 266 removed outlier: 3.570A pdb=" N GLN V 264 " --> pdb=" O ASN V 260 " (cutoff:3.500A) Processing helix chain 'V' and resid 272 through 289 removed outlier: 3.841A pdb=" N ASN V 289 " --> pdb=" O LYS V 285 " (cutoff:3.500A) Processing helix chain 'V' and resid 331 through 335 Processing helix chain 'V' and resid 345 through 354 Processing helix chain 'V' and resid 379 through 389 Processing helix chain 'V' and resid 405 through 424 Processing helix chain 'V' and resid 429 through 433 removed outlier: 3.597A pdb=" N LYS V 432 " --> pdb=" O HIS V 429 " (cutoff:3.500A) Processing helix chain 'V' and resid 434 through 449 removed outlier: 3.843A pdb=" N VAL V 438 " --> pdb=" O SER V 434 " (cutoff:3.500A) Processing helix chain 'V' and resid 452 through 458 removed outlier: 3.808A pdb=" N ASP V 456 " --> pdb=" O SER V 453 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG V 457 " --> pdb=" O GLN V 454 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LYS V 458 " --> pdb=" O TRP V 455 " (cutoff:3.500A) Processing helix chain 'V' and resid 459 through 477 Processing helix chain 'V' and resid 497 through 513 Processing helix chain 'V' and resid 516 through 520 removed outlier: 4.176A pdb=" N ASP V 520 " --> pdb=" O PRO V 517 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.524A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE K 230 " --> pdb=" O ALA K 323 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLU K 325 " --> pdb=" O PHE K 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU K 232 " --> pdb=" O GLU K 325 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N LEU K 322 " --> pdb=" O PRO K 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR K 358 " --> pdb=" O SER K 378 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE K 297 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU K 311 " --> pdb=" O ILE K 297 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 83 through 84 removed outlier: 7.048A pdb=" N ARG L 83 " --> pdb=" O VAL M 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 118 through 119 Processing sheet with id=AB6, first strand: chain 'M' and resid 96 through 98 removed outlier: 5.952A pdb=" N THR M 96 " --> pdb=" O THR R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'N' and resid 42 through 43 removed outlier: 7.424A pdb=" N ARG N 42 " --> pdb=" O ILE O 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'N' and resid 77 through 78 Processing sheet with id=AB9, first strand: chain 'N' and resid 101 through 102 removed outlier: 7.519A pdb=" N THR N 101 " --> pdb=" O TYR Q 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'P' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG P 83 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'P' and resid 118 through 119 Processing sheet with id=AC3, first strand: chain 'R' and resid 42 through 43 removed outlier: 7.003A pdb=" N ARG R 42 " --> pdb=" O ILE S 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'R' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'V' and resid 206 through 208 removed outlier: 5.865A pdb=" N PHE V 230 " --> pdb=" O ALA V 323 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU V 325 " --> pdb=" O PHE V 230 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LEU V 232 " --> pdb=" O GLU V 325 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N LEU V 322 " --> pdb=" O PRO V 361 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR V 358 " --> pdb=" O SER V 378 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'V' and resid 296 through 298 removed outlier: 3.602A pdb=" N ILE V 297 " --> pdb=" O LEU V 311 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU V 311 " --> pdb=" O ILE V 297 " (cutoff:3.500A) 1092 hydrogen bonds defined for protein. 3222 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 728 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 286 basepair parallelities 510 stacking parallelities Total time for adding SS restraints: 16.37 Time building geometry restraints manager: 17.84 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: 14133 32.34 - 64.68: 2753 64.68 - 97.02: 74 97.02 - 129.36: 2 129.36 - 161.70: 4 Dihedral angle restraints: 16966 sinusoidal: 10556 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 16963 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 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. 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.440 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.270 Process input model: 93.610 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 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 : 24.745 161.695 12818 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer Outliers : 0.11 % 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 *********************** 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 : 2.541 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 outliers start: 2 outliers final: 0 residues processed: 555 average time/residue: 0.4382 time to fit residues: 369.2539 Evaluate side-chains 252 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 252 time to evaluate : 2.864 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2870 ------------------------------------------------------------------------------- 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: 5.9990 chunk 112 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 137 optimal weight: 5.9990 chunk 108 optimal weight: 40.0000 chunk 210 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 chunk 156 optimal weight: 10.0000 chunk 243 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 64 ASN B 93 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 V 449 ASN V 473 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.064 31458 Z= 0.289 Angle : 0.699 8.405 44954 Z= 0.408 Chirality : 0.039 0.187 5072 Planarity : 0.006 0.060 3660 Dihedral : 30.834 166.351 8340 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.00 % 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: -0.69 (0.16), residues: 2162 helix: 0.36 (0.12), residues: 1396 sheet: -2.72 (0.40), residues: 106 loop : -1.69 (0.22), residues: 660 *********************** 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 314 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.561 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 outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.4226 time to fit residues: 207.2233 Evaluate side-chains 193 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 2.253 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8450 ------------------------------------------------------------------------------- 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: 7.9990 chunk 165 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 243 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 217 optimal weight: 20.0000 chunk 241 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 overall best weight: 4.3586 ------------------------------------------------------------------------------- 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 ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN ** K 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 89 ASN N 110 ASN O 95 GLN S 67 ASN ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.4289 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= 0.234 Angle : 0.618 7.468 44954 Z= 0.365 Chirality : 0.036 0.148 5072 Planarity : 0.005 0.054 3660 Dihedral : 30.903 171.757 8340 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.05 % 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: -0.15 (0.17), residues: 2162 helix: 0.80 (0.13), residues: 1380 sheet: -2.69 (0.48), residues: 84 loop : -1.52 (0.22), residues: 698 *********************** 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 287 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 286 time to evaluate : 2.095 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 outliers start: 1 outliers final: 0 residues processed: 287 average time/residue: 0.4343 time to fit residues: 195.9296 Evaluate side-chains 196 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.490 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0963 ------------------------------------------------------------------------------- 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: 2.9990 chunk 183 optimal weight: 0.2980 chunk 126 optimal weight: 50.0000 chunk 26 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 259 optimal weight: 20.0000 chunk 127 optimal weight: 8.9990 chunk 231 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN D 95 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 429 HIS ** K 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 507 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6892 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 31458 Z= 0.182 Angle : 0.577 6.890 44954 Z= 0.339 Chirality : 0.035 0.186 5072 Planarity : 0.005 0.069 3660 Dihedral : 30.643 177.321 8340 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.17), residues: 2162 helix: 1.24 (0.13), residues: 1398 sheet: -2.73 (0.50), residues: 80 loop : -1.41 (0.22), residues: 684 *********************** 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 287 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 284 time to evaluate : 2.767 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 outliers start: 3 outliers final: 2 residues processed: 287 average time/residue: 0.3947 time to fit residues: 181.3514 Evaluate side-chains 195 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 2.609 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.2934 time to fit residues: 4.1568 ------------------------------------------------------------------------------- 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: 0.9980 chunk 3 optimal weight: 7.9990 chunk 192 optimal weight: 6.9990 chunk 106 optimal weight: 0.0270 chunk 221 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 overall best weight: 3.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN F 64 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** Q 27 GLN Q 64 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 31458 Z= 0.209 Angle : 0.594 7.038 44954 Z= 0.349 Chirality : 0.036 0.189 5072 Planarity : 0.005 0.059 3660 Dihedral : 30.753 179.989 8340 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer Outliers : 0.05 % 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: 0.43 (0.17), residues: 2162 helix: 1.26 (0.13), residues: 1384 sheet: -2.55 (0.50), residues: 80 loop : -1.33 (0.22), residues: 698 *********************** 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 275 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 274 time to evaluate : 2.573 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 outliers start: 1 outliers final: 0 residues processed: 275 average time/residue: 0.3872 time to fit residues: 172.6080 Evaluate side-chains 196 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 2.411 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.0836 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 30.0000 chunk 152 optimal weight: 20.0000 chunk 63 optimal weight: 0.8980 chunk 259 optimal weight: 30.0000 chunk 215 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 overall best weight: 5.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.045 31458 Z= 0.255 Angle : 0.637 8.307 44954 Z= 0.373 Chirality : 0.037 0.183 5072 Planarity : 0.005 0.062 3660 Dihedral : 31.249 176.581 8340 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer Outliers : 0.21 % 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: 0.28 (0.17), residues: 2162 helix: 1.13 (0.13), residues: 1352 sheet: -2.50 (0.51), residues: 80 loop : -1.24 (0.22), residues: 730 *********************** 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 274 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 270 time to evaluate : 2.792 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 outliers start: 4 outliers final: 1 residues processed: 272 average time/residue: 0.3945 time to fit residues: 173.6745 Evaluate side-chains 195 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 2.531 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3130 time to fit residues: 3.6046 ------------------------------------------------------------------------------- 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: 30.0000 chunk 29 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 189 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 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** ** 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: 0.7032 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 31458 Z= 0.219 Angle : 0.611 7.257 44954 Z= 0.359 Chirality : 0.037 0.198 5072 Planarity : 0.005 0.054 3660 Dihedral : 31.237 178.969 8340 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.11 % 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: 0.43 (0.17), residues: 2162 helix: 1.21 (0.13), residues: 1364 sheet: -2.24 (0.58), residues: 68 loop : -1.19 (0.22), residues: 730 *********************** 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 274 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 2.464 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 outliers start: 2 outliers final: 1 residues processed: 274 average time/residue: 0.3907 time to fit residues: 173.1325 Evaluate side-chains 197 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 196 time to evaluate : 2.518 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3009 time to fit residues: 3.6915 ------------------------------------------------------------------------------- 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: 20.0000 chunk 103 optimal weight: 9.9990 chunk 154 optimal weight: 0.0670 chunk 77 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 127 optimal weight: 0.1980 chunk 24 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 234 optimal weight: 4.9990 overall best weight: 1.8522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 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** ** 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: 0.6938 moved from start: 0.6557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 31458 Z= 0.174 Angle : 0.584 9.052 44954 Z= 0.341 Chirality : 0.036 0.186 5072 Planarity : 0.004 0.044 3660 Dihedral : 30.954 178.515 8340 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer Outliers : 0.05 % 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: 0.70 (0.17), residues: 2162 helix: 1.43 (0.13), residues: 1376 sheet: -2.16 (0.59), residues: 68 loop : -1.14 (0.22), residues: 718 *********************** 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 284 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 283 time to evaluate : 2.666 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 outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.3978 time to fit residues: 183.7149 Evaluate side-chains 201 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 201 time to evaluate : 2.650 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2334 ------------------------------------------------------------------------------- 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: 9.9990 chunk 225 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 189 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 217 optimal weight: 20.0000 chunk 227 optimal weight: 10.0000 chunk 239 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 overall best weight: 8.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 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** G 68 ASN K 342 ASN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 HIS ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 68 ASN 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.7551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 31458 Z= 0.366 Angle : 0.752 13.575 44954 Z= 0.432 Chirality : 0.041 0.237 5072 Planarity : 0.006 0.064 3660 Dihedral : 31.827 176.653 8340 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 33.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer Outliers : 0.05 % 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: -0.18 (0.17), residues: 2162 helix: 0.63 (0.13), residues: 1362 sheet: -2.38 (0.60), residues: 68 loop : -1.20 (0.22), residues: 732 *********************** 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 252 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 2.679 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 outliers start: 1 outliers final: 0 residues processed: 252 average time/residue: 0.4127 time to fit residues: 172.0457 Evaluate side-chains 171 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 2.719 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3373 ------------------------------------------------------------------------------- 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: 8.9990 chunk 120 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 266 optimal weight: 30.0000 chunk 245 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 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** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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: 0.7155 moved from start: 0.7931 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= 0.283 Angle : 0.685 13.516 44954 Z= 0.397 Chirality : 0.039 0.284 5072 Planarity : 0.006 0.079 3660 Dihedral : 31.992 177.402 8340 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 27.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 0.05 % 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: -0.20 (0.17), residues: 2162 helix: 0.62 (0.13), residues: 1370 sheet: -2.49 (0.59), residues: 68 loop : -1.24 (0.22), residues: 724 ********************** 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 257 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 256 time to evaluate : 2.450 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 outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.3771 time to fit residues: 157.3741 Evaluate side-chains 178 residues out of total 1898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 2.487 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.9662 ------------------------------------------------------------------------------- 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: 3.9990 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 212 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 218 optimal weight: 20.0000 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 186 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 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** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.077424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.055185 restraints weight = 305543.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.055359 restraints weight = 223213.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.055999 restraints weight = 172408.748| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.8017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 31458 Z= 0.214 Angle : 0.623 7.557 44954 Z= 0.364 Chirality : 0.038 0.195 5072 Planarity : 0.005 0.060 3660 Dihedral : 31.724 179.691 8340 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer Outliers : 0.05 % 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: 0.28 (0.17), residues: 2162 helix: 1.04 (0.13), residues: 1362 sheet: -2.48 (0.58), residues: 68 loop : -1.11 (0.22), residues: 732 =============================================================================== Job complete usr+sys time: 4799.25 seconds wall clock time: 89 minutes 24.62 seconds (5364.62 seconds total)