Starting phenix.real_space_refine on Fri Feb 6 01:00:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.map" model { file = "/net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v2r_64738/02_2026/9v2r_64738.cif" } resolution = 4.4 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 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= 0.009 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 13272 2.51 5 N 3513 2.21 5 O 4167 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21060 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "B" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "C" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "D" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "E" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "F" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "H" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "J" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "L" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Chain: "G" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 986 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 123} Chain: "I" Number of atoms: 3482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3482 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 436} Chain breaks: 1 Chain: "K" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 817 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 103} Chain: "M" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 908 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "O" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 827 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 101} Time building chain proxies: 5.37, per 1000 atoms: 0.25 Number of scatterers: 21060 At special positions: 0 Unit cell: (146, 144, 145, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4167 8.00 N 3513 7.00 C 13272 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.02 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 37 " - pdb=" SG CYS H 439 " distance=2.03 Simple disulfide: pdb=" SG CYS H 69 " - pdb=" SG CYS H 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 290 " distance=2.03 Simple disulfide: pdb=" SG CYS H 313 " - pdb=" SG CYS H 343 " distance=2.03 Simple disulfide: pdb=" SG CYS H 322 " - pdb=" SG CYS H 333 " distance=2.04 Simple disulfide: pdb=" SG CYS H 358 " - pdb=" SG CYS H 367 " distance=2.04 Simple disulfide: pdb=" SG CYS H 382 " - pdb=" SG CYS H 393 " distance=2.03 Simple disulfide: pdb=" SG CYS H 416 " - pdb=" SG CYS H 422 " distance=2.02 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 90 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 37 " - pdb=" SG CYS I 439 " distance=2.03 Simple disulfide: pdb=" SG CYS I 69 " - pdb=" SG CYS I 212 " distance=2.03 Simple disulfide: pdb=" SG CYS I 155 " - pdb=" SG CYS I 290 " distance=2.03 Simple disulfide: pdb=" SG CYS I 313 " - pdb=" SG CYS I 343 " distance=2.03 Simple disulfide: pdb=" SG CYS I 322 " - pdb=" SG CYS I 333 " distance=2.04 Simple disulfide: pdb=" SG CYS I 358 " - pdb=" SG CYS I 367 " distance=2.04 Simple disulfide: pdb=" SG CYS I 382 " - pdb=" SG CYS I 393 " distance=2.03 Simple disulfide: pdb=" SG CYS I 416 " - pdb=" SG CYS I 422 " distance=2.02 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 90 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5022 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 57 sheets defined 19.6% alpha, 26.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.952A pdb=" N ASP A 90 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N THR A 91 " --> pdb=" O ARG A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 91' Processing helix chain 'B' and resid 77 through 97 removed outlier: 3.605A pdb=" N GLN B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 159 Processing helix chain 'B' and resid 163 through 171 removed outlier: 3.674A pdb=" N ILE B 167 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 203 removed outlier: 3.610A pdb=" N LEU B 203 " --> pdb=" O ILE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 217 through 226 removed outlier: 3.923A pdb=" N GLU B 222 " --> pdb=" O GLU B 218 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 223 " --> pdb=" O THR B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 285 Processing helix chain 'B' and resid 292 through 296 removed outlier: 3.639A pdb=" N VAL B 296 " --> pdb=" O LYS B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 3.834A pdb=" N ASN B 371 " --> pdb=" O ASP B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 385 Processing helix chain 'B' and resid 445 through 447 No H-bonds generated for 'chain 'B' and resid 445 through 447' Processing helix chain 'B' and resid 473 through 478 Processing helix chain 'B' and resid 491 through 513 Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.667A pdb=" N GLU C 85 " --> pdb=" O PRO C 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.967A pdb=" N THR D 91 " --> pdb=" O VAL D 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 85 removed outlier: 4.126A pdb=" N GLU E 85 " --> pdb=" O PRO E 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 87 through 91 removed outlier: 3.947A pdb=" N ASP F 90 " --> pdb=" O ARG F 87 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N THR F 91 " --> pdb=" O ARG F 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 87 through 91' Processing helix chain 'H' and resid 77 through 97 Processing helix chain 'H' and resid 149 through 159 Processing helix chain 'H' and resid 163 through 171 removed outlier: 3.672A pdb=" N ILE H 167 " --> pdb=" O GLU H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 203 removed outlier: 3.607A pdb=" N LEU H 203 " --> pdb=" O ILE H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 217 through 226 removed outlier: 3.887A pdb=" N GLU H 222 " --> pdb=" O GLU H 218 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE H 223 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 removed outlier: 4.067A pdb=" N VAL H 239 " --> pdb=" O ARG H 235 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASN H 240 " --> pdb=" O GLU H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 262 Processing helix chain 'H' and resid 267 through 277 Processing helix chain 'H' and resid 277 through 285 Processing helix chain 'H' and resid 292 through 296 removed outlier: 3.648A pdb=" N VAL H 296 " --> pdb=" O LYS H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 368 through 372 removed outlier: 3.768A pdb=" N ASN H 371 " --> pdb=" O ASP H 368 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER H 372 " --> pdb=" O THR H 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 368 through 372' Processing helix chain 'H' and resid 379 through 385 Processing helix chain 'H' and resid 445 through 447 No H-bonds generated for 'chain 'H' and resid 445 through 447' Processing helix chain 'H' and resid 473 through 478 Processing helix chain 'H' and resid 492 through 513 Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.670A pdb=" N GLU J 85 " --> pdb=" O PRO J 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.859A pdb=" N THR L 91 " --> pdb=" O VAL L 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.983A pdb=" N GLU N 85 " --> pdb=" O PRO N 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.944A pdb=" N ASP G 90 " --> pdb=" O ARG G 87 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR G 91 " --> pdb=" O ARG G 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 87 through 91' Processing helix chain 'I' and resid 77 through 97 removed outlier: 3.672A pdb=" N GLN I 81 " --> pdb=" O LYS I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 159 Processing helix chain 'I' and resid 163 through 171 removed outlier: 3.654A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 195 through 203 removed outlier: 3.620A pdb=" N LEU I 203 " --> pdb=" O ILE I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 208 Processing helix chain 'I' and resid 217 through 226 removed outlier: 3.913A pdb=" N GLU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE I 223 " --> pdb=" O THR I 219 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 241 Processing helix chain 'I' and resid 253 through 262 Processing helix chain 'I' and resid 267 through 277 Processing helix chain 'I' and resid 277 through 285 Processing helix chain 'I' and resid 292 through 296 removed outlier: 3.685A pdb=" N VAL I 296 " --> pdb=" O LYS I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 368 through 372 removed outlier: 3.730A pdb=" N ASN I 371 " --> pdb=" O ASP I 368 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER I 372 " --> pdb=" O THR I 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 368 through 372' Processing helix chain 'I' and resid 379 through 385 Processing helix chain 'I' and resid 445 through 447 No H-bonds generated for 'chain 'I' and resid 445 through 447' Processing helix chain 'I' and resid 473 through 478 Processing helix chain 'I' and resid 491 through 513 Processing helix chain 'K' and resid 81 through 85 removed outlier: 3.692A pdb=" N GLU K 85 " --> pdb=" O PRO K 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.911A pdb=" N THR M 91 " --> pdb=" O VAL M 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 85 removed outlier: 4.017A pdb=" N GLU O 85 " --> pdb=" O PRO O 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.969A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE A 34 " --> pdb=" O LEU A 50 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 50 " --> pdb=" O PHE A 34 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP A 36 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 11 removed outlier: 6.438A pdb=" N GLY A 10 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL A 115 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.927A pdb=" N GLU B 30 " --> pdb=" O LYS B 465 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU B 467 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE B 32 " --> pdb=" O LEU B 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA6, first strand: chain 'B' and resid 176 through 177 removed outlier: 6.270A pdb=" N VAL B 56 " --> pdb=" O PHE B 190 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL B 192 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N THR B 58 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASP B 194 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N GLU B 60 " --> pdb=" O ASP B 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 321 through 322 removed outlier: 3.688A pdb=" N LEU B 334 " --> pdb=" O LEU B 321 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 359 through 360 Processing sheet with id=AA9, first strand: chain 'B' and resid 405 through 408 removed outlier: 3.887A pdb=" N GLY B 411 " --> pdb=" O THR B 408 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.586A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.688A pdb=" N THR C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLN C 39 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LEU C 48 " --> pdb=" O GLN C 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.688A pdb=" N THR C 108 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 19 through 23 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 11 removed outlier: 5.806A pdb=" N GLY D 10 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 19 through 22 Processing sheet with id=AB7, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AB8, first strand: chain 'E' and resid 37 through 39 removed outlier: 5.977A pdb=" N GLN E 39 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N VAL E 48 " --> pdb=" O GLN E 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 88 Processing sheet with id=AC1, first strand: chain 'E' and resid 91 through 92 removed outlier: 3.561A pdb=" N SER E 92 " --> pdb=" O VAL E 100 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 7 removed outlier: 4.088A pdb=" N GLN F 3 " --> pdb=" O SER F 25 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N SER F 25 " --> pdb=" O GLN F 3 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER F 21 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.840A pdb=" N PHE F 34 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LEU F 50 " --> pdb=" O PHE F 34 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.544A pdb=" N ARG F 98 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL F 115 " --> pdb=" O ARG F 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 29 through 32 removed outlier: 3.899A pdb=" N GLU H 30 " --> pdb=" O LYS H 465 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU H 467 " --> pdb=" O GLU H 30 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE H 32 " --> pdb=" O LEU H 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 38 through 39 Processing sheet with id=AC7, first strand: chain 'H' and resid 176 through 177 removed outlier: 6.213A pdb=" N VAL H 56 " --> pdb=" O PHE H 190 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL H 192 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR H 58 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ASP H 194 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLU H 60 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER H 287 " --> pdb=" O THR H 244 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 321 through 322 removed outlier: 3.571A pdb=" N LEU H 321 " --> pdb=" O LEU H 334 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU H 334 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE H 395 " --> pdb=" O ASP H 489 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ASP H 489 " --> pdb=" O ILE H 395 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR H 397 " --> pdb=" O GLU H 487 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N GLU H 487 " --> pdb=" O THR H 397 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 359 through 361 Processing sheet with id=AD1, first strand: chain 'H' and resid 405 through 408 removed outlier: 3.819A pdb=" N GLY H 411 " --> pdb=" O THR H 408 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 430 through 434 removed outlier: 6.602A pdb=" N ALA H 424 " --> pdb=" O ILE H 432 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR H 434 " --> pdb=" O CYS H 422 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N CYS H 422 " --> pdb=" O THR H 434 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 9 through 11 removed outlier: 3.638A pdb=" N THR J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLN J 39 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N LEU J 48 " --> pdb=" O GLN J 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 9 through 11 removed outlier: 3.638A pdb=" N THR J 108 " --> pdb=" O VAL J 10 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 19 through 23 Processing sheet with id=AD6, first strand: chain 'L' and resid 6 through 7 Processing sheet with id=AD7, first strand: chain 'L' and resid 10 through 11 removed outlier: 5.946A pdb=" N GLY L 10 " --> pdb=" O THR L 119 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG L 38 " --> pdb=" O TRP L 47 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N TRP L 47 " --> pdb=" O ARG L 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AD9, first strand: chain 'N' and resid 37 through 38 Processing sheet with id=AE1, first strand: chain 'N' and resid 86 through 88 Processing sheet with id=AE2, first strand: chain 'N' and resid 91 through 92 removed outlier: 3.544A pdb=" N SER N 92 " --> pdb=" O VAL N 100 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 3 through 7 removed outlier: 4.100A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N SER G 25 " --> pdb=" O GLN G 3 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU G 79 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 10 through 12 removed outlier: 7.894A pdb=" N PHE G 34 " --> pdb=" O LEU G 50 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N TRP G 36 " --> pdb=" O LEU G 48 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 29 through 32 removed outlier: 6.055A pdb=" N GLU I 30 " --> pdb=" O LEU I 467 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 38 through 40 Processing sheet with id=AE7, first strand: chain 'I' and resid 176 through 177 removed outlier: 6.312A pdb=" N VAL I 56 " --> pdb=" O PHE I 190 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL I 192 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N THR I 58 " --> pdb=" O VAL I 192 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASP I 194 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU I 60 " --> pdb=" O ASP I 194 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 321 through 322 removed outlier: 3.755A pdb=" N LEU I 334 " --> pdb=" O LEU I 321 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 359 through 361 Processing sheet with id=AF1, first strand: chain 'I' and resid 405 through 408 removed outlier: 3.949A pdb=" N GLY I 411 " --> pdb=" O THR I 408 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 430 through 434 removed outlier: 6.565A pdb=" N ALA I 424 " --> pdb=" O ILE I 432 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR I 434 " --> pdb=" O CYS I 422 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N CYS I 422 " --> pdb=" O THR I 434 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN K 39 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N LEU K 48 " --> pdb=" O GLN K 39 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 9 through 11 removed outlier: 3.658A pdb=" N THR K 108 " --> pdb=" O VAL K 10 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF6, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.909A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG M 38 " --> pdb=" O TRP M 47 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N TRP M 47 " --> pdb=" O ARG M 38 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'M' and resid 10 through 11 removed outlier: 5.909A pdb=" N GLY M 10 " --> pdb=" O THR M 119 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS M 96 " --> pdb=" O TRP M 112 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N TRP M 112 " --> pdb=" O CYS M 96 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ARG M 98 " --> pdb=" O ASP M 110 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 19 through 22 Processing sheet with id=AF9, first strand: chain 'O' and resid 18 through 23 Processing sheet with id=AG1, first strand: chain 'O' and resid 37 through 39 removed outlier: 5.826A pdb=" N GLN O 39 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL O 48 " --> pdb=" O GLN O 39 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 86 through 88 Processing sheet with id=AG3, first strand: chain 'O' and resid 91 through 92 removed outlier: 3.595A pdb=" N SER O 92 " --> pdb=" O VAL O 100 " (cutoff:3.500A) 778 hydrogen bonds defined for protein. 1914 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 6792 1.35 - 1.48: 5372 1.48 - 1.60: 9151 1.60 - 1.73: 0 1.73 - 1.85: 144 Bond restraints: 21459 Sorted by residual: bond pdb=" C VAL B 76 " pdb=" N LYS B 77 " ideal model delta sigma weight residual 1.332 1.291 0.042 1.40e-02 5.10e+03 8.94e+00 bond pdb=" N GLU L 16 " pdb=" CA GLU L 16 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.34e+00 bond pdb=" N GLY L 102 " pdb=" CA GLY L 102 " ideal model delta sigma weight residual 1.446 1.477 -0.031 1.06e-02 8.90e+03 8.31e+00 bond pdb=" N GLY D 102 " pdb=" CA GLY D 102 " ideal model delta sigma weight residual 1.446 1.476 -0.030 1.06e-02 8.90e+03 8.04e+00 bond pdb=" N VAL L 103 " pdb=" CA VAL L 103 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 8.04e+00 ... (remaining 21454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 28419 2.69 - 5.39: 608 5.39 - 8.08: 64 8.08 - 10.77: 24 10.77 - 13.47: 3 Bond angle restraints: 29118 Sorted by residual: angle pdb=" N SER M 30 " pdb=" CA SER M 30 " pdb=" C SER M 30 " ideal model delta sigma weight residual 114.62 108.98 5.64 1.14e+00 7.69e-01 2.45e+01 angle pdb=" C ILE B 506 " pdb=" N ARG B 507 " pdb=" CA ARG B 507 " ideal model delta sigma weight residual 122.06 113.08 8.98 1.86e+00 2.89e-01 2.33e+01 angle pdb=" N SER D 30 " pdb=" CA SER D 30 " pdb=" C SER D 30 " ideal model delta sigma weight residual 114.75 108.82 5.93 1.26e+00 6.30e-01 2.21e+01 angle pdb=" CB MET G 113 " pdb=" CG MET G 113 " pdb=" SD MET G 113 " ideal model delta sigma weight residual 112.70 126.17 -13.47 3.00e+00 1.11e-01 2.01e+01 angle pdb=" CB MET A 113 " pdb=" CG MET A 113 " pdb=" SD MET A 113 " ideal model delta sigma weight residual 112.70 126.16 -13.46 3.00e+00 1.11e-01 2.01e+01 ... (remaining 29113 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 11565 17.14 - 34.28: 1001 34.28 - 51.42: 228 51.42 - 68.55: 31 68.55 - 85.69: 21 Dihedral angle restraints: 12846 sinusoidal: 4965 harmonic: 7881 Sorted by residual: dihedral pdb=" CB CYS M 22 " pdb=" SG CYS M 22 " pdb=" SG CYS M 96 " pdb=" CB CYS M 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.16 85.16 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 96 " pdb=" CB CYS L 96 " ideal model delta sinusoidal sigma weight residual 93.00 175.39 -82.39 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 96 " pdb=" CB CYS D 96 " ideal model delta sinusoidal sigma weight residual -86.00 -166.41 80.41 1 1.00e+01 1.00e-02 8.00e+01 ... (remaining 12843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2351 0.050 - 0.100: 720 0.100 - 0.149: 220 0.149 - 0.199: 47 0.199 - 0.249: 10 Chirality restraints: 3348 Sorted by residual: chirality pdb=" CB ILE L 69 " pdb=" CA ILE L 69 " pdb=" CG1 ILE L 69 " pdb=" CG2 ILE L 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB ILE D 69 " pdb=" CA ILE D 69 " pdb=" CG1 ILE D 69 " pdb=" CG2 ILE D 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CB ILE M 69 " pdb=" CA ILE M 69 " pdb=" CG1 ILE M 69 " pdb=" CG2 ILE M 69 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 3345 not shown) Planarity restraints: 3699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG M 67 " 0.454 9.50e-02 1.11e+02 2.04e-01 2.54e+01 pdb=" NE ARG M 67 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG M 67 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG M 67 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG M 67 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 67 " 0.412 9.50e-02 1.11e+02 1.85e-01 2.09e+01 pdb=" NE ARG D 67 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 67 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG D 67 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG D 67 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 67 " -0.375 9.50e-02 1.11e+02 1.68e-01 1.73e+01 pdb=" NE ARG L 67 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG L 67 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG L 67 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 67 " -0.012 2.00e-02 2.50e+03 ... (remaining 3696 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 12028 3.02 - 3.49: 23221 3.49 - 3.96: 35354 3.96 - 4.43: 40528 4.43 - 4.90: 64033 Nonbonded interactions: 175164 Sorted by model distance: nonbonded pdb=" CA GLU C 85 " pdb=" O LEU C 107 " model vdw 2.554 2.776 nonbonded pdb=" CA GLU K 85 " pdb=" O LEU K 107 " model vdw 2.554 2.776 nonbonded pdb=" CA GLU J 85 " pdb=" O LEU J 107 " model vdw 2.562 2.776 nonbonded pdb=" O ILE B 506 " pdb=" CA ARG B 507 " model vdw 2.567 2.776 nonbonded pdb=" N VAL H 482 " pdb=" N PHE H 483 " model vdw 2.572 2.560 ... (remaining 175159 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'N' selection = chain 'O' } 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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.020 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 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 : 0.005 0.072 21495 Z= 0.249 Angle : 0.960 13.466 29190 Z= 0.523 Chirality : 0.055 0.249 3348 Planarity : 0.008 0.204 3699 Dihedral : 13.590 85.692 7716 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 0.17 % Allowed : 0.96 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.15), residues: 2712 helix: -0.84 (0.24), residues: 414 sheet: -1.41 (0.17), residues: 810 loop : -1.64 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 49 TYR 0.024 0.002 TYR A 32 PHE 0.028 0.003 PHE B 488 TRP 0.018 0.003 TRP I 52 HIS 0.008 0.002 HIS E 36 Details of bonding type rmsd covalent geometry : bond 0.00482 (21459) covalent geometry : angle 0.95745 (29118) SS BOND : bond 0.00554 ( 36) SS BOND : angle 1.58927 ( 72) hydrogen bonds : bond 0.12928 ( 748) hydrogen bonds : angle 7.51973 ( 1914) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 102 time to evaluate : 0.798 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: A 32 TYR cc_start: 0.9117 (m-10) cc_final: 0.8883 (m-10) REVERT: A 101 GLU cc_start: 0.7200 (mp0) cc_final: 0.6021 (mp0) REVERT: B 45 LEU cc_start: 0.9051 (mt) cc_final: 0.8847 (tp) REVERT: B 264 MET cc_start: 0.8808 (pmm) cc_final: 0.8389 (pmm) REVERT: B 370 MET cc_start: 0.9167 (ppp) cc_final: 0.8875 (ppp) REVERT: B 457 TYR cc_start: 0.8047 (m-80) cc_final: 0.7782 (m-80) REVERT: C 85 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8964 (pm20) REVERT: D 79 LEU cc_start: 0.8523 (tp) cc_final: 0.8262 (tp) REVERT: D 104 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6790 (tmm) REVERT: F 101 GLU cc_start: 0.7955 (mp0) cc_final: 0.7344 (mp0) REVERT: H 45 LEU cc_start: 0.8829 (mt) cc_final: 0.8606 (mt) REVERT: H 97 MET cc_start: 0.8802 (mmm) cc_final: 0.8492 (mmm) REVERT: H 264 MET cc_start: 0.8668 (pmm) cc_final: 0.8359 (pmm) REVERT: H 370 MET cc_start: 0.9137 (ppp) cc_final: 0.8500 (ppp) REVERT: L 34 MET cc_start: 0.8922 (mmp) cc_final: 0.8712 (mmm) REVERT: N 85 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7284 (tt0) REVERT: G 101 GLU cc_start: 0.7925 (mp0) cc_final: 0.7155 (mp0) REVERT: I 251 MET cc_start: 0.9193 (mtm) cc_final: 0.8973 (mtm) REVERT: I 264 MET cc_start: 0.8677 (pmm) cc_final: 0.8444 (pmm) REVERT: I 288 ILE cc_start: 0.9218 (tp) cc_final: 0.8730 (tt) REVERT: I 370 MET cc_start: 0.9269 (ppp) cc_final: 0.9068 (ppp) REVERT: I 457 TYR cc_start: 0.8384 (m-80) cc_final: 0.7931 (m-80) REVERT: K 85 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8932 (pm20) REVERT: M 79 LEU cc_start: 0.8345 (tp) cc_final: 0.7913 (tp) outliers start: 4 outliers final: 1 residues processed: 104 average time/residue: 0.1465 time to fit residues: 24.2391 Evaluate side-chains 93 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 91 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 20.0000 chunk 111 optimal weight: 9.9990 overall best weight: 5.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN D 77 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN L 77 ASN N 53 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** O 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 HIS O 91 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.027825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2620 r_free = 0.2620 target = 0.020700 restraints weight = 249064.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.021583 restraints weight = 146744.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.022225 restraints weight = 100309.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.022695 restraints weight = 74966.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.023042 restraints weight = 59867.924| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21495 Z= 0.208 Angle : 0.624 6.973 29190 Z= 0.335 Chirality : 0.041 0.145 3348 Planarity : 0.004 0.044 3699 Dihedral : 5.578 30.643 2958 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.51 % Favored : 90.49 % Rotamer: Outliers : 0.17 % Allowed : 6.39 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.15), residues: 2712 helix: 0.19 (0.25), residues: 426 sheet: -1.41 (0.17), residues: 822 loop : -1.52 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 49 TYR 0.014 0.001 TYR D 57 PHE 0.016 0.002 PHE H 190 TRP 0.012 0.002 TRP M 47 HIS 0.012 0.002 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00428 (21459) covalent geometry : angle 0.62213 (29118) SS BOND : bond 0.00337 ( 36) SS BOND : angle 1.14804 ( 72) hydrogen bonds : bond 0.03386 ( 748) hydrogen bonds : angle 6.07606 ( 1914) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.845 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: A 101 GLU cc_start: 0.7691 (mp0) cc_final: 0.6422 (mp0) REVERT: B 370 MET cc_start: 0.9163 (ppp) cc_final: 0.8759 (ppp) REVERT: C 85 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8941 (pm20) REVERT: D 79 LEU cc_start: 0.8468 (tp) cc_final: 0.8166 (tp) REVERT: F 101 GLU cc_start: 0.8337 (mp0) cc_final: 0.7295 (mp0) REVERT: H 370 MET cc_start: 0.9161 (ppp) cc_final: 0.8741 (ppp) REVERT: G 101 GLU cc_start: 0.8335 (mp0) cc_final: 0.7322 (mp0) REVERT: I 370 MET cc_start: 0.9252 (ppp) cc_final: 0.8895 (ppp) REVERT: M 79 LEU cc_start: 0.8606 (tp) cc_final: 0.8114 (tp) REVERT: O 55 HIS cc_start: 0.9246 (m90) cc_final: 0.9005 (m-70) outliers start: 4 outliers final: 0 residues processed: 102 average time/residue: 0.1374 time to fit residues: 22.9437 Evaluate side-chains 87 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 186 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 252 optimal weight: 9.9990 chunk 192 optimal weight: 10.0000 chunk 10 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 51 optimal weight: 7.9990 chunk 173 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 25 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 268 ASN B 283 GLN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 277 ASN H 283 GLN ** H 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 74 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 268 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 GLN M 74 ASN M 77 ASN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.026884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.020010 restraints weight = 264810.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.020846 restraints weight = 155438.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.021439 restraints weight = 105707.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.021878 restraints weight = 79293.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.022169 restraints weight = 63736.962| |-----------------------------------------------------------------------------| r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21495 Z= 0.305 Angle : 0.725 7.895 29190 Z= 0.389 Chirality : 0.043 0.153 3348 Planarity : 0.005 0.040 3699 Dihedral : 6.010 42.333 2958 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 23.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.25 % Allowed : 8.40 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.16), residues: 2712 helix: 0.27 (0.25), residues: 426 sheet: -1.51 (0.17), residues: 873 loop : -1.56 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 49 TYR 0.019 0.002 TYR A 32 PHE 0.022 0.002 PHE H 190 TRP 0.012 0.002 TRP G 106 HIS 0.007 0.002 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00622 (21459) covalent geometry : angle 0.72258 (29118) SS BOND : bond 0.00480 ( 36) SS BOND : angle 1.44902 ( 72) hydrogen bonds : bond 0.03763 ( 748) hydrogen bonds : angle 6.24093 ( 1914) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8075 (mp0) cc_final: 0.7016 (pm20) REVERT: B 45 LEU cc_start: 0.8974 (mt) cc_final: 0.8725 (mt) REVERT: B 264 MET cc_start: 0.9020 (pmm) cc_final: 0.8703 (pmm) REVERT: B 370 MET cc_start: 0.9208 (ppp) cc_final: 0.8793 (ppp) REVERT: D 79 LEU cc_start: 0.8634 (tp) cc_final: 0.8362 (tp) REVERT: F 101 GLU cc_start: 0.8632 (mp0) cc_final: 0.7513 (mp0) REVERT: H 370 MET cc_start: 0.9212 (ppp) cc_final: 0.8793 (ppp) REVERT: L 28 MET cc_start: 0.9012 (tpp) cc_final: 0.8750 (tmm) REVERT: L 34 MET cc_start: 0.8907 (mmm) cc_final: 0.8619 (mpp) REVERT: G 101 GLU cc_start: 0.8476 (mp0) cc_final: 0.7328 (mp0) REVERT: I 251 MET cc_start: 0.9191 (mtm) cc_final: 0.8984 (mtm) REVERT: I 370 MET cc_start: 0.9348 (ppp) cc_final: 0.9048 (ppp) REVERT: M 79 LEU cc_start: 0.8873 (tp) cc_final: 0.8431 (tp) outliers start: 6 outliers final: 1 residues processed: 96 average time/residue: 0.1521 time to fit residues: 23.6354 Evaluate side-chains 78 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 244 optimal weight: 20.0000 chunk 217 optimal weight: 6.9990 chunk 75 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 34 optimal weight: 0.0470 chunk 57 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 80 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 361 GLN J 6 GLN ** J 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN I 501 GLN K 6 GLN ** K 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.027472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.020433 restraints weight = 256450.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.021309 restraints weight = 148806.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.021944 restraints weight = 100680.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.022375 restraints weight = 74952.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.022717 restraints weight = 60507.436| |-----------------------------------------------------------------------------| r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21495 Z= 0.195 Angle : 0.638 7.881 29190 Z= 0.341 Chirality : 0.043 0.148 3348 Planarity : 0.004 0.040 3699 Dihedral : 5.741 43.334 2958 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 20.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.08 % Allowed : 4.47 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.16), residues: 2712 helix: 0.58 (0.26), residues: 426 sheet: -1.50 (0.17), residues: 873 loop : -1.56 (0.16), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 98 TYR 0.024 0.002 TYR J 89 PHE 0.045 0.002 PHE I 237 TRP 0.013 0.002 TRP G 106 HIS 0.017 0.002 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00412 (21459) covalent geometry : angle 0.63641 (29118) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.16513 ( 72) hydrogen bonds : bond 0.03323 ( 748) hydrogen bonds : angle 5.94016 ( 1914) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.710 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: A 101 GLU cc_start: 0.7863 (mp0) cc_final: 0.6810 (pm20) REVERT: D 79 LEU cc_start: 0.8658 (tp) cc_final: 0.8274 (tp) REVERT: E 68 LYS cc_start: 0.9456 (pptt) cc_final: 0.9138 (pttm) REVERT: F 101 GLU cc_start: 0.8448 (mp0) cc_final: 0.7197 (mp0) REVERT: H 264 MET cc_start: 0.8933 (pmm) cc_final: 0.8504 (pmm) REVERT: H 370 MET cc_start: 0.9193 (ppp) cc_final: 0.8808 (ppp) REVERT: L 34 MET cc_start: 0.8956 (mmm) cc_final: 0.8703 (mpp) REVERT: I 264 MET cc_start: 0.8881 (pmm) cc_final: 0.8485 (pmm) REVERT: I 300 VAL cc_start: 0.9138 (t) cc_final: 0.8835 (t) REVERT: I 370 MET cc_start: 0.9390 (ppp) cc_final: 0.9014 (ppp) REVERT: I 426 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.6363 (p0) REVERT: I 457 TYR cc_start: 0.8235 (m-80) cc_final: 0.7977 (m-80) REVERT: M 79 LEU cc_start: 0.8867 (tp) cc_final: 0.8636 (tp) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1476 time to fit residues: 21.6523 Evaluate side-chains 81 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 202 optimal weight: 0.8980 chunk 193 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 91 GLN J 16 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 361 GLN I 501 GLN O 1 GLN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 HIS ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.027571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2609 r_free = 0.2609 target = 0.020595 restraints weight = 247344.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.021472 restraints weight = 144984.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.022105 restraints weight = 98571.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.022514 restraints weight = 73332.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.022874 restraints weight = 59642.413| |-----------------------------------------------------------------------------| r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21495 Z= 0.157 Angle : 0.615 7.591 29190 Z= 0.326 Chirality : 0.042 0.182 3348 Planarity : 0.004 0.038 3699 Dihedral : 5.535 43.169 2958 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.28 % Favored : 88.72 % Rotamer: Outliers : 0.08 % Allowed : 3.55 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.16), residues: 2712 helix: 0.76 (0.26), residues: 426 sheet: -1.47 (0.17), residues: 885 loop : -1.51 (0.16), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 98 TYR 0.020 0.001 TYR A 32 PHE 0.013 0.001 PHE H 190 TRP 0.013 0.002 TRP M 112 HIS 0.016 0.002 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00338 (21459) covalent geometry : angle 0.61321 (29118) SS BOND : bond 0.00339 ( 36) SS BOND : angle 1.15723 ( 72) hydrogen bonds : bond 0.03207 ( 748) hydrogen bonds : angle 5.76554 ( 1914) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 87 time to evaluate : 1.014 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: A 101 GLU cc_start: 0.7782 (mp0) cc_final: 0.7062 (pm20) REVERT: B 45 LEU cc_start: 0.8987 (mt) cc_final: 0.8674 (mt) REVERT: B 264 MET cc_start: 0.9045 (pmm) cc_final: 0.8680 (pmm) REVERT: B 370 MET cc_start: 0.9234 (ppp) cc_final: 0.9015 (ppp) REVERT: D 79 LEU cc_start: 0.8611 (tp) cc_final: 0.8378 (tp) REVERT: H 264 MET cc_start: 0.8936 (pmm) cc_final: 0.8536 (pmm) REVERT: H 370 MET cc_start: 0.9189 (ppp) cc_final: 0.8786 (ppp) REVERT: I 97 MET cc_start: 0.8955 (tpt) cc_final: 0.8747 (mmm) REVERT: I 264 MET cc_start: 0.8828 (pmm) cc_final: 0.8526 (pmm) REVERT: I 300 VAL cc_start: 0.9243 (t) cc_final: 0.8967 (t) REVERT: I 370 MET cc_start: 0.9378 (ppp) cc_final: 0.8988 (ppp) REVERT: M 79 LEU cc_start: 0.8851 (tp) cc_final: 0.8635 (tp) outliers start: 2 outliers final: 0 residues processed: 89 average time/residue: 0.1607 time to fit residues: 23.1145 Evaluate side-chains 77 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 241 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 140 optimal weight: 20.0000 chunk 229 optimal weight: 9.9990 chunk 264 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 104 optimal weight: 0.0970 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 501 GLN D 74 ASN E 1 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN H 501 GLN J 16 GLN N 1 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.027340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.020379 restraints weight = 258410.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.021251 restraints weight = 150187.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.021875 restraints weight = 101011.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2693 r_free = 0.2693 target = 0.022340 restraints weight = 74871.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.022648 restraints weight = 59794.200| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21495 Z= 0.198 Angle : 0.643 8.567 29190 Z= 0.341 Chirality : 0.042 0.141 3348 Planarity : 0.004 0.048 3699 Dihedral : 5.599 42.685 2958 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.58 % Favored : 88.42 % Rotamer: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.16), residues: 2712 helix: 0.83 (0.26), residues: 426 sheet: -1.60 (0.17), residues: 915 loop : -1.48 (0.16), residues: 1371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 49 TYR 0.022 0.002 TYR A 32 PHE 0.017 0.002 PHE B 483 TRP 0.011 0.002 TRP F 106 HIS 0.006 0.001 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00416 (21459) covalent geometry : angle 0.64028 (29118) SS BOND : bond 0.00400 ( 36) SS BOND : angle 1.26254 ( 72) hydrogen bonds : bond 0.03225 ( 748) hydrogen bonds : angle 5.76888 ( 1914) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 85 time to evaluate : 0.830 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: A 32 TYR cc_start: 0.9330 (m-10) cc_final: 0.9110 (m-10) REVERT: A 101 GLU cc_start: 0.7898 (mp0) cc_final: 0.6755 (mp0) REVERT: B 45 LEU cc_start: 0.9017 (mt) cc_final: 0.8744 (mt) REVERT: B 264 MET cc_start: 0.9044 (pmm) cc_final: 0.8703 (pmm) REVERT: D 79 LEU cc_start: 0.8694 (tp) cc_final: 0.8439 (tp) REVERT: F 39 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7938 (tt0) REVERT: H 264 MET cc_start: 0.9018 (pmm) cc_final: 0.8810 (pmm) REVERT: H 370 MET cc_start: 0.9221 (ppp) cc_final: 0.8807 (ppp) REVERT: G 101 GLU cc_start: 0.8241 (mp0) cc_final: 0.7313 (mp0) REVERT: I 97 MET cc_start: 0.9008 (tpt) cc_final: 0.8799 (mmm) REVERT: I 300 VAL cc_start: 0.9306 (t) cc_final: 0.9033 (t) REVERT: I 370 MET cc_start: 0.9387 (ppp) cc_final: 0.8967 (ppp) REVERT: M 79 LEU cc_start: 0.8872 (tp) cc_final: 0.8663 (tp) outliers start: 3 outliers final: 0 residues processed: 88 average time/residue: 0.1516 time to fit residues: 21.7441 Evaluate side-chains 79 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 177 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 109 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 24 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 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 501 GLN E 1 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 GLN J 16 GLN N 91 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.027576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.020639 restraints weight = 256516.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.021512 restraints weight = 149465.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.022133 restraints weight = 101188.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.022591 restraints weight = 75443.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.022907 restraints weight = 60411.906| |-----------------------------------------------------------------------------| r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 21495 Z= 0.166 Angle : 0.625 8.320 29190 Z= 0.329 Chirality : 0.042 0.204 3348 Planarity : 0.004 0.040 3699 Dihedral : 5.477 42.223 2958 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.04 % Allowed : 2.09 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.16), residues: 2712 helix: 0.92 (0.26), residues: 426 sheet: -1.54 (0.17), residues: 912 loop : -1.45 (0.16), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 364 TYR 0.018 0.001 TYR A 32 PHE 0.016 0.002 PHE I 483 TRP 0.012 0.002 TRP F 106 HIS 0.007 0.001 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00356 (21459) covalent geometry : angle 0.62275 (29118) SS BOND : bond 0.00360 ( 36) SS BOND : angle 1.22775 ( 72) hydrogen bonds : bond 0.03094 ( 748) hydrogen bonds : angle 5.68723 ( 1914) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.808 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: A 101 GLU cc_start: 0.7958 (mp0) cc_final: 0.6861 (pm20) REVERT: B 370 MET cc_start: 0.9329 (ppp) cc_final: 0.8965 (ppp) REVERT: D 79 LEU cc_start: 0.8678 (tp) cc_final: 0.8420 (tp) REVERT: F 32 TYR cc_start: 0.9273 (m-10) cc_final: 0.9063 (m-10) REVERT: H 251 MET cc_start: 0.9229 (mtm) cc_final: 0.8922 (mtm) REVERT: H 370 MET cc_start: 0.9218 (ppp) cc_final: 0.8805 (ppp) REVERT: J 16 GLN cc_start: 0.8025 (pt0) cc_final: 0.7507 (pp30) REVERT: I 264 MET cc_start: 0.8910 (pmm) cc_final: 0.8548 (pmm) REVERT: I 370 MET cc_start: 0.9383 (ppp) cc_final: 0.8966 (ppp) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.1595 time to fit residues: 21.7677 Evaluate side-chains 73 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 172 optimal weight: 9.9990 chunk 232 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 74 ASN E 1 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN J 97 ASN L 74 ASN ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 277 ASN ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 426 ASN ** I 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.028347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.022560 restraints weight = 287074.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.023402 restraints weight = 157249.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.023976 restraints weight = 102083.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.024344 restraints weight = 73862.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.024613 restraints weight = 58508.812| |-----------------------------------------------------------------------------| r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 21495 Z= 0.311 Angle : 0.751 8.135 29190 Z= 0.400 Chirality : 0.044 0.190 3348 Planarity : 0.005 0.074 3699 Dihedral : 6.012 40.824 2958 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 27.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.09 % Favored : 86.91 % Rotamer: Outliers : 0.08 % Allowed : 3.09 % Favored : 96.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.03 (0.16), residues: 2712 helix: 0.50 (0.25), residues: 423 sheet: -1.70 (0.17), residues: 906 loop : -1.64 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 49 TYR 0.026 0.002 TYR A 32 PHE 0.023 0.002 PHE I 483 TRP 0.013 0.003 TRP M 112 HIS 0.010 0.002 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00637 (21459) covalent geometry : angle 0.74829 (29118) SS BOND : bond 0.00676 ( 36) SS BOND : angle 1.54412 ( 72) hydrogen bonds : bond 0.03753 ( 748) hydrogen bonds : angle 6.14455 ( 1914) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 86 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.8160 (mp0) cc_final: 0.7163 (pm20) REVERT: B 370 MET cc_start: 0.9378 (ppp) cc_final: 0.9061 (ppp) REVERT: D 79 LEU cc_start: 0.8852 (tp) cc_final: 0.8312 (tp) REVERT: E 68 LYS cc_start: 0.9492 (pptt) cc_final: 0.9185 (pttm) REVERT: F 101 GLU cc_start: 0.8673 (mp0) cc_final: 0.7560 (mp0) REVERT: H 370 MET cc_start: 0.9323 (ppp) cc_final: 0.8929 (ppp) REVERT: G 101 GLU cc_start: 0.8455 (mp0) cc_final: 0.7343 (mp0) REVERT: I 370 MET cc_start: 0.9468 (ppp) cc_final: 0.9105 (ppp) REVERT: I 426 ASN cc_start: 0.9109 (OUTLIER) cc_final: 0.6453 (p0) REVERT: M 79 LEU cc_start: 0.8983 (tp) cc_final: 0.8454 (tp) outliers start: 2 outliers final: 0 residues processed: 88 average time/residue: 0.1477 time to fit residues: 20.9748 Evaluate side-chains 74 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 235 optimal weight: 5.9990 chunk 80 optimal weight: 0.0000 chunk 22 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 130 optimal weight: 8.9990 chunk 85 optimal weight: 0.3980 chunk 25 optimal weight: 10.0000 overall best weight: 3.6790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN E 1 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 GLN J 16 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.027229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2594 r_free = 0.2594 target = 0.020389 restraints weight = 249247.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.2640 r_free = 0.2640 target = 0.021252 restraints weight = 145319.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.021886 restraints weight = 98333.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.022341 restraints weight = 73002.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.022687 restraints weight = 58242.626| |-----------------------------------------------------------------------------| r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 21495 Z= 0.172 Angle : 0.664 9.346 29190 Z= 0.349 Chirality : 0.043 0.169 3348 Planarity : 0.004 0.046 3699 Dihedral : 5.690 39.897 2958 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 21.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.73 % Favored : 88.27 % Rotamer: Outliers : 0.04 % Allowed : 1.00 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.16), residues: 2712 helix: 0.74 (0.26), residues: 426 sheet: -1.44 (0.18), residues: 855 loop : -1.62 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 49 TYR 0.022 0.002 TYR A 32 PHE 0.060 0.002 PHE I 237 TRP 0.017 0.002 TRP D 112 HIS 0.006 0.002 HIS O 55 Details of bonding type rmsd covalent geometry : bond 0.00372 (21459) covalent geometry : angle 0.66219 (29118) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.22814 ( 72) hydrogen bonds : bond 0.03267 ( 748) hydrogen bonds : angle 5.87597 ( 1914) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 TYR cc_start: 0.9336 (m-10) cc_final: 0.9135 (m-10) REVERT: A 101 GLU cc_start: 0.7811 (mp0) cc_final: 0.6689 (mp0) REVERT: B 370 MET cc_start: 0.9320 (ppp) cc_final: 0.8964 (ppp) REVERT: D 79 LEU cc_start: 0.8774 (tp) cc_final: 0.8513 (tp) REVERT: F 32 TYR cc_start: 0.9299 (m-10) cc_final: 0.9058 (m-10) REVERT: H 274 MET cc_start: 0.9334 (ttm) cc_final: 0.8953 (ttp) REVERT: H 370 MET cc_start: 0.9181 (ppp) cc_final: 0.8859 (ppp) REVERT: L 100 LEU cc_start: 0.9223 (mm) cc_final: 0.8958 (mp) REVERT: I 264 MET cc_start: 0.8810 (pmm) cc_final: 0.8442 (pmm) REVERT: I 300 VAL cc_start: 0.9138 (t) cc_final: 0.8930 (t) REVERT: I 370 MET cc_start: 0.9357 (ppp) cc_final: 0.9013 (ppp) REVERT: M 79 LEU cc_start: 0.8899 (tp) cc_final: 0.8407 (tp) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.1510 time to fit residues: 19.9760 Evaluate side-chains 72 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 23 optimal weight: 5.9990 chunk 154 optimal weight: 10.0000 chunk 261 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 259 optimal weight: 0.0670 chunk 66 optimal weight: 9.9990 chunk 94 optimal weight: 0.0000 chunk 242 optimal weight: 20.0000 chunk 210 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 3.6128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN E 1 GLN ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN O 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.027411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.020529 restraints weight = 256185.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.021405 restraints weight = 147527.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.022038 restraints weight = 99235.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.022505 restraints weight = 73519.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.022832 restraints weight = 58638.391| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21495 Z= 0.167 Angle : 0.650 7.841 29190 Z= 0.342 Chirality : 0.043 0.154 3348 Planarity : 0.004 0.046 3699 Dihedral : 5.562 39.697 2958 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 20.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.09 % Favored : 87.91 % Rotamer: Outliers : 0.04 % Allowed : 1.04 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.16), residues: 2712 helix: 0.79 (0.26), residues: 426 sheet: -1.41 (0.18), residues: 855 loop : -1.59 (0.16), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 76 TYR 0.020 0.002 TYR A 32 PHE 0.015 0.002 PHE H 483 TRP 0.012 0.002 TRP D 112 HIS 0.006 0.002 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00360 (21459) covalent geometry : angle 0.64806 (29118) SS BOND : bond 0.00389 ( 36) SS BOND : angle 1.20004 ( 72) hydrogen bonds : bond 0.03172 ( 748) hydrogen bonds : angle 5.78819 ( 1914) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5424 Ramachandran restraints generated. 2712 Oldfield, 0 Emsley, 2712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.7878 (mp0) cc_final: 0.7108 (pm20) REVERT: B 370 MET cc_start: 0.9309 (ppp) cc_final: 0.9046 (ppp) REVERT: D 79 LEU cc_start: 0.8681 (tp) cc_final: 0.8440 (tp) REVERT: H 251 MET cc_start: 0.9070 (mtm) cc_final: 0.8854 (mtm) REVERT: H 274 MET cc_start: 0.9337 (ttm) cc_final: 0.8957 (ttp) REVERT: H 370 MET cc_start: 0.9186 (ppp) cc_final: 0.8774 (ppp) REVERT: I 251 MET cc_start: 0.9111 (mtm) cc_final: 0.8792 (mtm) REVERT: I 264 MET cc_start: 0.8802 (pmm) cc_final: 0.8441 (pmm) REVERT: I 370 MET cc_start: 0.9367 (ppp) cc_final: 0.9008 (ppp) REVERT: M 79 LEU cc_start: 0.8854 (tp) cc_final: 0.8371 (tp) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1501 time to fit residues: 19.6868 Evaluate side-chains 70 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 241 optimal weight: 5.9990 chunk 135 optimal weight: 20.0000 chunk 184 optimal weight: 10.0000 chunk 187 optimal weight: 8.9990 chunk 79 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 247 optimal weight: 8.9990 chunk 200 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 1 GLN ** E 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 GLN N 1 GLN ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 501 GLN O 1 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.026939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2581 r_free = 0.2581 target = 0.020160 restraints weight = 255654.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.021021 restraints weight = 148480.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2659 r_free = 0.2659 target = 0.021646 restraints weight = 99926.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.022105 restraints weight = 74070.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.022429 restraints weight = 59106.604| |-----------------------------------------------------------------------------| r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21495 Z= 0.207 Angle : 0.673 7.756 29190 Z= 0.356 Chirality : 0.043 0.151 3348 Planarity : 0.004 0.051 3699 Dihedral : 5.658 39.566 2958 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.46 % Favored : 87.54 % Rotamer: Outliers : 0.13 % Allowed : 0.75 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.16), residues: 2712 helix: 0.81 (0.26), residues: 423 sheet: -1.59 (0.18), residues: 894 loop : -1.59 (0.16), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 49 TYR 0.021 0.002 TYR A 32 PHE 0.018 0.002 PHE H 483 TRP 0.011 0.002 TRP D 112 HIS 0.006 0.001 HIS N 40 Details of bonding type rmsd covalent geometry : bond 0.00434 (21459) covalent geometry : angle 0.67044 (29118) SS BOND : bond 0.00401 ( 36) SS BOND : angle 1.27191 ( 72) hydrogen bonds : bond 0.03273 ( 748) hydrogen bonds : angle 5.85808 ( 1914) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.54 seconds wall clock time: 44 minutes 56.82 seconds (2696.82 seconds total)