Starting phenix.real_space_refine on Fri Aug 7 10:39:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.map" model { file = "/net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vwe_65394/08_2026/9vwe_65394.cif" } resolution = 2.06 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= 0.006 sd= 0.088 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 105 5.16 5 C 13077 2.51 5 N 3432 2.21 5 O 4101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20715 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3360 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "D" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 874 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "E" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 805 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 994 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "L" Number of atoms: 872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 872 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 103} Restraints were copied for chains: B, C, F, G, I, J, K, M, N, O Time building chain proxies: 3.84, per 1000 atoms: 0.19 Number of scatterers: 20715 At special positions: 0 Unit cell: (150.15, 152.75, 129.35, 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 105 16.00 O 4101 8.00 N 3432 7.00 C 13077 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 149 " - pdb=" SG CYS B 458 " distance=2.34 Simple disulfide: pdb=" SG CYS A 155 " - pdb=" SG CYS A 290 " distance=2.35 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.21 Simple disulfide: pdb=" SG CYS A 458 " - pdb=" SG CYS C 149 " distance=2.34 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 86 " distance=1.98 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 149 " - pdb=" SG CYS C 458 " distance=2.34 Simple disulfide: pdb=" SG CYS B 155 " - pdb=" SG CYS B 290 " distance=2.35 Simple disulfide: pdb=" SG CYS C 155 " - pdb=" SG CYS C 290 " distance=2.35 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.21 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.21 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 86 " distance=1.98 Simple disulfide: pdb=" SG CYS J 21 " - pdb=" SG CYS J 86 " distance=1.98 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 93 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 93 " 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: 1.60 Conformation dependent library (CDL) restraints added in 779.3 milliseconds 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4950 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 51 sheets defined 19.9% alpha, 39.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 73 through 98 removed outlier: 3.655A pdb=" N GLN A 98 " --> pdb=" O GLN A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 202 Processing helix chain 'A' and resid 203 through 207 Processing helix chain 'A' and resid 216 through 239 removed outlier: 4.155A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.580A pdb=" N GLN A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 376 through 384 removed outlier: 3.725A pdb=" N ASN A 380 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.812A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 506 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 86 through 90 removed outlier: 3.926A pdb=" N THR D 90 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 28 removed outlier: 3.687A pdb=" N ALA E 27 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 81 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 109 through 114 removed outlier: 3.580A pdb=" N GLY H 114 " --> pdb=" O TYR H 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 98 removed outlier: 3.655A pdb=" N GLN B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 203 through 207 Processing helix chain 'B' and resid 216 through 239 removed outlier: 4.155A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 277 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.581A pdb=" N GLN B 283 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 356 No H-bonds generated for 'chain 'B' and resid 354 through 356' Processing helix chain 'B' and resid 376 through 384 removed outlier: 3.726A pdb=" N ASN B 380 " --> pdb=" O SER B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.812A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 506 Processing helix chain 'F' and resid 63 through 65 No H-bonds generated for 'chain 'F' and resid 63 through 65' Processing helix chain 'F' and resid 86 through 90 removed outlier: 3.926A pdb=" N THR F 90 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 28 removed outlier: 3.687A pdb=" N ALA I 27 " --> pdb=" O ASP I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 81 Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 109 through 114 removed outlier: 3.580A pdb=" N GLY K 114 " --> pdb=" O TYR K 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 98 removed outlier: 3.655A pdb=" N GLN C 98 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 203 through 207 Processing helix chain 'C' and resid 216 through 239 removed outlier: 4.155A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 277 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.580A pdb=" N GLN C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 356 No H-bonds generated for 'chain 'C' and resid 354 through 356' Processing helix chain 'C' and resid 376 through 384 removed outlier: 3.725A pdb=" N ASN C 380 " --> pdb=" O SER C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.812A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 506 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 86 through 90 removed outlier: 3.927A pdb=" N THR G 90 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 28 removed outlier: 3.687A pdb=" N ALA J 27 " --> pdb=" O ASP J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 77 through 81 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 109 through 114 removed outlier: 3.580A pdb=" N GLY M 114 " --> pdb=" O TYR M 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 360 removed outlier: 5.451A pdb=" N VAL A 40 " --> pdb=" O HIS A 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS A 317 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS A 42 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS A 315 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU A 48 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE A 309 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP A 341 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 6.505A pdb=" N GLU A 30 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N VAL A 469 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE A 32 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 11.102A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.634A pdb=" N ALA A 424 " --> pdb=" O ILE A 432 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR A 434 " --> pdb=" O CYS A 422 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS A 422 " --> pdb=" O THR A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AA8, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.179A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.935A pdb=" N SER D 105 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY D 99 " --> pdb=" O PHE D 103 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 8 through 11 removed outlier: 6.278A pdb=" N VAL E 9 " --> pdb=" O THR E 104 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP E 33 " --> pdb=" O LEU E 45 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 8 through 11 removed outlier: 6.278A pdb=" N VAL E 9 " --> pdb=" O THR E 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 16 through 22 Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB5, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.180A pdb=" N GLY H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.892A pdb=" N ASP L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.577A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.573A pdb=" N THR L 103 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 358 through 360 removed outlier: 5.451A pdb=" N VAL B 40 " --> pdb=" O HIS B 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS B 317 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LYS B 42 " --> pdb=" O LYS B 315 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS B 315 " --> pdb=" O LYS B 42 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N LEU B 48 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ILE B 309 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP B 341 " --> pdb=" O PHE B 352 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 358 through 360 removed outlier: 6.505A pdb=" N GLU B 30 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL B 469 " --> pdb=" O GLU B 30 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE B 32 " --> pdb=" O VAL B 469 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.101A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AC5, first strand: chain 'B' and resid 430 through 434 removed outlier: 6.634A pdb=" N ALA B 424 " --> pdb=" O ILE B 432 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR B 434 " --> pdb=" O CYS B 422 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N CYS B 422 " --> pdb=" O THR B 434 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.179A pdb=" N TRP F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR F 50 " --> pdb=" O TRP F 34 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.935A pdb=" N SER F 105 " --> pdb=" O ARG F 97 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY F 99 " --> pdb=" O PHE F 103 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 8 through 11 removed outlier: 6.278A pdb=" N VAL I 9 " --> pdb=" O THR I 104 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP I 33 " --> pdb=" O LEU I 45 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 8 through 11 removed outlier: 6.278A pdb=" N VAL I 9 " --> pdb=" O THR I 104 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 16 through 22 Processing sheet with id=AD3, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.181A pdb=" N GLY K 10 " --> pdb=" O THR K 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'N' and resid 4 through 6 removed outlier: 3.891A pdb=" N ASP N 75 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU N 38 " --> pdb=" O TYR N 54 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N TYR N 54 " --> pdb=" O LEU N 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP N 40 " --> pdb=" O LEU N 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.572A pdb=" N THR N 103 " --> pdb=" O GLN N 95 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 358 through 360 removed outlier: 5.451A pdb=" N VAL C 40 " --> pdb=" O HIS C 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N HIS C 317 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N LYS C 42 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS C 315 " --> pdb=" O LYS C 42 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU C 48 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE C 309 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TRP C 341 " --> pdb=" O PHE C 352 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 358 through 360 removed outlier: 6.505A pdb=" N GLU C 30 " --> pdb=" O LEU C 467 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL C 469 " --> pdb=" O GLU C 30 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE C 32 " --> pdb=" O VAL C 469 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.101A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AE3, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AE4, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.634A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.179A pdb=" N TRP G 34 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N TYR G 50 " --> pdb=" O TRP G 34 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.935A pdb=" N SER G 105 " --> pdb=" O ARG G 97 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N GLY G 99 " --> pdb=" O PHE G 103 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N PHE G 103 " --> pdb=" O GLY G 99 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'J' and resid 8 through 11 removed outlier: 6.279A pdb=" N VAL J 9 " --> pdb=" O THR J 104 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP J 33 " --> pdb=" O LEU J 45 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 8 through 11 removed outlier: 6.279A pdb=" N VAL J 9 " --> pdb=" O THR J 104 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 16 through 22 Processing sheet with id=AF2, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.180A pdb=" N GLY M 10 " --> pdb=" O THR M 125 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE M 34 " --> pdb=" O TYR M 50 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR M 50 " --> pdb=" O ILE M 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.892A pdb=" N ASP O 75 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.576A pdb=" N LEU O 38 " --> pdb=" O TYR O 54 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR O 54 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.573A pdb=" N THR O 103 " --> pdb=" O GLN O 95 " (cutoff:3.500A) 987 hydrogen bonds defined for protein. 2457 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6648 1.34 - 1.46: 5109 1.46 - 1.58: 9240 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 21129 Sorted by residual: bond pdb=" CA PHE L 60 " pdb=" C PHE L 60 " ideal model delta sigma weight residual 1.527 1.468 0.059 1.34e-02 5.57e+03 1.93e+01 bond pdb=" CA PHE O 60 " pdb=" C PHE O 60 " ideal model delta sigma weight residual 1.527 1.468 0.059 1.34e-02 5.57e+03 1.91e+01 bond pdb=" CA PHE N 60 " pdb=" C PHE N 60 " ideal model delta sigma weight residual 1.527 1.468 0.058 1.34e-02 5.57e+03 1.88e+01 bond pdb=" CA SER L 57 " pdb=" CB SER L 57 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.51e-02 4.39e+03 1.28e+01 bond pdb=" CA SER O 57 " pdb=" CB SER O 57 " ideal model delta sigma weight residual 1.531 1.477 0.054 1.51e-02 4.39e+03 1.27e+01 ... (remaining 21124 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 27720 1.56 - 3.13: 791 3.13 - 4.69: 145 4.69 - 6.25: 24 6.25 - 7.81: 21 Bond angle restraints: 28701 Sorted by residual: angle pdb=" CA PHE N 60 " pdb=" CB PHE N 60 " pdb=" CG PHE N 60 " ideal model delta sigma weight residual 113.80 119.28 -5.48 1.00e+00 1.00e+00 3.00e+01 angle pdb=" CA PHE L 60 " pdb=" CB PHE L 60 " pdb=" CG PHE L 60 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" CA PHE O 60 " pdb=" CB PHE O 60 " pdb=" CG PHE O 60 " ideal model delta sigma weight residual 113.80 119.23 -5.43 1.00e+00 1.00e+00 2.95e+01 angle pdb=" N SER G 62 " pdb=" CA SER G 62 " pdb=" C SER G 62 " ideal model delta sigma weight residual 114.64 107.38 7.26 1.52e+00 4.33e-01 2.28e+01 angle pdb=" N SER F 62 " pdb=" CA SER F 62 " pdb=" C SER F 62 " ideal model delta sigma weight residual 114.64 107.38 7.26 1.52e+00 4.33e-01 2.28e+01 ... (remaining 28696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 11302 17.77 - 35.54: 1070 35.54 - 53.31: 243 53.31 - 71.08: 69 71.08 - 88.85: 21 Dihedral angle restraints: 12705 sinusoidal: 4953 harmonic: 7752 Sorted by residual: dihedral pdb=" CA SER N 7 " pdb=" C SER N 7 " pdb=" N PRO N 8 " pdb=" CA PRO N 8 " ideal model delta harmonic sigma weight residual 180.00 128.12 51.88 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA SER L 7 " pdb=" C SER L 7 " pdb=" N PRO L 8 " pdb=" CA PRO L 8 " ideal model delta harmonic sigma weight residual 180.00 128.13 51.87 0 5.00e+00 4.00e-02 1.08e+02 dihedral pdb=" CA SER O 7 " pdb=" C SER O 7 " pdb=" N PRO O 8 " pdb=" CA PRO O 8 " ideal model delta harmonic sigma weight residual 180.00 128.14 51.86 0 5.00e+00 4.00e-02 1.08e+02 ... (remaining 12702 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2156 0.039 - 0.078: 781 0.078 - 0.117: 308 0.117 - 0.156: 40 0.156 - 0.196: 12 Chirality restraints: 3297 Sorted by residual: chirality pdb=" CB ILE A 292 " pdb=" CA ILE A 292 " pdb=" CG1 ILE A 292 " pdb=" CG2 ILE A 292 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" CB ILE C 292 " pdb=" CA ILE C 292 " pdb=" CG1 ILE C 292 " pdb=" CG2 ILE C 292 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB ILE B 292 " pdb=" CA ILE B 292 " pdb=" CG1 ILE B 292 " pdb=" CG2 ILE B 292 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.31e-01 ... (remaining 3294 not shown) Planarity restraints: 3651 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG O 59 " 0.515 9.50e-02 1.11e+02 2.31e-01 3.26e+01 pdb=" NE ARG O 59 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG O 59 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG O 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG O 59 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 59 " 0.515 9.50e-02 1.11e+02 2.31e-01 3.26e+01 pdb=" NE ARG L 59 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG L 59 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG L 59 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG L 59 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 59 " -0.514 9.50e-02 1.11e+02 2.31e-01 3.25e+01 pdb=" NE ARG N 59 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG N 59 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG N 59 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG N 59 " -0.018 2.00e-02 2.50e+03 ... (remaining 3648 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3561 2.77 - 3.30: 18239 3.30 - 3.83: 34169 3.83 - 4.37: 41512 4.37 - 4.90: 72878 Nonbonded interactions: 170359 Sorted by model distance: nonbonded pdb=" O TYR H 103 " pdb=" OG SER H 104 " model vdw 2.236 3.040 nonbonded pdb=" O TYR K 103 " pdb=" OG SER K 104 " model vdw 2.236 3.040 nonbonded pdb=" O TYR M 103 " pdb=" OG SER M 104 " model vdw 2.236 3.040 nonbonded pdb=" OD2 ASP B 92 " pdb=" OG SER B 238 " model vdw 2.252 3.040 nonbonded pdb=" OD2 ASP A 92 " pdb=" OG SER A 238 " model vdw 2.252 3.040 ... (remaining 170354 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'E' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'H' selection = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' 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=0.59 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 17.460 Find NCS groups from input model: 0.180 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:5.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.008 0.320 21168 Z= 0.386 Angle : 0.717 16.109 28779 Z= 0.411 Chirality : 0.046 0.196 3297 Planarity : 0.010 0.231 3651 Dihedral : 15.070 88.854 7638 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.13 % Allowed : 12.18 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.08 (0.16), residues: 2646 helix: -0.13 (0.24), residues: 417 sheet: 0.67 (0.16), residues: 1014 loop : -0.32 (0.18), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 364 TYR 0.018 0.002 TYR C 198 PHE 0.030 0.002 PHE C 190 TRP 0.013 0.001 TRP K 118 HIS 0.002 0.001 HIS N 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.26 (21129) covalent geometry : angle 0.67139 / 0.39 (28701) SS BOND : bond 0.13327 / 8.33 ( 39) SS BOND : angle 4.88127 / 3.13 ( 78) hydrogen bonds : bond 0.20954 / 13.83 ( 927) hydrogen bonds : angle 8.07965 / 5.72 ( 2457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 0.570 Fit side-chains REVERT: C 218 GLU cc_start: 0.7829 (mp0) cc_final: 0.7555 (mp0) outliers start: 3 outliers final: 1 residues processed: 575 average time/residue: 0.4875 time to fit residues: 323.6189 Evaluate side-chains 519 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 518 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.0970 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 258 optimal weight: 50.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 225 GLN A 227 ASN A 277 ASN A 361 GLN A 460 ASN E 48 GLN H 39 GLN B 202 GLN B 216 ASN B 224 GLN B 225 GLN B 270 GLN B 277 ASN B 284 GLN B 361 GLN I 48 GLN K 3 GLN K 39 GLN C 34 GLN C 227 ASN C 277 ASN C 361 GLN C 371 ASN C 380 ASN C 494 GLN G 58 ASN J 35 GLN J 48 GLN M 39 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.155707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131950 restraints weight = 23898.300| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.55 r_work: 0.3693 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21168 Z= 0.126 Angle : 0.563 9.081 28779 Z= 0.297 Chirality : 0.044 0.170 3297 Planarity : 0.005 0.056 3651 Dihedral : 5.582 87.321 2906 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.61 % Allowed : 14.47 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.63 (0.16), residues: 2646 helix: 1.17 (0.26), residues: 420 sheet: 0.94 (0.16), residues: 957 loop : -0.19 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 339 TYR 0.014 0.002 TYR A 299 PHE 0.014 0.001 PHE K 29 TRP 0.016 0.001 TRP G 34 HIS 0.003 0.001 HIS O 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (21129) covalent geometry : angle 0.56056 / 0.30 (28701) SS BOND : bond 0.00222 / 0.13 ( 39) SS BOND : angle 1.08161 / 0.69 ( 78) hydrogen bonds : bond 0.04480 / 2.92 ( 927) hydrogen bonds : angle 5.39449 / 3.80 ( 2457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 542 time to evaluate : 0.758 Fit side-chains REVERT: A 218 GLU cc_start: 0.8020 (mp0) cc_final: 0.7692 (mp0) REVERT: B 69 CYS cc_start: 0.6442 (p) cc_final: 0.6006 (p) REVERT: C 64 ILE cc_start: 0.7765 (mm) cc_final: 0.7545 (mm) REVERT: C 218 GLU cc_start: 0.7956 (mp0) cc_final: 0.7677 (mp0) REVERT: C 477 PHE cc_start: 0.8676 (m-10) cc_final: 0.8443 (m-10) outliers start: 38 outliers final: 18 residues processed: 560 average time/residue: 0.5187 time to fit residues: 333.8460 Evaluate side-chains 537 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 519 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 398 SER Chi-restraints excluded: chain O residue 36 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 146 optimal weight: 2.9990 chunk 210 optimal weight: 3.9990 chunk 195 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 259 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 216 ASN A 225 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN D 58 ASN E 48 GLN B 202 GLN B 224 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 36 GLN I 87 GLN C 225 GLN C 227 ASN C 317 HIS ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.154783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130143 restraints weight = 23907.450| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.73 r_work: 0.3657 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3497 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3489 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3489 r_free = 0.3489 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3489 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 21168 Z= 0.162 Angle : 0.570 10.003 28779 Z= 0.301 Chirality : 0.044 0.161 3297 Planarity : 0.005 0.059 3651 Dihedral : 5.566 85.273 2904 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.78 % Allowed : 15.40 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.74 (0.16), residues: 2646 helix: 1.51 (0.26), residues: 420 sheet: 0.94 (0.16), residues: 954 loop : -0.15 (0.18), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 55 TYR 0.016 0.002 TYR B 198 PHE 0.016 0.002 PHE I 30 TRP 0.016 0.002 TRP F 34 HIS 0.005 0.001 HIS O 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (21129) covalent geometry : angle 0.56768 / 0.30 (28701) SS BOND : bond 0.00266 / 0.16 ( 39) SS BOND : angle 1.15812 / 0.72 ( 78) hydrogen bonds : bond 0.04384 / 2.85 ( 927) hydrogen bonds : angle 5.17109 / 3.64 ( 2457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 520 time to evaluate : 0.554 Fit side-chains REVERT: A 218 GLU cc_start: 0.8076 (mp0) cc_final: 0.7771 (mp0) REVERT: B 69 CYS cc_start: 0.6583 (p) cc_final: 0.6141 (p) outliers start: 42 outliers final: 27 residues processed: 538 average time/residue: 0.5397 time to fit residues: 332.8265 Evaluate side-chains 536 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 509 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 36 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 195 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 229 optimal weight: 3.9990 chunk 232 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 chunk 235 optimal weight: 0.9980 chunk 204 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 216 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN D 58 ASN E 48 GLN H 82 GLN B 202 GLN B 224 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN C 227 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN M 82 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.155341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131277 restraints weight = 23849.505| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.56 r_work: 0.3687 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21168 Z= 0.143 Angle : 0.547 9.929 28779 Z= 0.288 Chirality : 0.044 0.166 3297 Planarity : 0.005 0.058 3651 Dihedral : 5.437 82.684 2904 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.90 % Allowed : 15.65 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.85 (0.17), residues: 2646 helix: 1.69 (0.26), residues: 420 sheet: 0.91 (0.16), residues: 981 loop : -0.04 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 339 TYR 0.014 0.002 TYR B 457 PHE 0.015 0.001 PHE I 30 TRP 0.014 0.001 TRP F 34 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (21129) covalent geometry : angle 0.54524 / 0.29 (28701) SS BOND : bond 0.00269 / 0.16 ( 39) SS BOND : angle 0.98229 / 0.62 ( 78) hydrogen bonds : bond 0.03991 / 2.60 ( 927) hydrogen bonds : angle 5.00580 / 3.52 ( 2457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 529 time to evaluate : 0.809 Fit side-chains REVERT: A 218 GLU cc_start: 0.7998 (mp0) cc_final: 0.7709 (mp0) REVERT: B 69 CYS cc_start: 0.6688 (p) cc_final: 0.6234 (p) REVERT: F 84 SER cc_start: 0.8349 (m) cc_final: 0.8071 (p) REVERT: C 64 ILE cc_start: 0.7777 (mm) cc_final: 0.7548 (mm) outliers start: 45 outliers final: 30 residues processed: 551 average time/residue: 0.5452 time to fit residues: 345.2559 Evaluate side-chains 550 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 520 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 215 optimal weight: 0.0670 chunk 107 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 13 optimal weight: 0.0570 chunk 94 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 239 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.9438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 216 ASN A 225 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 94 GLN B 202 GLN B 224 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 87 GLN C 227 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.154549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.131094 restraints weight = 24290.231| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 1.54 r_work: 0.3683 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3532 r_free = 0.3532 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21168 Z= 0.146 Angle : 0.547 9.808 28779 Z= 0.290 Chirality : 0.044 0.162 3297 Planarity : 0.005 0.059 3651 Dihedral : 5.368 79.573 2904 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.03 % Allowed : 15.69 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.86 (0.17), residues: 2646 helix: 1.70 (0.26), residues: 420 sheet: 0.92 (0.16), residues: 984 loop : -0.04 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 339 TYR 0.015 0.002 TYR B 457 PHE 0.019 0.001 PHE B 190 TRP 0.015 0.001 TRP F 34 HIS 0.003 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (21129) covalent geometry : angle 0.54478 / 0.29 (28701) SS BOND : bond 0.00283 / 0.16 ( 39) SS BOND : angle 1.15630 / 0.76 ( 78) hydrogen bonds : bond 0.03974 / 2.59 ( 927) hydrogen bonds : angle 4.97054 / 3.49 ( 2457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 528 time to evaluate : 0.812 Fit side-chains REVERT: A 218 GLU cc_start: 0.7998 (mp0) cc_final: 0.7701 (mp0) REVERT: F 84 SER cc_start: 0.8377 (m) cc_final: 0.8125 (p) REVERT: C 64 ILE cc_start: 0.7765 (mm) cc_final: 0.7537 (mm) REVERT: C 218 GLU cc_start: 0.7775 (mp0) cc_final: 0.7567 (mp0) REVERT: C 378 GLU cc_start: 0.7655 (mp0) cc_final: 0.7422 (mp0) outliers start: 48 outliers final: 36 residues processed: 551 average time/residue: 0.5681 time to fit residues: 358.9787 Evaluate side-chains 560 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 524 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 14 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 118 optimal weight: 0.9990 chunk 89 optimal weight: 0.0470 chunk 52 optimal weight: 0.7980 chunk 241 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 114 optimal weight: 0.0020 overall best weight: 0.7690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 216 ASN A 225 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 34 GLN B 94 GLN B 202 GLN B 224 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN C 227 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 460 ASN J 48 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.156142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132303 restraints weight = 23780.952| |-----------------------------------------------------------------------------| r_work (start): 0.3807 rms_B_bonded: 1.55 r_work: 0.3697 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 21168 Z= 0.131 Angle : 0.548 12.605 28779 Z= 0.289 Chirality : 0.043 0.152 3297 Planarity : 0.005 0.058 3651 Dihedral : 5.259 75.212 2904 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.12 % Allowed : 15.69 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.91 (0.17), residues: 2646 helix: 1.75 (0.26), residues: 420 sheet: 0.96 (0.16), residues: 987 loop : -0.01 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.017 0.002 TYR B 457 PHE 0.014 0.001 PHE I 30 TRP 0.013 0.001 TRP F 34 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (21129) covalent geometry : angle 0.53525 / 0.28 (28701) SS BOND : bond 0.00330 / 0.18 ( 39) SS BOND : angle 2.33681 / 1.52 ( 78) hydrogen bonds : bond 0.03760 / 2.45 ( 927) hydrogen bonds : angle 4.88757 / 3.43 ( 2457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 520 time to evaluate : 0.818 Fit side-chains REVERT: A 218 GLU cc_start: 0.8000 (mp0) cc_final: 0.7709 (mp0) REVERT: F 84 SER cc_start: 0.8375 (m) cc_final: 0.8121 (p) REVERT: C 64 ILE cc_start: 0.7769 (mm) cc_final: 0.7545 (mm) REVERT: C 97 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8174 (ttm) REVERT: C 218 GLU cc_start: 0.7750 (mp0) cc_final: 0.7537 (mp0) REVERT: C 378 GLU cc_start: 0.7651 (mp0) cc_final: 0.7414 (mp0) outliers start: 50 outliers final: 37 residues processed: 548 average time/residue: 0.5817 time to fit residues: 365.5086 Evaluate side-chains 543 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 505 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 151 optimal weight: 6.9990 chunk 169 optimal weight: 0.0770 chunk 148 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 251 optimal weight: 0.0670 chunk 243 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 154 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.3880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 225 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN H 39 GLN B 34 GLN B 94 GLN B 202 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 87 GLN K 39 GLN C 225 GLN C 227 ASN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 GLN M 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.154529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129413 restraints weight = 23732.101| |-----------------------------------------------------------------------------| r_work (start): 0.3779 rms_B_bonded: 1.75 r_work: 0.3655 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3472 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3472 r_free = 0.3472 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3472 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.131 21168 Z= 0.201 Angle : 0.599 14.882 28779 Z= 0.317 Chirality : 0.045 0.180 3297 Planarity : 0.005 0.060 3651 Dihedral : 5.401 69.787 2904 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.12 % Allowed : 16.20 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % 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: 0.87 (0.17), residues: 2646 helix: 1.69 (0.26), residues: 420 sheet: 0.92 (0.16), residues: 987 loop : -0.02 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 235 TYR 0.020 0.002 TYR B 457 PHE 0.018 0.002 PHE I 30 TRP 0.015 0.002 TRP F 34 HIS 0.003 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (21129) covalent geometry : angle 0.58110 / 0.31 (28701) SS BOND : bond 0.00386 / 0.22 ( 39) SS BOND : angle 2.83795 / 1.91 ( 78) hydrogen bonds : bond 0.04337 / 2.82 ( 927) hydrogen bonds : angle 5.06941 / 3.56 ( 2457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 535 time to evaluate : 0.776 Fit side-chains REVERT: A 218 GLU cc_start: 0.8112 (mp0) cc_final: 0.7792 (mp0) REVERT: N 24 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7576 (mptm) REVERT: C 97 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8224 (ttm) REVERT: C 378 GLU cc_start: 0.7771 (mp0) cc_final: 0.7506 (mp0) outliers start: 50 outliers final: 35 residues processed: 561 average time/residue: 0.5032 time to fit residues: 325.3968 Evaluate side-chains 575 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 538 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain L residue 90 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 451 SER Chi-restraints excluded: chain I residue 67 THR Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 98 GLN Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain C residue 458 CYS Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 116 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 258 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 201 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 34 GLN B 94 GLN B 202 GLN B 225 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN C 34 GLN C 227 ASN C 388 ASN C 454 ASN J 48 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.153877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.129678 restraints weight = 23650.967| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 1.55 r_work: 0.3664 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3508 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3508 r_free = 0.3508 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3508 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 21168 Z= 0.248 Angle : 0.633 12.954 28779 Z= 0.338 Chirality : 0.047 0.212 3297 Planarity : 0.005 0.062 3651 Dihedral : 5.517 59.722 2904 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.21 % Favored : 96.75 % Rotamer: Outliers : 1.78 % Allowed : 16.96 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: 0.75 (0.17), residues: 2646 helix: 1.54 (0.26), residues: 420 sheet: 0.82 (0.16), residues: 987 loop : -0.06 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 49 TYR 0.021 0.002 TYR C 457 PHE 0.020 0.002 PHE I 30 TRP 0.016 0.002 TRP F 34 HIS 0.004 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (21129) covalent geometry : angle 0.62150 / 0.33 (28701) SS BOND : bond 0.00409 / 0.24 ( 39) SS BOND : angle 2.38618 / 1.54 ( 78) hydrogen bonds : bond 0.04707 / 3.05 ( 927) hydrogen bonds : angle 5.18997 / 3.65 ( 2457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 528 time to evaluate : 0.830 Fit side-chains REVERT: A 218 GLU cc_start: 0.8043 (mp0) cc_final: 0.7720 (mp0) REVERT: A 289 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7186 (tpt) REVERT: N 24 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7617 (mptm) REVERT: C 97 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8186 (ttm) REVERT: C 378 GLU cc_start: 0.7737 (mp0) cc_final: 0.7486 (mp0) REVERT: O 24 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7712 (mptm) outliers start: 42 outliers final: 30 residues processed: 549 average time/residue: 0.5474 time to fit residues: 343.9577 Evaluate side-chains 561 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 527 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 289 MET Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 61 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 237 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 chunk 254 optimal weight: 0.9980 chunk 251 optimal weight: 30.0000 chunk 167 optimal weight: 1.9990 chunk 245 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 216 ASN A 227 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 34 GLN B 94 GLN B 202 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN I 87 GLN C 34 GLN C 227 ASN C 388 ASN J 48 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.131045 restraints weight = 23781.111| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 1.56 r_work: 0.3683 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 21168 Z= 0.168 Angle : 0.582 10.162 28779 Z= 0.309 Chirality : 0.045 0.179 3297 Planarity : 0.005 0.059 3651 Dihedral : 5.221 50.727 2904 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.73 % Allowed : 17.17 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: 0.81 (0.17), residues: 2646 helix: 1.69 (0.26), residues: 420 sheet: 0.84 (0.16), residues: 987 loop : -0.04 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.016 0.002 TYR G 94 PHE 0.026 0.002 PHE B 190 TRP 0.015 0.002 TRP F 34 HIS 0.003 0.001 HIS L 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 (21129) covalent geometry : angle 0.57189 / 0.31 (28701) SS BOND : bond 0.00359 / 0.20 ( 39) SS BOND : angle 2.10233 / 1.49 ( 78) hydrogen bonds : bond 0.04087 / 2.65 ( 927) hydrogen bonds : angle 5.01172 / 3.52 ( 2457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 520 time to evaluate : 0.791 Fit side-chains REVERT: N 24 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (mptm) REVERT: C 97 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8127 (ttm) REVERT: C 378 GLU cc_start: 0.7726 (mp0) cc_final: 0.7454 (mp0) REVERT: O 24 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7691 (mptm) outliers start: 41 outliers final: 30 residues processed: 541 average time/residue: 0.5222 time to fit residues: 325.4866 Evaluate side-chains 552 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 519 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain F residue 19 SER Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 152 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 172 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 105 optimal weight: 0.7980 chunk 124 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN A 225 GLN A 227 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 34 GLN B 94 GLN B 202 GLN B 227 ASN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN C 227 ASN J 48 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.155805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132199 restraints weight = 24479.757| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 1.56 r_work: 0.3692 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.094 21168 Z= 0.130 Angle : 0.550 9.586 28779 Z= 0.292 Chirality : 0.044 0.160 3297 Planarity : 0.005 0.059 3651 Dihedral : 4.911 45.575 2904 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.35 % Allowed : 17.68 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: 0.89 (0.17), residues: 2646 helix: 1.82 (0.26), residues: 420 sheet: 0.88 (0.16), residues: 987 loop : -0.00 (0.19), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.014 0.002 TYR G 94 PHE 0.022 0.001 PHE B 190 TRP 0.014 0.001 TRP F 34 HIS 0.002 0.001 HIS A 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (21129) covalent geometry : angle 0.54234 / 0.29 (28701) SS BOND : bond 0.00308 / 0.17 ( 39) SS BOND : angle 1.82662 / 1.37 ( 78) hydrogen bonds : bond 0.03694 / 2.39 ( 927) hydrogen bonds : angle 4.87439 / 3.42 ( 2457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5292 Ramachandran restraints generated. 2646 Oldfield, 0 Emsley, 2646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 530 time to evaluate : 0.705 Fit side-chains REVERT: N 24 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7553 (mptm) REVERT: C 64 ILE cc_start: 0.7767 (mm) cc_final: 0.7530 (mm) REVERT: C 97 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8164 (ttm) REVERT: C 378 GLU cc_start: 0.7689 (mp0) cc_final: 0.7411 (mp0) REVERT: O 24 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7637 (mptm) outliers start: 32 outliers final: 27 residues processed: 547 average time/residue: 0.4933 time to fit residues: 309.9025 Evaluate side-chains 555 residues out of total 2364 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 525 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 186 SER Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain K residue 115 LEU Chi-restraints excluded: chain N residue 13 VAL Chi-restraints excluded: chain N residue 24 LYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 451 SER Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain O residue 24 LYS Chi-restraints excluded: chain O residue 36 THR Chi-restraints excluded: chain O residue 78 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 237 optimal weight: 3.9990 chunk 212 optimal weight: 0.4980 chunk 109 optimal weight: 0.8980 chunk 171 optimal weight: 20.0000 chunk 73 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 195 optimal weight: 0.8980 chunk 155 optimal weight: 0.0170 chunk 161 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 199 optimal weight: 0.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 94 GLN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN E 48 GLN B 94 GLN B 202 GLN B 270 GLN B 284 GLN ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 48 GLN C 227 ASN J 15 GLN J 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.156887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.132450 restraints weight = 23994.572| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.61 r_work: 0.3693 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 21168 Z= 0.115 Angle : 0.535 9.357 28779 Z= 0.283 Chirality : 0.043 0.147 3297 Planarity : 0.004 0.058 3651 Dihedral : 4.689 42.566 2904 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.44 % Allowed : 17.64 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 2.78 % Twisted General : 0.08 % 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: 0.94 (0.17), residues: 2646 helix: 1.87 (0.26), residues: 420 sheet: 0.93 (0.16), residues: 981 loop : 0.00 (0.19), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 339 TYR 0.013 0.001 TYR G 94 PHE 0.022 0.001 PHE B 190 TRP 0.014 0.001 TRP F 34 HIS 0.002 0.001 HIS C 317 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (21129) covalent geometry : angle 0.52835 / 0.28 (28701) SS BOND : bond 0.00298 / 0.17 ( 39) SS BOND : angle 1.64947 / 1.23 ( 78) hydrogen bonds : bond 0.03507 / 2.28 ( 927) hydrogen bonds : angle 4.79120 / 3.37 ( 2457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13950.46 seconds wall clock time: 236 minutes 45.05 seconds (14205.05 seconds total)