Starting phenix.real_space_refine on Sat Aug 23 15:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qrh_18614/08_2025/8qrh_18614.map" } resolution = 3.6 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= 0.003 sd= 0.037 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 81 5.16 5 C 8220 2.51 5 N 2274 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12951 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "B" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "C" Number of atoms: 3746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3746 Classifications: {'peptide': 492} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 472} Chain: "D" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "E" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "F" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 557 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 2, 'TRANS': 68} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.38, per 1000 atoms: 0.26 Number of scatterers: 12951 At special positions: 0 Unit cell: (114.75, 195.075, 94.35, 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 81 16.00 O 2376 8.00 N 2274 7.00 C 8220 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 30 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 105 " distance=2.04 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 116 " distance=2.03 Simple disulfide: pdb=" SG CYS A 186 " - pdb=" SG CYS A 290 " distance=2.03 Simple disulfide: pdb=" SG CYS A 307 " - pdb=" SG CYS A 338 " distance=2.02 Simple disulfide: pdb=" SG CYS B 3 " - pdb=" SG CYS B 30 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 105 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 116 " distance=2.03 Simple disulfide: pdb=" SG CYS B 186 " - pdb=" SG CYS B 290 " distance=2.03 Simple disulfide: pdb=" SG CYS B 307 " - pdb=" SG CYS B 338 " distance=2.03 Simple disulfide: pdb=" SG CYS C 3 " - pdb=" SG CYS C 30 " distance=2.03 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 116 " distance=2.03 Simple disulfide: pdb=" SG CYS C 186 " - pdb=" SG CYS C 290 " distance=2.03 Simple disulfide: pdb=" SG CYS C 307 " - pdb=" SG CYS C 338 " distance=2.02 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 Links applied NAG-ASN " NAG A 500 " - " ASN A 154 " " NAG B 500 " - " ASN B 154 " " NAG C 500 " - " ASN C 154 " Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 588.0 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 27 sheets defined 31.8% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 Processing helix chain 'A' and resid 82 through 86 removed outlier: 3.618A pdb=" N HIS A 86 " --> pdb=" O ALA A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.595A pdb=" N HIS A 104 " --> pdb=" O TRP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 237 through 240 Processing helix chain 'A' and resid 260 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 308 through 310 No H-bonds generated for 'chain 'A' and resid 308 through 310' Processing helix chain 'A' and resid 397 through 417 removed outlier: 3.753A pdb=" N VAL A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 423 removed outlier: 3.591A pdb=" N TRP A 421 " --> pdb=" O GLU A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 Processing helix chain 'A' and resid 453 through 467 Processing helix chain 'A' and resid 473 through 476 removed outlier: 4.378A pdb=" N MET A 476 " --> pdb=" O ASN A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 492 removed outlier: 4.051A pdb=" N LEU A 481 " --> pdb=" O SER A 477 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 187 through 191 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 237 through 240 Processing helix chain 'B' and resid 260 through 268 Processing helix chain 'B' and resid 397 through 417 Processing helix chain 'B' and resid 418 through 423 Processing helix chain 'B' and resid 427 through 450 removed outlier: 3.995A pdb=" N THR B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 471 Processing helix chain 'B' and resid 474 through 492 removed outlier: 4.121A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) Processing helix chain 'C' and resid 1 through 6 removed outlier: 3.508A pdb=" N THR C 4 " --> pdb=" O SER C 1 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 removed outlier: 3.661A pdb=" N HIS C 86 " --> pdb=" O ALA C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 188 through 191 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 260 through 268 Processing helix chain 'C' and resid 397 through 420 removed outlier: 3.591A pdb=" N THR C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N VAL C 415 " --> pdb=" O GLU C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 427 through 448 removed outlier: 4.232A pdb=" N VAL C 433 " --> pdb=" O PHE C 429 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 470 Processing helix chain 'C' and resid 473 through 492 Processing helix chain 'D' and resid 20 through 52 removed outlier: 3.590A pdb=" N SER D 24 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D 25 " --> pdb=" O GLU D 21 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS D 28 " --> pdb=" O SER D 24 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU D 29 " --> pdb=" O LEU D 25 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU D 41 " --> pdb=" O TRP D 37 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'E' and resid 26 through 54 removed outlier: 4.017A pdb=" N THR E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG E 31 " --> pdb=" O THR E 27 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL E 32 " --> pdb=" O HIS E 28 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU E 41 " --> pdb=" O TRP E 37 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU E 42 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 71 removed outlier: 3.805A pdb=" N ARG E 60 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL E 61 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA E 62 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 10 Processing helix chain 'F' and resid 20 through 28 removed outlier: 4.161A pdb=" N ARG F 26 " --> pdb=" O GLY F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 39 Processing helix chain 'F' and resid 39 through 54 Processing helix chain 'F' and resid 58 through 71 removed outlier: 5.689A pdb=" N LEU F 64 " --> pdb=" O ARG F 60 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.806A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR A 140 " --> pdb=" O ASP A 46 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ILE A 48 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N VAL A 138 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.806A pdb=" N ASP A 10 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR A 34 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N VAL A 12 " --> pdb=" O THR A 34 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 212 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA A 127 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU A 58 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLY A 129 " --> pdb=" O THR A 56 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A 54 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 26 Processing sheet with id=AA4, first strand: chain 'A' and resid 63 through 73 removed outlier: 4.287A pdb=" N THR A 68 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS A 116 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 70 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL A 114 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ALA A 72 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N SER A 112 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 242 through 244 Processing sheet with id=AA6, first strand: chain 'A' and resid 312 through 320 removed outlier: 6.172A pdb=" N GLU A 329 " --> pdb=" O LYS A 315 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ILE A 317 " --> pdb=" O VAL A 327 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 327 " --> pdb=" O ILE A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA8, first strand: chain 'A' and resid 342 through 344 Processing sheet with id=AA9, first strand: chain 'A' and resid 379 through 380 Processing sheet with id=AB1, first strand: chain 'B' and resid 9 through 10 removed outlier: 6.965A pdb=" N THR B 140 " --> pdb=" O ASP B 46 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE B 48 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL B 138 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 212 through 216 removed outlier: 6.433A pdb=" N ALA B 127 " --> pdb=" O GLU B 58 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU B 58 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY B 129 " --> pdb=" O THR B 56 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 63 through 72 removed outlier: 4.332A pdb=" N THR B 68 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 116 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL B 70 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL B 114 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA B 72 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N SER B 112 " --> pdb=" O ALA B 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 242 through 244 Processing sheet with id=AB7, first strand: chain 'B' and resid 312 through 320 removed outlier: 5.568A pdb=" N TRP B 314 " --> pdb=" O ALA B 331 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ALA B 331 " --> pdb=" O TRP B 314 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N VAL B 327 " --> pdb=" O PRO B 318 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 338 through 339 Processing sheet with id=AB9, first strand: chain 'B' and resid 342 through 346 Processing sheet with id=AC1, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.940A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 12 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N THR C 140 " --> pdb=" O ASP C 46 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ILE C 48 " --> pdb=" O VAL C 138 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N VAL C 138 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 9 through 14 removed outlier: 6.940A pdb=" N ASP C 10 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N THR C 34 " --> pdb=" O ASP C 10 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL C 12 " --> pdb=" O THR C 34 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ALA C 35 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA C 212 " --> pdb=" O ALA C 274 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA C 127 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU C 58 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 129 " --> pdb=" O THR C 56 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 20 through 26 removed outlier: 4.641A pdb=" N THR C 289 " --> pdb=" O ARG C 187 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 63 through 72 removed outlier: 4.342A pdb=" N THR C 68 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N CYS C 116 " --> pdb=" O THR C 68 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL C 70 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL C 114 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA C 72 " --> pdb=" O SER C 112 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N SER C 112 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 172 through 177 removed outlier: 4.920A pdb=" N GLY C 180 " --> pdb=" O MET C 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 242 through 244 Processing sheet with id=AC7, first strand: chain 'C' and resid 312 through 320 removed outlier: 6.452A pdb=" N GLU C 329 " --> pdb=" O LYS C 315 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N ILE C 317 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL C 327 " --> pdb=" O ILE C 317 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 338 through 339 Processing sheet with id=AC9, first strand: chain 'C' and resid 342 through 346 601 hydrogen bonds defined for protein. 1605 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: 2.31 Time building geometry restraints manager: 1.41 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: 4214 1.34 - 1.46: 3032 1.46 - 1.59: 5870 1.59 - 1.71: 0 1.71 - 1.83: 123 Bond restraints: 13239 Sorted by residual: bond pdb=" CA GLY C 180 " pdb=" C GLY C 180 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.04e-02 9.25e+03 2.77e+00 bond pdb=" C1 NAG B 500 " pdb=" O5 NAG B 500 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N GLY C 180 " pdb=" CA GLY C 180 " ideal model delta sigma weight residual 1.464 1.450 0.014 1.12e-02 7.97e+03 1.67e+00 bond pdb=" C5 NAG C 500 " pdb=" O5 NAG C 500 " ideal model delta sigma weight residual 1.413 1.438 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 500 " pdb=" O5 NAG C 500 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.34e+00 ... (remaining 13234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 17086 1.53 - 3.06: 774 3.06 - 4.60: 95 4.60 - 6.13: 21 6.13 - 7.66: 3 Bond angle restraints: 17979 Sorted by residual: angle pdb=" N ARG E 40 " pdb=" CA ARG E 40 " pdb=" C ARG E 40 " ideal model delta sigma weight residual 110.80 118.46 -7.66 2.13e+00 2.20e-01 1.29e+01 angle pdb=" C LEU B 448 " pdb=" N PHE B 449 " pdb=" CA PHE B 449 " ideal model delta sigma weight residual 120.68 126.32 -5.64 1.70e+00 3.46e-01 1.10e+01 angle pdb=" N GLY C 180 " pdb=" CA GLY C 180 " pdb=" C GLY C 180 " ideal model delta sigma weight residual 111.67 114.69 -3.02 9.20e-01 1.18e+00 1.08e+01 angle pdb=" CA TRP D 19 " pdb=" CB TRP D 19 " pdb=" CG TRP D 19 " ideal model delta sigma weight residual 113.60 119.46 -5.86 1.90e+00 2.77e-01 9.51e+00 angle pdb=" CA LYS B 457 " pdb=" CB LYS B 457 " pdb=" CG LYS B 457 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.08e+00 ... (remaining 17974 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 7342 17.79 - 35.58: 424 35.58 - 53.37: 58 53.37 - 71.16: 20 71.16 - 88.94: 7 Dihedral angle restraints: 7851 sinusoidal: 3102 harmonic: 4749 Sorted by residual: dihedral pdb=" CA GLY C 427 " pdb=" C GLY C 427 " pdb=" N GLY C 428 " pdb=" CA GLY C 428 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASN E 39 " pdb=" C ASN E 39 " pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta harmonic sigma weight residual -180.00 -151.19 -28.81 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA ASN D 39 " pdb=" C ASN D 39 " pdb=" N ARG D 40 " pdb=" CA ARG D 40 " ideal model delta harmonic sigma weight residual -180.00 -151.24 -28.76 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 7848 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1275 0.036 - 0.071: 566 0.071 - 0.107: 161 0.107 - 0.143: 78 0.143 - 0.178: 5 Chirality restraints: 2085 Sorted by residual: chirality pdb=" CB ILE B 33 " pdb=" CA ILE B 33 " pdb=" CG1 ILE B 33 " pdb=" CG2 ILE B 33 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.95e-01 chirality pdb=" CA ASN E 39 " pdb=" N ASN E 39 " pdb=" C ASN E 39 " pdb=" CB ASN E 39 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CA HIS A 260 " pdb=" N HIS A 260 " pdb=" C HIS A 260 " pdb=" CB HIS A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 ... (remaining 2082 not shown) Planarity restraints: 2259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 412 " 0.346 9.50e-02 1.11e+02 1.56e-01 1.79e+01 pdb=" NE ARG A 412 " -0.031 2.00e-02 2.50e+03 pdb=" CZ ARG A 412 " 0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 412 " -0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 412 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 414 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C THR C 414 " -0.068 2.00e-02 2.50e+03 pdb=" O THR C 414 " 0.025 2.00e-02 2.50e+03 pdb=" N VAL C 415 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 413 " 0.019 2.00e-02 2.50e+03 3.78e-02 1.43e+01 pdb=" C LEU A 413 " -0.065 2.00e-02 2.50e+03 pdb=" O LEU A 413 " 0.024 2.00e-02 2.50e+03 pdb=" N THR A 414 " 0.022 2.00e-02 2.50e+03 ... (remaining 2256 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2395 2.78 - 3.31: 12361 3.31 - 3.84: 19975 3.84 - 4.37: 23233 4.37 - 4.90: 40823 Nonbonded interactions: 98787 Sorted by model distance: nonbonded pdb=" O ALA B 426 " pdb=" OG1 THR B 431 " model vdw 2.255 3.040 nonbonded pdb=" OE2 GLU B 411 " pdb=" NH2 ARG D 15 " model vdw 2.316 3.120 nonbonded pdb=" O LEU E 54 " pdb=" NE ARG E 60 " model vdw 2.339 3.120 nonbonded pdb=" O SER F 24 " pdb=" OG1 THR F 27 " model vdw 2.359 3.040 nonbonded pdb=" O PRO B 474 " pdb=" OG SER B 477 " model vdw 2.379 3.040 ... (remaining 98782 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.530 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.003 0.031 13260 Z= 0.149 Angle : 0.722 7.661 18024 Z= 0.423 Chirality : 0.046 0.178 2085 Planarity : 0.008 0.156 2256 Dihedral : 12.207 88.944 4761 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.83 (0.19), residues: 1677 helix: -0.19 (0.22), residues: 411 sheet: -0.53 (0.22), residues: 486 loop : -0.62 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.031 0.003 ARG A 412 TYR 0.014 0.003 TYR A 384 PHE 0.033 0.002 PHE A 480 TRP 0.031 0.002 TRP D 19 HIS 0.006 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00274 (13239) covalent geometry : angle 0.71761 (17979) SS BOND : bond 0.00462 ( 18) SS BOND : angle 1.29485 ( 36) hydrogen bonds : bond 0.13053 ( 589) hydrogen bonds : angle 7.57219 ( 1605) link_NAG-ASN : bond 0.00465 ( 3) link_NAG-ASN : angle 2.93828 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 TRP cc_start: 0.6129 (m100) cc_final: 0.5220 (m100) REVERT: A 251 LYS cc_start: 0.8399 (mttt) cc_final: 0.8182 (tptt) REVERT: A 476 MET cc_start: 0.3698 (mmt) cc_final: 0.2739 (mmt) REVERT: B 87 GLN cc_start: 0.7292 (mt0) cc_final: 0.6881 (mp10) REVERT: B 306 MET cc_start: 0.7705 (mmm) cc_final: 0.7419 (mmt) REVERT: B 316 ARG cc_start: 0.7456 (ttt180) cc_final: 0.4952 (tpp80) REVERT: B 404 GLN cc_start: 0.8053 (tp40) cc_final: 0.7563 (tm-30) REVERT: C 8 ASN cc_start: 0.8254 (t0) cc_final: 0.7219 (t0) REVERT: C 41 MET cc_start: 0.9013 (mmt) cc_final: 0.8062 (mmt) REVERT: C 87 GLN cc_start: 0.6680 (mt0) cc_final: 0.6130 (mp10) REVERT: C 252 MET cc_start: 0.8429 (ttt) cc_final: 0.8177 (ttm) REVERT: C 306 MET cc_start: 0.8649 (mmt) cc_final: 0.8337 (mmt) REVERT: E 52 LEU cc_start: 0.9508 (mt) cc_final: 0.9225 (mt) REVERT: F 7 HIS cc_start: 0.6800 (t-90) cc_final: 0.5181 (m-70) REVERT: F 19 TRP cc_start: 0.7321 (m100) cc_final: 0.6713 (m-10) REVERT: F 41 LEU cc_start: 0.9037 (mt) cc_final: 0.8750 (pt) REVERT: F 46 MET cc_start: 0.9498 (mmm) cc_final: 0.9138 (mmp) REVERT: F 50 VAL cc_start: 0.9528 (t) cc_final: 0.9273 (p) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1278 time to fit residues: 58.1064 Evaluate side-chains 200 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 149 optimal weight: 30.0000 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 HIS A 221 ASN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN B 366 ASN B 375 GLN B 419 HIS ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 473 ASN E 7 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.147306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109618 restraints weight = 22604.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112992 restraints weight = 11922.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.115241 restraints weight = 8047.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.116331 restraints weight = 6244.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117146 restraints weight = 5415.771| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13260 Z= 0.301 Angle : 0.759 9.505 18024 Z= 0.404 Chirality : 0.049 0.225 2085 Planarity : 0.005 0.050 2256 Dihedral : 6.803 51.160 1845 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.57 % Allowed : 8.80 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.20), residues: 1677 helix: 1.02 (0.25), residues: 393 sheet: -0.47 (0.23), residues: 467 loop : -0.45 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 94 TYR 0.033 0.003 TYR A 304 PHE 0.025 0.003 PHE A 480 TRP 0.033 0.003 TRP C 101 HIS 0.009 0.002 HIS B 419 Details of bonding type rmsd covalent geometry : bond 0.00710 (13239) covalent geometry : angle 0.75815 (17979) SS BOND : bond 0.00598 ( 18) SS BOND : angle 0.95976 ( 36) hydrogen bonds : bond 0.04839 ( 589) hydrogen bonds : angle 6.15731 ( 1605) link_NAG-ASN : bond 0.00642 ( 3) link_NAG-ASN : angle 1.60675 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8612 (mtpp) REVERT: A 394 GLN cc_start: 0.8605 (tp40) cc_final: 0.8356 (tp40) REVERT: B 87 GLN cc_start: 0.7338 (mt0) cc_final: 0.7061 (mp10) REVERT: B 404 GLN cc_start: 0.7933 (tp40) cc_final: 0.7496 (tm-30) REVERT: B 478 MET cc_start: 0.8660 (mpp) cc_final: 0.8403 (ppp) REVERT: C 86 HIS cc_start: 0.7890 (m-70) cc_final: 0.7404 (m-70) REVERT: C 367 ASN cc_start: 0.7984 (t0) cc_final: 0.7750 (t0) REVERT: E 39 ASN cc_start: 0.7854 (t0) cc_final: 0.7189 (t0) REVERT: E 46 MET cc_start: 0.8341 (ptm) cc_final: 0.8133 (ptt) REVERT: E 48 THR cc_start: 0.9280 (p) cc_final: 0.8976 (t) REVERT: E 52 LEU cc_start: 0.9455 (mt) cc_final: 0.9062 (mt) REVERT: F 7 HIS cc_start: 0.7481 (t-90) cc_final: 0.5339 (m-70) REVERT: F 46 MET cc_start: 0.9337 (mmm) cc_final: 0.9004 (mmp) outliers start: 22 outliers final: 18 residues processed: 239 average time/residue: 0.1055 time to fit residues: 37.2971 Evaluate side-chains 221 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 202 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 55 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 243 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 51 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 89 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 21 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 164 optimal weight: 30.0000 chunk 104 optimal weight: 5.9990 chunk 59 optimal weight: 9.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN B 375 GLN C 196 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.150585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.112909 restraints weight = 22596.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.116574 restraints weight = 11494.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.118925 restraints weight = 7520.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.120334 restraints weight = 5765.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.121201 restraints weight = 4915.035| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13260 Z= 0.144 Angle : 0.629 10.963 18024 Z= 0.328 Chirality : 0.044 0.162 2085 Planarity : 0.004 0.042 2256 Dihedral : 6.086 45.825 1845 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.43 % Allowed : 11.80 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.20), residues: 1677 helix: 1.29 (0.25), residues: 389 sheet: -0.27 (0.24), residues: 467 loop : -0.28 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 94 TYR 0.038 0.002 TYR A 304 PHE 0.023 0.002 PHE B 454 TRP 0.023 0.002 TRP E 35 HIS 0.006 0.001 HIS C 229 Details of bonding type rmsd covalent geometry : bond 0.00314 (13239) covalent geometry : angle 0.62840 (17979) SS BOND : bond 0.00321 ( 18) SS BOND : angle 0.73246 ( 36) hydrogen bonds : bond 0.04135 ( 589) hydrogen bonds : angle 5.74605 ( 1605) link_NAG-ASN : bond 0.00238 ( 3) link_NAG-ASN : angle 1.49975 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.8412 (mmt) cc_final: 0.8185 (mmt) REVERT: A 196 GLN cc_start: 0.8377 (mm110) cc_final: 0.8095 (mm110) REVERT: A 476 MET cc_start: 0.4029 (mmt) cc_final: 0.3770 (mmp) REVERT: A 486 LEU cc_start: 0.7885 (mt) cc_final: 0.7407 (tp) REVERT: B 316 ARG cc_start: 0.7468 (ttt180) cc_final: 0.7011 (ttp80) REVERT: B 367 ASN cc_start: 0.7696 (p0) cc_final: 0.7495 (p0) REVERT: B 395 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8746 (ptpp) REVERT: B 404 GLN cc_start: 0.7910 (tp40) cc_final: 0.7378 (tm-30) REVERT: C 86 HIS cc_start: 0.7852 (m-70) cc_final: 0.7449 (m-70) REVERT: C 87 GLN cc_start: 0.7162 (mp10) cc_final: 0.6822 (mp10) REVERT: C 367 ASN cc_start: 0.7896 (t0) cc_final: 0.7642 (t0) REVERT: D 46 MET cc_start: 0.7854 (mmm) cc_final: 0.7242 (mmm) REVERT: E 35 TRP cc_start: 0.8382 (t-100) cc_final: 0.8105 (t-100) REVERT: E 39 ASN cc_start: 0.8062 (t0) cc_final: 0.7401 (t0) REVERT: E 40 ARG cc_start: 0.6870 (ptp-170) cc_final: 0.6449 (ptp-170) REVERT: E 52 LEU cc_start: 0.9420 (mt) cc_final: 0.9083 (mt) REVERT: E 64 LEU cc_start: 0.9689 (mt) cc_final: 0.9234 (pp) REVERT: F 7 HIS cc_start: 0.7472 (t-90) cc_final: 0.5319 (m-70) outliers start: 20 outliers final: 12 residues processed: 232 average time/residue: 0.1018 time to fit residues: 35.1168 Evaluate side-chains 204 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 196 GLN Chi-restraints excluded: chain C residue 263 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 39 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 166 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 150 optimal weight: 20.0000 chunk 92 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 ASN ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS B 260 HIS B 366 ASN B 375 GLN C 233 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.146040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.108483 restraints weight = 22651.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.111657 restraints weight = 12880.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115043 restraints weight = 7816.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.114355 restraints weight = 6547.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114453 restraints weight = 5762.036| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 13260 Z= 0.355 Angle : 0.766 10.619 18024 Z= 0.404 Chirality : 0.049 0.180 2085 Planarity : 0.005 0.052 2256 Dihedral : 6.411 56.637 1845 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 3.15 % Allowed : 12.80 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.20), residues: 1677 helix: 1.01 (0.26), residues: 386 sheet: -0.76 (0.23), residues: 473 loop : -0.75 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.032 0.003 TYR A 304 PHE 0.024 0.003 PHE B 449 TRP 0.026 0.002 TRP C 101 HIS 0.010 0.002 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00834 (13239) covalent geometry : angle 0.76440 (17979) SS BOND : bond 0.00632 ( 18) SS BOND : angle 1.11942 ( 36) hydrogen bonds : bond 0.04494 ( 589) hydrogen bonds : angle 5.89487 ( 1605) link_NAG-ASN : bond 0.00665 ( 3) link_NAG-ASN : angle 1.51640 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 367 ASN cc_start: 0.8354 (p0) cc_final: 0.8146 (p0) REVERT: A 486 LEU cc_start: 0.7762 (mt) cc_final: 0.7365 (tp) REVERT: B 87 GLN cc_start: 0.7785 (mt0) cc_final: 0.7281 (mp10) REVERT: B 316 ARG cc_start: 0.7825 (ttt180) cc_final: 0.7555 (ttt180) REVERT: B 367 ASN cc_start: 0.7903 (p0) cc_final: 0.7678 (p0) REVERT: B 404 GLN cc_start: 0.7955 (tp40) cc_final: 0.7530 (tm-30) REVERT: C 86 HIS cc_start: 0.7949 (m-70) cc_final: 0.7630 (m-70) REVERT: C 87 GLN cc_start: 0.7373 (mp10) cc_final: 0.7131 (mp10) REVERT: C 367 ASN cc_start: 0.8039 (t0) cc_final: 0.7734 (t0) REVERT: E 35 TRP cc_start: 0.8512 (t-100) cc_final: 0.8219 (t-100) REVERT: E 39 ASN cc_start: 0.8600 (t0) cc_final: 0.8117 (t0) REVERT: E 52 LEU cc_start: 0.9476 (mt) cc_final: 0.9179 (mt) REVERT: E 64 LEU cc_start: 0.9731 (mt) cc_final: 0.9268 (pp) REVERT: F 7 HIS cc_start: 0.7450 (t-90) cc_final: 0.5368 (m-70) outliers start: 44 outliers final: 35 residues processed: 223 average time/residue: 0.1000 time to fit residues: 33.0628 Evaluate side-chains 226 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 234 ASN Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 405 LYS Chi-restraints excluded: chain B residue 31 VAL Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 34 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 0.0170 chunk 167 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.7218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.149599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112511 restraints weight = 22498.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116119 restraints weight = 11491.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.118259 restraints weight = 7512.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119738 restraints weight = 5788.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120650 restraints weight = 4921.058| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13260 Z= 0.113 Angle : 0.597 10.685 18024 Z= 0.309 Chirality : 0.043 0.150 2085 Planarity : 0.004 0.047 2256 Dihedral : 5.711 45.250 1845 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.93 % Allowed : 14.95 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.20), residues: 1677 helix: 1.11 (0.25), residues: 405 sheet: -0.39 (0.23), residues: 463 loop : -0.58 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 187 TYR 0.029 0.001 TYR A 304 PHE 0.025 0.001 PHE B 454 TRP 0.016 0.001 TRP E 51 HIS 0.005 0.001 HIS C 86 Details of bonding type rmsd covalent geometry : bond 0.00236 (13239) covalent geometry : angle 0.59564 (17979) SS BOND : bond 0.00307 ( 18) SS BOND : angle 0.78101 ( 36) hydrogen bonds : bond 0.03784 ( 589) hydrogen bonds : angle 5.54399 ( 1605) link_NAG-ASN : bond 0.00102 ( 3) link_NAG-ASN : angle 1.35293 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 215 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.7657 (ttm-80) cc_final: 0.7444 (ttm-80) REVERT: A 486 LEU cc_start: 0.7709 (mt) cc_final: 0.7319 (tp) REVERT: B 87 GLN cc_start: 0.7452 (mt0) cc_final: 0.7219 (mp10) REVERT: B 304 TYR cc_start: 0.7503 (m-10) cc_final: 0.7215 (m-80) REVERT: B 395 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8830 (ptpp) REVERT: B 404 GLN cc_start: 0.7875 (tp40) cc_final: 0.7400 (tm-30) REVERT: B 478 MET cc_start: 0.8158 (mpp) cc_final: 0.7766 (ppp) REVERT: C 252 MET cc_start: 0.8756 (ttt) cc_final: 0.8498 (ttm) REVERT: C 306 MET cc_start: 0.8777 (mmt) cc_final: 0.8481 (mmt) REVERT: D 46 MET cc_start: 0.7897 (mmm) cc_final: 0.7252 (mmm) REVERT: E 39 ASN cc_start: 0.8501 (t0) cc_final: 0.7992 (t0) REVERT: E 52 LEU cc_start: 0.9368 (mt) cc_final: 0.9071 (mt) REVERT: F 7 HIS cc_start: 0.7557 (t-90) cc_final: 0.5346 (m-70) outliers start: 27 outliers final: 19 residues processed: 232 average time/residue: 0.1061 time to fit residues: 36.5006 Evaluate side-chains 212 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 192 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 47 optimal weight: 6.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN B 470 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.148800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110949 restraints weight = 22149.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.114608 restraints weight = 11358.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.116863 restraints weight = 7441.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.118299 restraints weight = 5728.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118875 restraints weight = 4889.366| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13260 Z= 0.178 Angle : 0.636 10.303 18024 Z= 0.327 Chirality : 0.044 0.148 2085 Planarity : 0.004 0.056 2256 Dihedral : 5.670 48.099 1845 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.43 % Allowed : 15.81 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.20), residues: 1677 helix: 1.17 (0.26), residues: 405 sheet: -0.48 (0.24), residues: 463 loop : -0.64 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 40 TYR 0.029 0.002 TYR A 304 PHE 0.021 0.002 PHE B 454 TRP 0.034 0.002 TRP E 35 HIS 0.006 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00411 (13239) covalent geometry : angle 0.63548 (17979) SS BOND : bond 0.00358 ( 18) SS BOND : angle 0.81432 ( 36) hydrogen bonds : bond 0.03841 ( 589) hydrogen bonds : angle 5.49349 ( 1605) link_NAG-ASN : bond 0.00317 ( 3) link_NAG-ASN : angle 1.29514 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.7771 (ttm-80) cc_final: 0.7537 (ttm-80) REVERT: A 486 LEU cc_start: 0.7682 (mt) cc_final: 0.7294 (tp) REVERT: B 395 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8876 (ptpp) REVERT: B 404 GLN cc_start: 0.7780 (tp40) cc_final: 0.7317 (tm-30) REVERT: C 69 LYS cc_start: 0.8671 (mttm) cc_final: 0.8430 (mttm) REVERT: C 252 MET cc_start: 0.8741 (ttt) cc_final: 0.8449 (ttm) REVERT: D 46 MET cc_start: 0.7941 (mmm) cc_final: 0.7308 (mmm) REVERT: E 52 LEU cc_start: 0.9377 (mt) cc_final: 0.9063 (mt) REVERT: F 7 HIS cc_start: 0.7521 (t-90) cc_final: 0.5353 (m-70) outliers start: 34 outliers final: 30 residues processed: 219 average time/residue: 0.0980 time to fit residues: 31.9015 Evaluate side-chains 215 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 184 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 4 THR Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 395 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 317 ILE Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 41 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 147 optimal weight: 0.0770 chunk 94 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 123 optimal weight: 0.0070 chunk 50 optimal weight: 0.0370 chunk 75 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.152158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.114930 restraints weight = 22117.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.118685 restraints weight = 11175.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.121042 restraints weight = 7264.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122452 restraints weight = 5544.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.123107 restraints weight = 4721.608| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13260 Z= 0.107 Angle : 0.615 14.235 18024 Z= 0.308 Chirality : 0.043 0.167 2085 Planarity : 0.004 0.066 2256 Dihedral : 5.297 40.994 1845 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.86 % Allowed : 17.02 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.20), residues: 1677 helix: 1.32 (0.26), residues: 399 sheet: -0.34 (0.24), residues: 468 loop : -0.47 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 40 TYR 0.031 0.001 TYR A 304 PHE 0.022 0.001 PHE B 454 TRP 0.046 0.001 TRP E 35 HIS 0.005 0.001 HIS B 86 Details of bonding type rmsd covalent geometry : bond 0.00221 (13239) covalent geometry : angle 0.61402 (17979) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.67716 ( 36) hydrogen bonds : bond 0.03603 ( 589) hydrogen bonds : angle 5.33564 ( 1605) link_NAG-ASN : bond 0.00090 ( 3) link_NAG-ASN : angle 1.25960 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ARG cc_start: 0.7638 (ttm-80) cc_final: 0.7372 (ttm-80) REVERT: A 486 LEU cc_start: 0.7725 (mt) cc_final: 0.7383 (tp) REVERT: B 101 TRP cc_start: 0.5767 (OUTLIER) cc_final: 0.4951 (m-10) REVERT: B 187 ARG cc_start: 0.7598 (mmt90) cc_final: 0.7357 (mmt90) REVERT: B 404 GLN cc_start: 0.7842 (tp40) cc_final: 0.7413 (tm-30) REVERT: B 469 LEU cc_start: 0.9178 (tp) cc_final: 0.8921 (pp) REVERT: B 490 MET cc_start: 0.7190 (mmp) cc_final: 0.6669 (mmp) REVERT: C 8 ASN cc_start: 0.8351 (t0) cc_final: 0.7559 (t0) REVERT: C 87 GLN cc_start: 0.6766 (mp10) cc_final: 0.6040 (mp10) REVERT: C 252 MET cc_start: 0.8767 (ttt) cc_final: 0.8461 (ttm) REVERT: D 46 MET cc_start: 0.8078 (mmm) cc_final: 0.7638 (mmm) REVERT: E 52 LEU cc_start: 0.9341 (mt) cc_final: 0.9038 (mt) REVERT: F 7 HIS cc_start: 0.7489 (t-90) cc_final: 0.5309 (m-70) outliers start: 26 outliers final: 14 residues processed: 230 average time/residue: 0.0948 time to fit residues: 32.7670 Evaluate side-chains 215 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 200 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain B residue 45 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 LYS Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain B residue 480 PHE Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 5.9990 chunk 159 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 146 optimal weight: 20.0000 chunk 59 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 164 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 165 optimal weight: 30.0000 chunk 77 optimal weight: 2.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 347 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.145227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107427 restraints weight = 22302.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.110848 restraints weight = 11556.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113067 restraints weight = 7696.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.114524 restraints weight = 5942.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.115165 restraints weight = 5053.632| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 13260 Z= 0.319 Angle : 0.753 11.261 18024 Z= 0.388 Chirality : 0.049 0.268 2085 Planarity : 0.005 0.057 2256 Dihedral : 5.939 55.675 1845 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.72 % Allowed : 16.88 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.20), residues: 1677 helix: 1.01 (0.25), residues: 401 sheet: -0.68 (0.23), residues: 467 loop : -0.85 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.022 0.003 TYR B 150 PHE 0.021 0.002 PHE B 454 TRP 0.045 0.003 TRP E 35 HIS 0.007 0.002 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00749 (13239) covalent geometry : angle 0.75049 (17979) SS BOND : bond 0.00562 ( 18) SS BOND : angle 1.43473 ( 36) hydrogen bonds : bond 0.04173 ( 589) hydrogen bonds : angle 5.62700 ( 1605) link_NAG-ASN : bond 0.00545 ( 3) link_NAG-ASN : angle 1.54758 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 199 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: A 471 MET cc_start: 0.5775 (mmt) cc_final: 0.5058 (mmt) REVERT: A 486 LEU cc_start: 0.7758 (mt) cc_final: 0.7367 (tp) REVERT: B 243 GLU cc_start: 0.7553 (tp30) cc_final: 0.7291 (tp30) REVERT: B 404 GLN cc_start: 0.7907 (tp40) cc_final: 0.7491 (tm-30) REVERT: C 87 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: D 46 MET cc_start: 0.8168 (mmm) cc_final: 0.7727 (mmm) REVERT: E 52 LEU cc_start: 0.9354 (mt) cc_final: 0.9054 (mt) REVERT: F 7 HIS cc_start: 0.7587 (t-90) cc_final: 0.5405 (m-70) outliers start: 38 outliers final: 27 residues processed: 224 average time/residue: 0.0987 time to fit residues: 32.9494 Evaluate side-chains 219 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 117 VAL Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 41 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 137 optimal weight: 0.3980 chunk 117 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN B 375 GLN C 347 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.150092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113394 restraints weight = 22125.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116932 restraints weight = 11379.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119204 restraints weight = 7499.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.120612 restraints weight = 5755.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121424 restraints weight = 4905.054| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13260 Z= 0.119 Angle : 0.661 13.102 18024 Z= 0.330 Chirality : 0.044 0.198 2085 Planarity : 0.004 0.070 2256 Dihedral : 5.447 43.762 1845 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.72 % Allowed : 17.88 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1677 helix: 1.16 (0.26), residues: 397 sheet: -0.52 (0.23), residues: 466 loop : -0.64 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 187 TYR 0.013 0.001 TYR A 304 PHE 0.021 0.001 PHE B 454 TRP 0.057 0.002 TRP E 35 HIS 0.007 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00247 (13239) covalent geometry : angle 0.65991 (17979) SS BOND : bond 0.00301 ( 18) SS BOND : angle 1.01858 ( 36) hydrogen bonds : bond 0.03720 ( 589) hydrogen bonds : angle 5.37506 ( 1605) link_NAG-ASN : bond 0.00101 ( 3) link_NAG-ASN : angle 1.32134 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 211 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8360 (m-30) REVERT: A 471 MET cc_start: 0.5534 (mmt) cc_final: 0.4960 (mmt) REVERT: A 486 LEU cc_start: 0.7600 (mt) cc_final: 0.7225 (tp) REVERT: B 404 GLN cc_start: 0.7744 (tp40) cc_final: 0.7329 (tm-30) REVERT: B 469 LEU cc_start: 0.9196 (tp) cc_final: 0.8960 (pp) REVERT: B 478 MET cc_start: 0.7917 (mpp) cc_final: 0.7334 (ppp) REVERT: B 490 MET cc_start: 0.7241 (mmp) cc_final: 0.6995 (mmp) REVERT: C 8 ASN cc_start: 0.8390 (t0) cc_final: 0.7679 (t0) REVERT: C 252 MET cc_start: 0.8780 (ttt) cc_final: 0.8432 (ttm) REVERT: C 306 MET cc_start: 0.8699 (mmt) cc_final: 0.8415 (mmt) REVERT: D 46 MET cc_start: 0.8147 (mmm) cc_final: 0.7699 (mmm) REVERT: E 52 LEU cc_start: 0.9254 (mt) cc_final: 0.8951 (mt) REVERT: E 70 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7957 (mp) REVERT: F 7 HIS cc_start: 0.7640 (t-90) cc_final: 0.5360 (m-70) outliers start: 24 outliers final: 20 residues processed: 224 average time/residue: 0.1058 time to fit residues: 35.4910 Evaluate side-chains 224 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 202 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 193 ASP Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain D residue 52 LEU Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 159 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 7.9990 chunk 92 optimal weight: 20.0000 overall best weight: 4.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 GLN C 347 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.147091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.109266 restraints weight = 22464.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112841 restraints weight = 11566.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.115003 restraints weight = 7628.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116474 restraints weight = 5899.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.117254 restraints weight = 5031.206| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13260 Z= 0.281 Angle : 0.750 10.997 18024 Z= 0.383 Chirality : 0.048 0.232 2085 Planarity : 0.005 0.064 2256 Dihedral : 5.820 53.485 1845 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.86 % Allowed : 18.24 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1677 helix: 1.07 (0.26), residues: 401 sheet: -0.77 (0.23), residues: 460 loop : -0.85 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 217 TYR 0.022 0.002 TYR B 150 PHE 0.020 0.002 PHE B 449 TRP 0.061 0.002 TRP E 35 HIS 0.014 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00656 (13239) covalent geometry : angle 0.74819 (17979) SS BOND : bond 0.00677 ( 18) SS BOND : angle 1.15982 ( 36) hydrogen bonds : bond 0.04056 ( 589) hydrogen bonds : angle 5.56203 ( 1605) link_NAG-ASN : bond 0.00490 ( 3) link_NAG-ASN : angle 1.51877 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3354 Ramachandran restraints generated. 1677 Oldfield, 0 Emsley, 1677 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8384 (m-30) REVERT: A 448 LEU cc_start: 0.9072 (tp) cc_final: 0.8852 (tp) REVERT: A 471 MET cc_start: 0.5480 (mmt) cc_final: 0.4816 (mmt) REVERT: A 486 LEU cc_start: 0.7746 (mt) cc_final: 0.7349 (tp) REVERT: B 243 GLU cc_start: 0.7545 (tp30) cc_final: 0.7260 (tp30) REVERT: B 266 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8168 (mppt) REVERT: B 374 MET cc_start: 0.8093 (ptp) cc_final: 0.7717 (ptp) REVERT: B 404 GLN cc_start: 0.7880 (tp40) cc_final: 0.7416 (tm-30) REVERT: B 490 MET cc_start: 0.7390 (mmp) cc_final: 0.6858 (mmp) REVERT: C 67 ASP cc_start: 0.8512 (t0) cc_final: 0.7974 (t0) REVERT: C 69 LYS cc_start: 0.8832 (mttm) cc_final: 0.8267 (mttm) REVERT: C 87 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: D 46 MET cc_start: 0.8132 (mmm) cc_final: 0.7695 (mmm) REVERT: E 52 LEU cc_start: 0.9329 (mt) cc_final: 0.9060 (mt) REVERT: F 7 HIS cc_start: 0.7575 (t-90) cc_final: 0.5359 (m-70) outliers start: 26 outliers final: 23 residues processed: 213 average time/residue: 0.0969 time to fit residues: 30.9997 Evaluate side-chains 226 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 201 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 146 HIS Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 98 ASP Chi-restraints excluded: chain B residue 101 TRP Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 288 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 448 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 87 GLN Chi-restraints excluded: chain C residue 190 SER Chi-restraints excluded: chain C residue 347 HIS Chi-restraints excluded: chain E residue 41 LEU Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 42 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 113 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 GLN C 347 HIS ** E 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.150413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.113255 restraints weight = 22314.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116926 restraints weight = 11239.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119165 restraints weight = 7330.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120690 restraints weight = 5631.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.121615 restraints weight = 4751.062| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13260 Z= 0.119 Angle : 0.686 14.706 18024 Z= 0.337 Chirality : 0.044 0.231 2085 Planarity : 0.004 0.073 2256 Dihedral : 5.413 43.822 1845 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.72 % Allowed : 18.53 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.20), residues: 1677 helix: 1.25 (0.26), residues: 397 sheet: -0.59 (0.23), residues: 470 loop : -0.68 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 217 TYR 0.010 0.001 TYR A 304 PHE 0.021 0.001 PHE B 454 TRP 0.060 0.002 TRP E 35 HIS 0.009 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00258 (13239) covalent geometry : angle 0.68447 (17979) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.03576 ( 36) hydrogen bonds : bond 0.03675 ( 589) hydrogen bonds : angle 5.35684 ( 1605) link_NAG-ASN : bond 0.00114 ( 3) link_NAG-ASN : angle 1.31462 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2144.84 seconds wall clock time: 37 minutes 46.40 seconds (2266.40 seconds total)