Starting phenix.real_space_refine on Fri Sep 19 03:30:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.cif Found real_map, /net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.map" model { file = "/net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5i08_8069/09_2025/5i08_8069.cif" } resolution = 4.04 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= 0.000 sd= 0.006 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 120 5.16 5 C 14499 2.51 5 N 3723 2.21 5 O 4341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 183 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22683 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 958, 7561 Classifications: {'peptide': 958} Link IDs: {'PTRANS': 31, 'TRANS': 926} Chain breaks: 7 Restraints were copied for chains: B, C Time building chain proxies: 7.66, per 1000 atoms: 0.34 Number of scatterers: 22683 At special positions: 0 Unit cell: (146.72, 141.48, 151.96, 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 120 16.00 O 4341 8.00 N 3723 7.00 C 14499 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.02 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.02 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.06 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.08 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.06 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.10 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.04 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.05 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.04 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.04 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.10 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.02 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.06 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.06 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.08 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.08 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.06 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.06 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.10 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.10 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.04 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.04 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.05 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.05 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.04 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.04 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.04 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.04 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.10 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.10 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.09 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 953.7 nanoseconds 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5442 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 42 sheets defined 27.8% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.106A pdb=" N GLU A 252 " --> pdb=" O THR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 284 Processing helix chain 'A' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 4.048A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY A 380 " --> pdb=" O SER A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 907 Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 914 through 924 Processing helix chain 'A' and resid 934 through 941 Processing helix chain 'A' and resid 951 through 968 Processing helix chain 'A' and resid 978 through 988 Processing helix chain 'A' and resid 995 through 1000 Processing helix chain 'A' and resid 1002 through 1017 Processing helix chain 'A' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA A1021 " --> pdb=" O GLY A1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1018 through 1021' Processing helix chain 'A' and resid 1024 through 1046 Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU A1062 " --> pdb=" O LEU A1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A1064 " --> pdb=" O GLU A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1111 Processing helix chain 'B' and resid 88 through 91 Processing helix chain 'B' and resid 248 through 252 removed outlier: 4.106A pdb=" N GLU B 252 " --> pdb=" O THR B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 284 Processing helix chain 'B' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 4.049A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE B 379 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 380 " --> pdb=" O SER B 376 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 823 through 833 Processing helix chain 'B' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE B 839 " --> pdb=" O PHE B 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN B 840 " --> pdb=" O CYS B 836 " (cutoff:3.500A) Processing helix chain 'B' and resid 903 through 907 Processing helix chain 'B' and resid 908 through 910 No H-bonds generated for 'chain 'B' and resid 908 through 910' Processing helix chain 'B' and resid 914 through 924 Processing helix chain 'B' and resid 934 through 941 Processing helix chain 'B' and resid 951 through 968 Processing helix chain 'B' and resid 978 through 988 Processing helix chain 'B' and resid 995 through 1000 Processing helix chain 'B' and resid 1002 through 1017 Processing helix chain 'B' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA B1021 " --> pdb=" O GLY B1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1018 through 1021' Processing helix chain 'B' and resid 1024 through 1046 Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU B1062 " --> pdb=" O LEU B1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG B1064 " --> pdb=" O GLU B1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1111 Processing helix chain 'C' and resid 88 through 91 Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.105A pdb=" N GLU C 252 " --> pdb=" O THR C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 284 Processing helix chain 'C' and resid 285 through 295 removed outlier: 4.035A pdb=" N GLN C 291 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 4.049A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 344 Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 374 through 381 removed outlier: 3.912A pdb=" N PHE C 379 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY C 380 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.957A pdb=" N GLN C 402 " --> pdb=" O ASP C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 703 Processing helix chain 'C' and resid 823 through 833 Processing helix chain 'C' and resid 835 through 863 removed outlier: 3.999A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 903 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 914 through 924 Processing helix chain 'C' and resid 934 through 941 Processing helix chain 'C' and resid 951 through 968 Processing helix chain 'C' and resid 978 through 988 Processing helix chain 'C' and resid 995 through 1000 Processing helix chain 'C' and resid 1002 through 1017 Processing helix chain 'C' and resid 1018 through 1021 removed outlier: 3.951A pdb=" N ALA C1021 " --> pdb=" O GLY C1018 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1018 through 1021' Processing helix chain 'C' and resid 1024 through 1046 Processing helix chain 'C' and resid 1047 through 1049 No H-bonds generated for 'chain 'C' and resid 1047 through 1049' Processing helix chain 'C' and resid 1058 through 1065 removed outlier: 3.741A pdb=" N LEU C1062 " --> pdb=" O LEU C1058 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C1064 " --> pdb=" O GLU C1060 " (cutoff:3.500A) Processing helix chain 'C' and resid 1067 through 1111 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 39 removed outlier: 4.059A pdb=" N ARG A 34 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N PHE A 74 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN A 73 " --> pdb=" O PRO A 260 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 54 through 55 removed outlier: 6.377A pdb=" N VAL A 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP C 650 " --> pdb=" O ILE C 655 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE C 655 " --> pdb=" O ASP C 650 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 67 removed outlier: 6.408A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 111 through 112 Processing sheet with id=AA7, first strand: chain 'A' and resid 303 through 306 Processing sheet with id=AA8, first strand: chain 'A' and resid 317 through 319 removed outlier: 5.974A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE A 655 " --> pdb=" O ASP A 650 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP A 650 " --> pdb=" O ILE A 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AB3, first strand: chain 'A' and resid 456 through 458 Processing sheet with id=AB4, first strand: chain 'A' and resid 742 through 745 Processing sheet with id=AB5, first strand: chain 'A' and resid 797 through 801 Processing sheet with id=AB6, first strand: chain 'A' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB8, first strand: chain 'B' and resid 34 through 39 removed outlier: 4.058A pdb=" N ARG B 34 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE B 74 " --> pdb=" O SER B 36 " (cutoff:3.500A) removed outlier: 8.406A pdb=" N ASN B 73 " --> pdb=" O PRO B 260 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 59 through 67 removed outlier: 6.407A pdb=" N LEU B 267 " --> pdb=" O ALA B 279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA B 279 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 111 through 112 Processing sheet with id=AC3, first strand: chain 'B' and resid 303 through 306 Processing sheet with id=AC4, first strand: chain 'B' and resid 317 through 319 removed outlier: 5.974A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 655 " --> pdb=" O ASP B 650 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP B 650 " --> pdb=" O ILE B 655 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AC6, first strand: chain 'B' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AC8, first strand: chain 'B' and resid 456 through 458 Processing sheet with id=AC9, first strand: chain 'B' and resid 742 through 745 Processing sheet with id=AD1, first strand: chain 'B' and resid 797 through 801 Processing sheet with id=AD2, first strand: chain 'B' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AD4, first strand: chain 'C' and resid 34 through 39 removed outlier: 4.059A pdb=" N ARG C 34 " --> pdb=" O ASP C 76 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE C 74 " --> pdb=" O SER C 36 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N ASN C 73 " --> pdb=" O PRO C 260 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 59 through 67 removed outlier: 6.408A pdb=" N LEU C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ALA C 279 " --> pdb=" O LEU C 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 95 through 97 removed outlier: 3.511A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 111 through 112 Processing sheet with id=AD8, first strand: chain 'C' and resid 303 through 306 Processing sheet with id=AD9, first strand: chain 'C' and resid 337 through 339 Processing sheet with id=AE1, first strand: chain 'C' and resid 345 through 349 removed outlier: 6.551A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AE3, first strand: chain 'C' and resid 456 through 458 Processing sheet with id=AE4, first strand: chain 'C' and resid 742 through 745 Processing sheet with id=AE5, first strand: chain 'C' and resid 797 through 801 Processing sheet with id=AE6, first strand: chain 'C' and resid 809 through 812 removed outlier: 3.871A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2541 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: 5.12 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5999 1.33 - 1.45: 6525 1.45 - 1.58: 10534 1.58 - 1.71: 0 1.71 - 1.83: 141 Bond restraints: 23199 Sorted by residual: bond pdb=" CA ASP B 281 " pdb=" C ASP B 281 " ideal model delta sigma weight residual 1.526 1.469 0.058 1.21e-02 6.83e+03 2.28e+01 bond pdb=" CA ASP A 281 " pdb=" C ASP A 281 " ideal model delta sigma weight residual 1.526 1.469 0.058 1.21e-02 6.83e+03 2.26e+01 bond pdb=" CA ASP C 281 " pdb=" C ASP C 281 " ideal model delta sigma weight residual 1.526 1.469 0.057 1.21e-02 6.83e+03 2.25e+01 bond pdb=" CA LEU C 624 " pdb=" C LEU C 624 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.44e+01 bond pdb=" CA LEU B 624 " pdb=" C LEU B 624 " ideal model delta sigma weight residual 1.521 1.477 0.044 1.17e-02 7.31e+03 1.42e+01 ... (remaining 23194 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 27928 2.57 - 5.14: 2988 5.14 - 7.71: 542 7.71 - 10.28: 81 10.28 - 12.85: 15 Bond angle restraints: 31554 Sorted by residual: angle pdb=" C LEU A 946 " pdb=" N PRO A 947 " pdb=" CA PRO A 947 " ideal model delta sigma weight residual 119.66 127.71 -8.05 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C LEU B 946 " pdb=" N PRO B 947 " pdb=" CA PRO B 947 " ideal model delta sigma weight residual 119.66 127.71 -8.05 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C LEU C 946 " pdb=" N PRO C 947 " pdb=" CA PRO C 947 " ideal model delta sigma weight residual 119.66 127.70 -8.04 7.20e-01 1.93e+00 1.25e+02 angle pdb=" C PRO B 947 " pdb=" N PRO B 948 " pdb=" CA PRO B 948 " ideal model delta sigma weight residual 119.85 130.45 -10.60 1.01e+00 9.80e-01 1.10e+02 angle pdb=" C PRO C 947 " pdb=" N PRO C 948 " pdb=" CA PRO C 948 " ideal model delta sigma weight residual 119.85 130.44 -10.59 1.01e+00 9.80e-01 1.10e+02 ... (remaining 31549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 13287 17.42 - 34.84: 321 34.84 - 52.26: 87 52.26 - 69.68: 24 69.68 - 87.10: 3 Dihedral angle restraints: 13722 sinusoidal: 5268 harmonic: 8454 Sorted by residual: dihedral pdb=" CB CYS B 814 " pdb=" SG CYS B 814 " pdb=" SG CYS B 836 " pdb=" CB CYS B 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.76 53.76 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS A 814 " pdb=" SG CYS A 814 " pdb=" SG CYS A 836 " pdb=" CB CYS A 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.76 53.76 1 1.00e+01 1.00e-02 3.92e+01 dihedral pdb=" CB CYS C 814 " pdb=" SG CYS C 814 " pdb=" SG CYS C 836 " pdb=" CB CYS C 836 " ideal model delta sinusoidal sigma weight residual -86.00 -139.75 53.75 1 1.00e+01 1.00e-02 3.92e+01 ... (remaining 13719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2781 0.103 - 0.207: 690 0.207 - 0.310: 84 0.310 - 0.414: 12 0.414 - 0.517: 3 Chirality restraints: 3570 Sorted by residual: chirality pdb=" CA PHE A 802 " pdb=" N PHE A 802 " pdb=" C PHE A 802 " pdb=" CB PHE A 802 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA PHE C 802 " pdb=" N PHE C 802 " pdb=" C PHE C 802 " pdb=" CB PHE C 802 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.68e+00 chirality pdb=" CA PHE B 802 " pdb=" N PHE B 802 " pdb=" C PHE B 802 " pdb=" CB PHE B 802 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.62e+00 ... (remaining 3567 not shown) Planarity restraints: 4047 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 218 " -0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO A 219 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO A 219 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 219 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET C 218 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO C 219 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO C 219 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 219 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 218 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO B 219 " -0.186 5.00e-02 4.00e+02 pdb=" CA PRO B 219 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 219 " 0.057 5.00e-02 4.00e+02 ... (remaining 4044 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 2441 2.72 - 3.26: 23866 3.26 - 3.81: 36374 3.81 - 4.35: 45822 4.35 - 4.90: 74355 Nonbonded interactions: 182858 Sorted by model distance: nonbonded pdb=" O PHE B 802 " pdb=" CD1 PHE B 802 " model vdw 2.174 3.340 nonbonded pdb=" O PHE A 802 " pdb=" CD1 PHE A 802 " model vdw 2.175 3.340 nonbonded pdb=" O PHE C 802 " pdb=" CD1 PHE C 802 " model vdw 2.175 3.340 nonbonded pdb=" OG1 THR B 123 " pdb=" O VAL B 139 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.283 3.040 ... (remaining 182853 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 24.470 Find NCS groups from input model: 0.320 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: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 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 : 0.014 0.072 23244 Z= 0.923 Angle : 1.751 12.847 31644 Z= 1.186 Chirality : 0.090 0.517 3570 Planarity : 0.009 0.108 4047 Dihedral : 8.794 87.098 8145 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.85 % Allowed : 7.01 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.15), residues: 2826 helix: 0.03 (0.17), residues: 657 sheet: 0.75 (0.19), residues: 612 loop : 0.53 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 397 TYR 0.043 0.007 TYR B 49 PHE 0.028 0.004 PHE C 98 TRP 0.032 0.007 TRP C 332 HIS 0.006 0.001 HIS B1145 Details of bonding type rmsd covalent geometry : bond 0.01433 (23199) covalent geometry : angle 1.74449 (31554) SS BOND : bond 0.03146 ( 45) SS BOND : angle 3.35486 ( 90) hydrogen bonds : bond 0.17787 ( 925) hydrogen bonds : angle 7.49426 ( 2541) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 614 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 267 LEU cc_start: 0.8863 (tp) cc_final: 0.8510 (tp) REVERT: A 578 ASP cc_start: 0.7728 (t0) cc_final: 0.7331 (t0) REVERT: A 593 ILE cc_start: 0.8164 (mt) cc_final: 0.7510 (mt) REVERT: A 967 MET cc_start: 0.6827 (tpp) cc_final: 0.6347 (tpp) REVERT: A 1094 SER cc_start: 0.8775 (m) cc_final: 0.8414 (p) REVERT: B 152 GLN cc_start: 0.7963 (mt0) cc_final: 0.7744 (pt0) REVERT: B 182 LEU cc_start: 0.7148 (mt) cc_final: 0.6564 (mt) REVERT: B 257 TRP cc_start: 0.6947 (m-10) cc_final: 0.6622 (m-10) REVERT: B 281 ASP cc_start: 0.7581 (t0) cc_final: 0.7132 (t0) REVERT: B 593 ILE cc_start: 0.8290 (mt) cc_final: 0.8012 (mm) REVERT: B 701 LEU cc_start: 0.8227 (tp) cc_final: 0.8007 (tt) REVERT: B 967 MET cc_start: 0.7211 (tpp) cc_final: 0.6880 (tpt) REVERT: C 135 TYR cc_start: 0.7971 (m-80) cc_final: 0.7322 (m-10) REVERT: C 137 ILE cc_start: 0.8394 (mt) cc_final: 0.8095 (mm) REVERT: C 152 GLN cc_start: 0.8069 (mt0) cc_final: 0.7683 (mt0) REVERT: C 182 LEU cc_start: 0.7501 (mt) cc_final: 0.7014 (mp) REVERT: C 203 TYR cc_start: 0.7779 (p90) cc_final: 0.7508 (p90) REVERT: C 257 TRP cc_start: 0.7399 (m-10) cc_final: 0.6701 (m-10) REVERT: C 281 ASP cc_start: 0.7796 (t0) cc_final: 0.7302 (t0) REVERT: C 425 LEU cc_start: 0.9024 (tp) cc_final: 0.8132 (tt) REVERT: C 439 PHE cc_start: 0.3510 (m-80) cc_final: 0.3207 (m-80) REVERT: C 593 ILE cc_start: 0.8479 (mt) cc_final: 0.8097 (mm) REVERT: C 770 PHE cc_start: 0.6292 (p90) cc_final: 0.6087 (p90) REVERT: C 1094 SER cc_start: 0.8704 (m) cc_final: 0.8372 (p) outliers start: 0 outliers final: 0 residues processed: 614 average time/residue: 0.1591 time to fit residues: 152.9932 Evaluate side-chains 280 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 269 ASN ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 470 ASN A 646 ASN A 838 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 269 ASN B 437 ASN B 470 ASN ** B 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1046 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS C 269 ASN C 437 ASN C 470 ASN ** C 646 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 821 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.112355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.098398 restraints weight = 55872.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.100718 restraints weight = 34088.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.102386 restraints weight = 23327.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.103574 restraints weight = 17423.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.104419 restraints weight = 13929.957| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23244 Z= 0.168 Angle : 0.754 9.332 31644 Z= 0.424 Chirality : 0.045 0.151 3570 Planarity : 0.005 0.081 4047 Dihedral : 6.196 26.781 3099 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.76 % Favored : 92.60 % Rotamer: Outliers : 0.16 % Allowed : 1.63 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.15), residues: 2826 helix: 1.17 (0.20), residues: 681 sheet: 0.20 (0.20), residues: 579 loop : -0.54 (0.15), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 398 TYR 0.025 0.002 TYR B 49 PHE 0.024 0.002 PHE C 968 TRP 0.027 0.002 TRP A 257 HIS 0.011 0.002 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00344 (23199) covalent geometry : angle 0.74858 (31554) SS BOND : bond 0.00498 ( 45) SS BOND : angle 1.80466 ( 90) hydrogen bonds : bond 0.06281 ( 925) hydrogen bonds : angle 6.04954 ( 2541) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 460 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8423 (mm) cc_final: 0.8133 (mt) REVERT: A 137 ILE cc_start: 0.9363 (mt) cc_final: 0.8930 (mm) REVERT: A 182 LEU cc_start: 0.8177 (mt) cc_final: 0.7514 (tt) REVERT: A 383 PHE cc_start: 0.7893 (m-80) cc_final: 0.7586 (m-80) REVERT: A 415 LYS cc_start: 0.6780 (mtmt) cc_final: 0.6314 (mttt) REVERT: A 470 ASN cc_start: 0.7829 (OUTLIER) cc_final: 0.7233 (m-40) REVERT: A 593 ILE cc_start: 0.9241 (mt) cc_final: 0.8931 (mt) REVERT: A 831 GLU cc_start: 0.7943 (pp20) cc_final: 0.7650 (pp20) REVERT: A 994 MET cc_start: 0.5254 (ttt) cc_final: 0.4835 (ttt) REVERT: A 1023 ASN cc_start: 0.7248 (p0) cc_final: 0.6504 (p0) REVERT: A 1038 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7241 (tm-30) REVERT: A 1094 SER cc_start: 0.8772 (m) cc_final: 0.8331 (p) REVERT: B 15 ILE cc_start: 0.8389 (mm) cc_final: 0.8054 (mt) REVERT: B 164 LYS cc_start: 0.8189 (mptt) cc_final: 0.7980 (mptt) REVERT: B 281 ASP cc_start: 0.7773 (t0) cc_final: 0.7010 (t0) REVERT: B 330 ASP cc_start: 0.7950 (p0) cc_final: 0.7514 (p0) REVERT: B 967 MET cc_start: 0.7724 (tpp) cc_final: 0.7170 (tpt) REVERT: B 1023 ASN cc_start: 0.7294 (p0) cc_final: 0.6616 (p0) REVERT: B 1045 GLN cc_start: 0.8636 (tt0) cc_final: 0.8324 (tp40) REVERT: B 1060 GLU cc_start: 0.7173 (tp30) cc_final: 0.6911 (tp30) REVERT: B 1079 ASN cc_start: 0.8317 (t0) cc_final: 0.7930 (t0) REVERT: B 1088 TYR cc_start: 0.9147 (t80) cc_final: 0.8931 (t80) REVERT: B 1122 ASN cc_start: 0.7078 (t0) cc_final: 0.6623 (t0) REVERT: C 137 ILE cc_start: 0.9394 (mt) cc_final: 0.8981 (mm) REVERT: C 206 ARG cc_start: 0.8036 (mtp-110) cc_final: 0.7832 (mtp85) REVERT: C 281 ASP cc_start: 0.7365 (t0) cc_final: 0.6820 (t0) REVERT: C 330 ASP cc_start: 0.8069 (p0) cc_final: 0.7489 (p0) REVERT: C 405 SER cc_start: 0.7790 (p) cc_final: 0.7542 (t) REVERT: C 439 PHE cc_start: 0.4302 (m-80) cc_final: 0.3777 (m-80) REVERT: C 851 ASP cc_start: 0.7640 (m-30) cc_final: 0.7421 (m-30) REVERT: C 967 MET cc_start: 0.7048 (tpt) cc_final: 0.5572 (tpp) REVERT: C 1023 ASN cc_start: 0.6996 (p0) cc_final: 0.6473 (p0) REVERT: C 1139 TYR cc_start: 0.8375 (m-80) cc_final: 0.8033 (m-10) outliers start: 4 outliers final: 0 residues processed: 463 average time/residue: 0.1414 time to fit residues: 107.1139 Evaluate side-chains 282 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 281 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 239 optimal weight: 20.0000 chunk 264 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 95 optimal weight: 8.9990 chunk 283 optimal weight: 1.9990 chunk 192 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN A 204 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 470 ASN B 595 ASN B 646 ASN B 859 ASN B 998 ASN ** B1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN C 821 ASN C 998 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.100372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.086805 restraints weight = 58037.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088795 restraints weight = 35602.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090329 restraints weight = 24791.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091372 restraints weight = 18760.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092133 restraints weight = 15163.074| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.065 23244 Z= 0.345 Angle : 0.908 9.741 31644 Z= 0.494 Chirality : 0.051 0.224 3570 Planarity : 0.006 0.070 4047 Dihedral : 6.528 33.362 3099 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.39 % Favored : 90.98 % Rotamer: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.09 (0.15), residues: 2826 helix: 0.45 (0.19), residues: 675 sheet: -0.89 (0.20), residues: 552 loop : -1.17 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 396 TYR 0.028 0.003 TYR A 49 PHE 0.035 0.003 PHE C 270 TRP 0.021 0.002 TRP A 444 HIS 0.019 0.004 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00773 (23199) covalent geometry : angle 0.90215 (31554) SS BOND : bond 0.00848 ( 45) SS BOND : angle 2.10548 ( 90) hydrogen bonds : bond 0.06235 ( 925) hydrogen bonds : angle 6.24658 ( 2541) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 351 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ASP cc_start: 0.7894 (t0) cc_final: 0.7150 (t0) REVERT: A 289 GLU cc_start: 0.8398 (tp30) cc_final: 0.8157 (tp30) REVERT: A 383 PHE cc_start: 0.8274 (m-80) cc_final: 0.7871 (m-80) REVERT: A 439 PHE cc_start: 0.5046 (m-80) cc_final: 0.4753 (m-80) REVERT: A 593 ILE cc_start: 0.9397 (mt) cc_final: 0.9180 (mm) REVERT: A 851 ASP cc_start: 0.7704 (m-30) cc_final: 0.7500 (m-30) REVERT: B 164 LYS cc_start: 0.8352 (mptt) cc_final: 0.8005 (mptt) REVERT: B 281 ASP cc_start: 0.8143 (t0) cc_final: 0.7655 (t70) REVERT: B 415 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6681 (mttt) REVERT: B 593 ILE cc_start: 0.9357 (mm) cc_final: 0.9093 (mt) REVERT: B 676 ARG cc_start: 0.7335 (ttp-110) cc_final: 0.7062 (ttp80) REVERT: B 851 ASP cc_start: 0.7484 (m-30) cc_final: 0.7238 (m-30) REVERT: B 952 GLU cc_start: 0.7688 (pp20) cc_final: 0.7359 (pp20) REVERT: B 967 MET cc_start: 0.7905 (tpp) cc_final: 0.7442 (tpt) REVERT: B 971 TRP cc_start: 0.2448 (m100) cc_final: 0.0438 (m100) REVERT: B 1023 ASN cc_start: 0.7169 (p0) cc_final: 0.6547 (p0) REVERT: B 1079 ASN cc_start: 0.8484 (t0) cc_final: 0.8276 (t0) REVERT: B 1097 THR cc_start: 0.9502 (m) cc_final: 0.9263 (p) REVERT: B 1122 ASN cc_start: 0.7299 (t0) cc_final: 0.6847 (t0) REVERT: C 281 ASP cc_start: 0.7928 (t0) cc_final: 0.7518 (t0) REVERT: C 289 GLU cc_start: 0.8376 (tp30) cc_final: 0.8080 (tp30) REVERT: C 330 ASP cc_start: 0.8329 (p0) cc_final: 0.8045 (p0) REVERT: C 405 SER cc_start: 0.8213 (p) cc_final: 0.7997 (t) REVERT: C 745 ASP cc_start: 0.6350 (t0) cc_final: 0.6148 (t0) REVERT: C 851 ASP cc_start: 0.7660 (m-30) cc_final: 0.7451 (m-30) REVERT: C 952 GLU cc_start: 0.7594 (pp20) cc_final: 0.7296 (pp20) REVERT: C 1023 ASN cc_start: 0.6841 (p0) cc_final: 0.6119 (p0) REVERT: C 1112 GLU cc_start: 0.7217 (tp30) cc_final: 0.6983 (tp30) REVERT: C 1116 SER cc_start: 0.8823 (m) cc_final: 0.8444 (t) outliers start: 5 outliers final: 0 residues processed: 354 average time/residue: 0.1358 time to fit residues: 80.0738 Evaluate side-chains 236 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 189 optimal weight: 0.7980 chunk 249 optimal weight: 6.9990 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 104 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 chunk 80 optimal weight: 0.4980 chunk 202 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 821 ASN A1034 ASN A1045 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN ** B 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** C 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 821 ASN C1034 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.105893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.092049 restraints weight = 55810.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094238 restraints weight = 33948.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095834 restraints weight = 23329.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096927 restraints weight = 17480.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.097784 restraints weight = 14037.812| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 23244 Z= 0.141 Angle : 0.694 12.485 31644 Z= 0.378 Chirality : 0.043 0.206 3570 Planarity : 0.005 0.066 4047 Dihedral : 5.926 32.935 3099 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.67 % Allowed : 8.21 % Favored : 91.12 % Rotamer: Outliers : 0.19 % Allowed : 2.13 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.97 (0.15), residues: 2826 helix: 1.11 (0.20), residues: 666 sheet: -0.85 (0.20), residues: 564 loop : -1.36 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 396 TYR 0.040 0.002 TYR A 266 PHE 0.021 0.002 PHE C 589 TRP 0.021 0.001 TRP C 332 HIS 0.012 0.002 HIS A 175 Details of bonding type rmsd covalent geometry : bond 0.00303 (23199) covalent geometry : angle 0.68977 (31554) SS BOND : bond 0.00716 ( 45) SS BOND : angle 1.58190 ( 90) hydrogen bonds : bond 0.05056 ( 925) hydrogen bonds : angle 5.73950 ( 2541) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 361 time to evaluate : 0.779 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 54 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8544 (ttm110) REVERT: A 77 LEU cc_start: 0.9039 (tp) cc_final: 0.8829 (tt) REVERT: A 231 ILE cc_start: 0.9249 (mm) cc_final: 0.8893 (tt) REVERT: A 254 LEU cc_start: 0.8310 (pt) cc_final: 0.7884 (mt) REVERT: A 330 ASP cc_start: 0.7909 (p0) cc_final: 0.7656 (p0) REVERT: A 593 ILE cc_start: 0.9417 (mt) cc_final: 0.9176 (mm) REVERT: A 952 GLU cc_start: 0.7250 (pp20) cc_final: 0.6945 (pp20) REVERT: A 1023 ASN cc_start: 0.7430 (p0) cc_final: 0.7003 (p0) REVERT: A 1094 SER cc_start: 0.8853 (m) cc_final: 0.8311 (p) REVERT: B 54 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8635 (ttm110) REVERT: B 164 LYS cc_start: 0.8235 (mptt) cc_final: 0.7966 (mptt) REVERT: B 593 ILE cc_start: 0.9389 (mm) cc_final: 0.9056 (mt) REVERT: B 813 ASP cc_start: 0.7643 (t0) cc_final: 0.7341 (t0) REVERT: B 851 ASP cc_start: 0.7660 (m-30) cc_final: 0.7444 (m-30) REVERT: B 952 GLU cc_start: 0.7598 (pp20) cc_final: 0.7361 (pp20) REVERT: B 967 MET cc_start: 0.8203 (tpp) cc_final: 0.7641 (tpt) REVERT: B 1023 ASN cc_start: 0.7268 (p0) cc_final: 0.6390 (p0) REVERT: B 1079 ASN cc_start: 0.8383 (t0) cc_final: 0.7976 (t0) REVERT: B 1122 ASN cc_start: 0.7063 (t0) cc_final: 0.6562 (t0) REVERT: C 15 ILE cc_start: 0.8795 (mm) cc_final: 0.8441 (mt) REVERT: C 405 SER cc_start: 0.8270 (p) cc_final: 0.7976 (t) REVERT: C 967 MET cc_start: 0.7880 (tpt) cc_final: 0.5709 (tpp) REVERT: C 1023 ASN cc_start: 0.6812 (p0) cc_final: 0.5989 (p0) REVERT: C 1112 GLU cc_start: 0.7285 (tp30) cc_final: 0.6978 (tp30) REVERT: C 1116 SER cc_start: 0.8536 (m) cc_final: 0.8201 (t) outliers start: 5 outliers final: 1 residues processed: 366 average time/residue: 0.1305 time to fit residues: 78.7325 Evaluate side-chains 249 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 248 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 189 optimal weight: 5.9990 chunk 282 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 234 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 185 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 281 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 265 optimal weight: 0.0010 chunk 100 optimal weight: 0.0570 overall best weight: 0.5706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 437 ASN A 595 ASN A 646 ASN A 821 ASN A1045 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 402 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B 821 ASN ** B1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 821 ASN ** C1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.107880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093750 restraints weight = 55450.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.096002 restraints weight = 33305.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097623 restraints weight = 22722.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098651 restraints weight = 16965.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099530 restraints weight = 13757.526| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 23244 Z= 0.132 Angle : 0.669 14.283 31644 Z= 0.361 Chirality : 0.042 0.294 3570 Planarity : 0.005 0.066 4047 Dihedral : 5.574 28.764 3099 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.89 % Favored : 91.47 % Rotamer: Outliers : 0.19 % Allowed : 1.86 % Favored : 97.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.86 (0.15), residues: 2826 helix: 1.36 (0.21), residues: 666 sheet: -0.52 (0.22), residues: 489 loop : -1.47 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 676 TYR 0.027 0.002 TYR B 266 PHE 0.018 0.001 PHE C 589 TRP 0.016 0.001 TRP A 444 HIS 0.007 0.001 HIS A1129 Details of bonding type rmsd covalent geometry : bond 0.00288 (23199) covalent geometry : angle 0.66074 (31554) SS BOND : bond 0.00589 ( 45) SS BOND : angle 2.06181 ( 90) hydrogen bonds : bond 0.04595 ( 925) hydrogen bonds : angle 5.47939 ( 2541) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 371 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8077 (mm) cc_final: 0.7731 (mt) REVERT: A 54 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8319 (ttm110) REVERT: A 77 LEU cc_start: 0.9042 (tp) cc_final: 0.8822 (tt) REVERT: A 231 ILE cc_start: 0.9259 (mm) cc_final: 0.8874 (tt) REVERT: A 254 LEU cc_start: 0.8543 (pt) cc_final: 0.8090 (mt) REVERT: A 578 ASP cc_start: 0.8076 (t70) cc_final: 0.7651 (t0) REVERT: A 593 ILE cc_start: 0.9418 (mt) cc_final: 0.9189 (mm) REVERT: A 863 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7954 (tm-30) REVERT: A 952 GLU cc_start: 0.7264 (pp20) cc_final: 0.7001 (pp20) REVERT: A 1023 ASN cc_start: 0.7632 (p0) cc_final: 0.7234 (p0) REVERT: B 54 ARG cc_start: 0.8825 (ttm110) cc_final: 0.8597 (ttm110) REVERT: B 164 LYS cc_start: 0.8303 (mptt) cc_final: 0.8057 (mptt) REVERT: B 231 ILE cc_start: 0.9072 (mm) cc_final: 0.8810 (tt) REVERT: B 578 ASP cc_start: 0.8024 (t70) cc_final: 0.7649 (t0) REVERT: B 967 MET cc_start: 0.8043 (tpp) cc_final: 0.7737 (tpp) REVERT: B 997 LEU cc_start: 0.7380 (tp) cc_final: 0.6930 (tp) REVERT: B 1023 ASN cc_start: 0.7254 (p0) cc_final: 0.6344 (p0) REVERT: B 1079 ASN cc_start: 0.8543 (t0) cc_final: 0.8185 (t0) REVERT: B 1094 SER cc_start: 0.9136 (m) cc_final: 0.8693 (p) REVERT: B 1122 ASN cc_start: 0.6962 (t0) cc_final: 0.6589 (t0) REVERT: C 15 ILE cc_start: 0.8426 (mm) cc_final: 0.8104 (mt) REVERT: C 330 ASP cc_start: 0.8326 (p0) cc_final: 0.8123 (p0) REVERT: C 649 TYR cc_start: 0.8025 (m-80) cc_final: 0.7793 (m-10) REVERT: C 676 ARG cc_start: 0.7101 (ttp80) cc_final: 0.6890 (mmp80) REVERT: C 829 LEU cc_start: 0.8135 (mt) cc_final: 0.7808 (mm) REVERT: C 851 ASP cc_start: 0.7509 (m-30) cc_final: 0.7254 (m-30) REVERT: C 967 MET cc_start: 0.7779 (tpt) cc_final: 0.5829 (tpp) REVERT: C 971 TRP cc_start: 0.2217 (m100) cc_final: 0.0643 (m100) REVERT: C 997 LEU cc_start: 0.7462 (tp) cc_final: 0.7079 (tp) REVERT: C 1023 ASN cc_start: 0.7112 (p0) cc_final: 0.6165 (p0) REVERT: C 1060 GLU cc_start: 0.6836 (tp30) cc_final: 0.6625 (tp30) REVERT: C 1116 SER cc_start: 0.8492 (m) cc_final: 0.8263 (t) outliers start: 5 outliers final: 0 residues processed: 376 average time/residue: 0.1266 time to fit residues: 78.1034 Evaluate side-chains 259 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 147 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 242 optimal weight: 0.8980 chunk 259 optimal weight: 3.9990 chunk 219 optimal weight: 6.9990 chunk 179 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 260 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 821 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 HIS B 175 HIS B 204 GLN B 470 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 821 ASN B 859 ASN ** B1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 175 HIS ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN ** C 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 646 ASN C 821 ASN C1145 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.102137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088644 restraints weight = 57204.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090677 restraints weight = 35204.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092146 restraints weight = 24461.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093187 restraints weight = 18579.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.093923 restraints weight = 15050.582| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23244 Z= 0.256 Angle : 0.779 12.938 31644 Z= 0.416 Chirality : 0.046 0.313 3570 Planarity : 0.005 0.069 4047 Dihedral : 5.857 32.202 3099 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.73 % Favored : 89.63 % Rotamer: Outliers : 0.19 % Allowed : 2.48 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.35 (0.15), residues: 2826 helix: 0.92 (0.21), residues: 660 sheet: -0.90 (0.21), residues: 522 loop : -1.73 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 206 TYR 0.031 0.002 TYR C 50 PHE 0.019 0.002 PHE C 270 TRP 0.021 0.002 TRP A 444 HIS 0.015 0.003 HIS C1129 Details of bonding type rmsd covalent geometry : bond 0.00585 (23199) covalent geometry : angle 0.77095 (31554) SS BOND : bond 0.00794 ( 45) SS BOND : angle 2.18338 ( 90) hydrogen bonds : bond 0.05182 ( 925) hydrogen bonds : angle 5.80853 ( 2541) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 315 time to evaluate : 0.915 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 54 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8603 (ttm110) REVERT: A 231 ILE cc_start: 0.9194 (mm) cc_final: 0.8812 (tt) REVERT: A 593 ILE cc_start: 0.9428 (mt) cc_final: 0.9187 (mm) REVERT: A 595 ASN cc_start: 0.8379 (m110) cc_final: 0.8166 (p0) REVERT: A 863 GLN cc_start: 0.8281 (tm-30) cc_final: 0.7971 (pp30) REVERT: A 997 LEU cc_start: 0.7998 (tp) cc_final: 0.7575 (tp) REVERT: A 1023 ASN cc_start: 0.7405 (p0) cc_final: 0.6976 (p0) REVERT: A 1094 SER cc_start: 0.8827 (m) cc_final: 0.8454 (p) REVERT: A 1111 ASN cc_start: 0.8700 (m-40) cc_final: 0.8486 (t0) REVERT: B 164 LYS cc_start: 0.8273 (mptt) cc_final: 0.8033 (mptt) REVERT: B 231 ILE cc_start: 0.9045 (mm) cc_final: 0.8719 (tt) REVERT: B 281 ASP cc_start: 0.7756 (t0) cc_final: 0.7037 (t0) REVERT: B 967 MET cc_start: 0.7952 (tpp) cc_final: 0.7655 (tpp) REVERT: B 1023 ASN cc_start: 0.7136 (p0) cc_final: 0.6199 (p0) REVERT: B 1122 ASN cc_start: 0.7021 (t0) cc_final: 0.6721 (t0) REVERT: C 15 ILE cc_start: 0.8654 (mm) cc_final: 0.8262 (mt) REVERT: C 77 LEU cc_start: 0.9019 (tp) cc_final: 0.8702 (tt) REVERT: C 330 ASP cc_start: 0.8179 (p0) cc_final: 0.7947 (p0) REVERT: C 439 PHE cc_start: 0.4565 (m-80) cc_final: 0.4007 (m-80) REVERT: C 1023 ASN cc_start: 0.6944 (p0) cc_final: 0.6200 (p0) REVERT: C 1111 ASN cc_start: 0.9017 (m-40) cc_final: 0.8320 (m110) REVERT: C 1116 SER cc_start: 0.8701 (m) cc_final: 0.8355 (t) REVERT: C 1122 ASN cc_start: 0.7103 (m110) cc_final: 0.6897 (m-40) outliers start: 5 outliers final: 0 residues processed: 320 average time/residue: 0.1425 time to fit residues: 75.3268 Evaluate side-chains 232 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 101 optimal weight: 0.0980 chunk 71 optimal weight: 7.9990 chunk 259 optimal weight: 3.9990 chunk 86 optimal weight: 5.9990 chunk 260 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 234 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 821 ASN A 938 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN ** B 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 ASN B1145 HIS C 152 GLN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN C 821 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.103164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.089291 restraints weight = 57103.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.091455 restraints weight = 34546.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.092990 restraints weight = 23715.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.094078 restraints weight = 17809.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.094877 restraints weight = 14308.810| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 23244 Z= 0.196 Angle : 0.734 15.089 31644 Z= 0.391 Chirality : 0.045 0.320 3570 Planarity : 0.005 0.062 4047 Dihedral : 5.747 30.658 3099 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.38 % Favored : 89.99 % Rotamer: Outliers : 0.08 % Allowed : 1.01 % Favored : 98.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.42 (0.15), residues: 2826 helix: 1.08 (0.21), residues: 651 sheet: -0.91 (0.22), residues: 462 loop : -1.86 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 75 TYR 0.023 0.002 TYR A 49 PHE 0.021 0.002 PHE C 18 TRP 0.014 0.001 TRP C 444 HIS 0.024 0.002 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00451 (23199) covalent geometry : angle 0.72556 (31554) SS BOND : bond 0.00748 ( 45) SS BOND : angle 2.20651 ( 90) hydrogen bonds : bond 0.04915 ( 925) hydrogen bonds : angle 5.72136 ( 2541) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8562 (mm) cc_final: 0.8090 (mt) REVERT: A 54 ARG cc_start: 0.8837 (ttm110) cc_final: 0.8518 (ttm110) REVERT: A 77 LEU cc_start: 0.9271 (tp) cc_final: 0.9038 (tt) REVERT: A 231 ILE cc_start: 0.9242 (mm) cc_final: 0.8887 (tt) REVERT: A 289 GLU cc_start: 0.8421 (tp30) cc_final: 0.8037 (tp30) REVERT: A 578 ASP cc_start: 0.8119 (t70) cc_final: 0.7688 (t0) REVERT: A 593 ILE cc_start: 0.9439 (mt) cc_final: 0.9163 (mm) REVERT: A 595 ASN cc_start: 0.8535 (m110) cc_final: 0.8209 (p0) REVERT: A 863 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7927 (pp30) REVERT: A 1023 ASN cc_start: 0.7476 (p0) cc_final: 0.7037 (p0) REVERT: A 1038 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7680 (tm-30) REVERT: A 1112 GLU cc_start: 0.6914 (tm-30) cc_final: 0.6638 (tm-30) REVERT: B 27 ASP cc_start: 0.8057 (m-30) cc_final: 0.7846 (t0) REVERT: B 54 ARG cc_start: 0.9038 (ttm110) cc_final: 0.8793 (ttm110) REVERT: B 164 LYS cc_start: 0.8277 (mptt) cc_final: 0.8017 (mptt) REVERT: B 289 GLU cc_start: 0.8523 (tp30) cc_final: 0.8009 (tp30) REVERT: B 578 ASP cc_start: 0.8180 (t70) cc_final: 0.7811 (t0) REVERT: B 967 MET cc_start: 0.7847 (tpp) cc_final: 0.7304 (tpp) REVERT: B 1023 ASN cc_start: 0.7157 (p0) cc_final: 0.6154 (p0) REVERT: B 1122 ASN cc_start: 0.6956 (t0) cc_final: 0.6565 (t0) REVERT: C 77 LEU cc_start: 0.9081 (tp) cc_final: 0.8771 (tt) REVERT: C 439 PHE cc_start: 0.4508 (m-80) cc_final: 0.4283 (m-80) REVERT: C 648 LEU cc_start: 0.7982 (tp) cc_final: 0.7760 (tt) REVERT: C 851 ASP cc_start: 0.7683 (m-30) cc_final: 0.7428 (m-30) REVERT: C 1023 ASN cc_start: 0.7072 (p0) cc_final: 0.6228 (p0) REVERT: C 1111 ASN cc_start: 0.8971 (m-40) cc_final: 0.8099 (m110) REVERT: C 1116 SER cc_start: 0.8600 (m) cc_final: 0.8299 (t) REVERT: C 1122 ASN cc_start: 0.7273 (m110) cc_final: 0.7018 (m-40) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.1366 time to fit residues: 73.6725 Evaluate side-chains 235 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 22 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 280 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 274 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 595 ASN B 646 ASN B 859 ASN B 938 GLN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.091120 restraints weight = 56103.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.093306 restraints weight = 33806.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094832 restraints weight = 23137.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095992 restraints weight = 17399.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.096684 restraints weight = 13914.859| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 23244 Z= 0.149 Angle : 0.687 15.696 31644 Z= 0.365 Chirality : 0.043 0.286 3570 Planarity : 0.005 0.093 4047 Dihedral : 5.497 27.371 3099 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.55 % Favored : 89.81 % Rotamer: Outliers : 0.08 % Allowed : 0.54 % Favored : 99.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.35 (0.15), residues: 2826 helix: 1.32 (0.21), residues: 651 sheet: -0.97 (0.21), residues: 504 loop : -1.87 (0.14), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 75 TYR 0.020 0.002 TYR B 266 PHE 0.021 0.001 PHE B 589 TRP 0.029 0.001 TRP A 444 HIS 0.013 0.002 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00336 (23199) covalent geometry : angle 0.68220 (31554) SS BOND : bond 0.00744 ( 45) SS BOND : angle 1.72550 ( 90) hydrogen bonds : bond 0.04558 ( 925) hydrogen bonds : angle 5.53031 ( 2541) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 308 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ILE cc_start: 0.8458 (mm) cc_final: 0.8026 (mt) REVERT: A 54 ARG cc_start: 0.8802 (ttm110) cc_final: 0.8138 (ttm110) REVERT: A 155 MET cc_start: 0.7412 (mtm) cc_final: 0.6965 (mtm) REVERT: A 231 ILE cc_start: 0.9214 (mm) cc_final: 0.8890 (tt) REVERT: A 578 ASP cc_start: 0.8135 (t70) cc_final: 0.7747 (t0) REVERT: A 593 ILE cc_start: 0.9381 (mt) cc_final: 0.9169 (mm) REVERT: A 863 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7858 (pp30) REVERT: A 952 GLU cc_start: 0.7175 (pp20) cc_final: 0.6820 (pp20) REVERT: A 1023 ASN cc_start: 0.7385 (p0) cc_final: 0.6931 (p0) REVERT: B 27 ASP cc_start: 0.8045 (m-30) cc_final: 0.7824 (t0) REVERT: B 164 LYS cc_start: 0.8231 (mptt) cc_final: 0.7970 (mptt) REVERT: B 289 GLU cc_start: 0.8416 (tp30) cc_final: 0.7908 (tp30) REVERT: B 578 ASP cc_start: 0.8127 (t70) cc_final: 0.7770 (t0) REVERT: B 967 MET cc_start: 0.7781 (tpp) cc_final: 0.7474 (tmm) REVERT: B 1023 ASN cc_start: 0.7285 (p0) cc_final: 0.6243 (p0) REVERT: B 1079 ASN cc_start: 0.8587 (t0) cc_final: 0.8193 (t0) REVERT: B 1122 ASN cc_start: 0.7082 (t0) cc_final: 0.6707 (t0) REVERT: C 15 ILE cc_start: 0.8191 (mm) cc_final: 0.7885 (mt) REVERT: C 77 LEU cc_start: 0.9103 (tp) cc_final: 0.8775 (tt) REVERT: C 330 ASP cc_start: 0.8131 (p0) cc_final: 0.7822 (p0) REVERT: C 439 PHE cc_start: 0.4445 (m-80) cc_final: 0.4002 (m-80) REVERT: C 648 LEU cc_start: 0.8078 (tp) cc_final: 0.7688 (tt) REVERT: C 649 TYR cc_start: 0.8186 (m-80) cc_final: 0.7804 (m-10) REVERT: C 851 ASP cc_start: 0.7634 (m-30) cc_final: 0.7348 (m-30) REVERT: C 971 TRP cc_start: 0.2515 (m100) cc_final: 0.0907 (m100) REVERT: C 1023 ASN cc_start: 0.7174 (p0) cc_final: 0.6241 (p0) REVERT: C 1112 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6416 (tm-30) REVERT: C 1116 SER cc_start: 0.8563 (m) cc_final: 0.8295 (t) outliers start: 2 outliers final: 0 residues processed: 310 average time/residue: 0.1316 time to fit residues: 68.5518 Evaluate side-chains 225 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 213 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 71 optimal weight: 7.9990 chunk 242 optimal weight: 0.0970 chunk 87 optimal weight: 3.9990 chunk 52 optimal weight: 10.0000 chunk 227 optimal weight: 1.9990 chunk 185 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B1086 ASN C 175 HIS ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.105623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091692 restraints weight = 56576.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.093895 restraints weight = 33935.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.095450 restraints weight = 23150.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096590 restraints weight = 17342.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.097408 restraints weight = 13831.748| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.5722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23244 Z= 0.137 Angle : 0.669 13.323 31644 Z= 0.353 Chirality : 0.043 0.254 3570 Planarity : 0.005 0.100 4047 Dihedral : 5.301 25.276 3099 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.70 % Favored : 90.66 % Rotamer: Outliers : 0.08 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.28 (0.15), residues: 2826 helix: 1.47 (0.21), residues: 663 sheet: -0.97 (0.20), residues: 516 loop : -1.89 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 75 TYR 0.018 0.001 TYR B 266 PHE 0.050 0.001 PHE C 18 TRP 0.020 0.001 TRP A 444 HIS 0.012 0.001 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00306 (23199) covalent geometry : angle 0.66454 (31554) SS BOND : bond 0.00754 ( 45) SS BOND : angle 1.62136 ( 90) hydrogen bonds : bond 0.04352 ( 925) hydrogen bonds : angle 5.42009 ( 2541) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 303 time to evaluate : 0.914 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 15 ILE cc_start: 0.8435 (mm) cc_final: 0.8035 (mt) REVERT: A 18 PHE cc_start: 0.4407 (t80) cc_final: 0.3585 (t80) REVERT: A 54 ARG cc_start: 0.8742 (ttm110) cc_final: 0.8082 (ttm110) REVERT: A 155 MET cc_start: 0.7435 (mtm) cc_final: 0.7039 (mtm) REVERT: A 182 LEU cc_start: 0.8139 (pt) cc_final: 0.7535 (tp) REVERT: A 231 ILE cc_start: 0.9203 (mm) cc_final: 0.8889 (tt) REVERT: A 863 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7802 (pp30) REVERT: A 1023 ASN cc_start: 0.7446 (p0) cc_final: 0.6939 (p0) REVERT: A 1038 GLN cc_start: 0.7942 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 1094 SER cc_start: 0.8741 (m) cc_final: 0.8364 (p) REVERT: B 27 ASP cc_start: 0.8045 (m-30) cc_final: 0.7820 (t0) REVERT: B 164 LYS cc_start: 0.8215 (mptt) cc_final: 0.7954 (mptt) REVERT: B 289 GLU cc_start: 0.8460 (tp30) cc_final: 0.7947 (tp30) REVERT: B 578 ASP cc_start: 0.8140 (t70) cc_final: 0.7774 (t0) REVERT: B 595 ASN cc_start: 0.8539 (m110) cc_final: 0.8043 (p0) REVERT: B 649 TYR cc_start: 0.7691 (m-80) cc_final: 0.7390 (m-80) REVERT: B 830 SER cc_start: 0.8880 (m) cc_final: 0.8539 (p) REVERT: B 1023 ASN cc_start: 0.7298 (p0) cc_final: 0.6243 (p0) REVERT: B 1079 ASN cc_start: 0.8645 (t0) cc_final: 0.8181 (t0) REVERT: B 1122 ASN cc_start: 0.6949 (t0) cc_final: 0.6703 (t0) REVERT: C 77 LEU cc_start: 0.9106 (tp) cc_final: 0.8765 (tt) REVERT: C 231 ILE cc_start: 0.9146 (mm) cc_final: 0.8767 (tt) REVERT: C 330 ASP cc_start: 0.8132 (p0) cc_final: 0.7811 (p0) REVERT: C 439 PHE cc_start: 0.4779 (m-80) cc_final: 0.4235 (m-80) REVERT: C 648 LEU cc_start: 0.7913 (tp) cc_final: 0.7683 (tp) REVERT: C 649 TYR cc_start: 0.8135 (m-80) cc_final: 0.7688 (m-10) REVERT: C 851 ASP cc_start: 0.7579 (m-30) cc_final: 0.7305 (m-30) REVERT: C 967 MET cc_start: 0.8483 (tmm) cc_final: 0.8205 (tmm) REVERT: C 971 TRP cc_start: 0.2363 (m100) cc_final: 0.0883 (m100) REVERT: C 1023 ASN cc_start: 0.7173 (p0) cc_final: 0.6256 (p0) REVERT: C 1112 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6603 (tm-30) REVERT: C 1116 SER cc_start: 0.8634 (m) cc_final: 0.8370 (t) outliers start: 2 outliers final: 0 residues processed: 305 average time/residue: 0.1207 time to fit residues: 62.5089 Evaluate side-chains 228 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 6.9990 chunk 157 optimal weight: 0.9990 chunk 177 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 chunk 1 optimal weight: 0.0670 chunk 268 optimal weight: 0.0020 chunk 230 optimal weight: 1.9990 chunk 252 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 83 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 overall best weight: 0.4726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 591 ASN A 646 ASN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN B1086 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 646 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.108044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.094166 restraints weight = 56060.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.096351 restraints weight = 34052.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097908 restraints weight = 23390.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.098928 restraints weight = 17570.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.099784 restraints weight = 14266.657| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23244 Z= 0.122 Angle : 0.652 13.713 31644 Z= 0.342 Chirality : 0.042 0.278 3570 Planarity : 0.005 0.089 4047 Dihedral : 5.125 25.442 3099 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.60 % Allowed : 8.60 % Favored : 90.80 % Rotamer: Outliers : 0.08 % Allowed : 0.43 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.15), residues: 2826 helix: 1.54 (0.21), residues: 660 sheet: -0.82 (0.21), residues: 516 loop : -1.85 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 75 TYR 0.018 0.001 TYR B 203 PHE 0.030 0.001 PHE B 835 TRP 0.014 0.001 TRP A 444 HIS 0.010 0.001 HIS B 175 Details of bonding type rmsd covalent geometry : bond 0.00258 (23199) covalent geometry : angle 0.64826 (31554) SS BOND : bond 0.00646 ( 45) SS BOND : angle 1.49404 ( 90) hydrogen bonds : bond 0.04160 ( 925) hydrogen bonds : angle 5.29698 ( 2541) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5652 Ramachandran restraints generated. 2826 Oldfield, 0 Emsley, 2826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 320 time to evaluate : 0.831 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 15 ILE cc_start: 0.8420 (mm) cc_final: 0.8056 (mt) REVERT: A 29 ASN cc_start: 0.7611 (p0) cc_final: 0.7406 (p0) REVERT: A 54 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8008 (ttm110) REVERT: A 182 LEU cc_start: 0.8029 (pt) cc_final: 0.7534 (tp) REVERT: A 231 ILE cc_start: 0.9140 (mm) cc_final: 0.8874 (tt) REVERT: A 595 ASN cc_start: 0.8425 (m110) cc_final: 0.8182 (p0) REVERT: A 851 ASP cc_start: 0.7473 (m-30) cc_final: 0.7273 (m-30) REVERT: A 863 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7599 (pp30) REVERT: A 997 LEU cc_start: 0.7817 (tp) cc_final: 0.7328 (tp) REVERT: A 1023 ASN cc_start: 0.7492 (p0) cc_final: 0.6912 (t0) REVERT: A 1094 SER cc_start: 0.8629 (m) cc_final: 0.8288 (p) REVERT: B 15 ILE cc_start: 0.8428 (mm) cc_final: 0.7875 (mt) REVERT: B 54 ARG cc_start: 0.8591 (ttm110) cc_final: 0.8334 (ttm110) REVERT: B 164 LYS cc_start: 0.8152 (mptt) cc_final: 0.7896 (mptt) REVERT: B 289 GLU cc_start: 0.8429 (tp30) cc_final: 0.7916 (tp30) REVERT: B 426 TYR cc_start: 0.8724 (m-80) cc_final: 0.8325 (m-80) REVERT: B 578 ASP cc_start: 0.7945 (t70) cc_final: 0.7664 (t0) REVERT: B 595 ASN cc_start: 0.8573 (m110) cc_final: 0.8031 (p0) REVERT: B 649 TYR cc_start: 0.7398 (m-80) cc_final: 0.7193 (m-80) REVERT: B 830 SER cc_start: 0.8770 (m) cc_final: 0.8460 (p) REVERT: B 851 ASP cc_start: 0.7567 (m-30) cc_final: 0.7288 (m-30) REVERT: B 952 GLU cc_start: 0.7470 (pp20) cc_final: 0.7243 (pp20) REVERT: B 1023 ASN cc_start: 0.7324 (p0) cc_final: 0.6244 (p0) REVERT: B 1079 ASN cc_start: 0.8523 (t0) cc_final: 0.8086 (t0) REVERT: C 77 LEU cc_start: 0.9018 (tp) cc_final: 0.8692 (tt) REVERT: C 180 GLU cc_start: 0.7592 (pm20) cc_final: 0.7385 (pm20) REVERT: C 231 ILE cc_start: 0.9091 (mm) cc_final: 0.8725 (tt) REVERT: C 330 ASP cc_start: 0.7941 (p0) cc_final: 0.7621 (p0) REVERT: C 439 PHE cc_start: 0.4610 (m-80) cc_final: 0.4066 (m-80) REVERT: C 649 TYR cc_start: 0.7873 (m-80) cc_final: 0.7545 (m-10) REVERT: C 851 ASP cc_start: 0.7488 (m-30) cc_final: 0.7283 (m-30) REVERT: C 971 TRP cc_start: 0.2425 (m100) cc_final: 0.1113 (m100) REVERT: C 1023 ASN cc_start: 0.7213 (p0) cc_final: 0.6289 (p0) REVERT: C 1112 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6764 (tm-30) outliers start: 2 outliers final: 0 residues processed: 322 average time/residue: 0.1272 time to fit residues: 69.4967 Evaluate side-chains 243 residues out of total 2580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 9 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 281 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 74 optimal weight: 0.0570 chunk 236 optimal weight: 3.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 HIS ** A 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 ASN A 998 ASN A1045 GLN ** A1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 470 ASN B 646 ASN ** C 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 402 GLN C 470 ASN C 646 ASN ** C1049 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091266 restraints weight = 56935.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093464 restraints weight = 34360.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.095013 restraints weight = 23508.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.096123 restraints weight = 17604.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096951 restraints weight = 14107.919| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 23244 Z= 0.161 Angle : 0.690 13.062 31644 Z= 0.362 Chirality : 0.044 0.254 3570 Planarity : 0.005 0.085 4047 Dihedral : 5.206 27.005 3099 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.57 % Allowed : 9.52 % Favored : 89.92 % Rotamer: Outliers : 0.08 % Allowed : 0.35 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.34 (0.15), residues: 2826 helix: 1.43 (0.21), residues: 669 sheet: -0.86 (0.21), residues: 489 loop : -1.98 (0.14), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 75 TYR 0.017 0.002 TYR A1088 PHE 0.029 0.001 PHE B 835 TRP 0.023 0.001 TRP A 444 HIS 0.014 0.002 HIS B1129 Details of bonding type rmsd covalent geometry : bond 0.00366 (23199) covalent geometry : angle 0.68507 (31554) SS BOND : bond 0.00725 ( 45) SS BOND : angle 1.67394 ( 90) hydrogen bonds : bond 0.04371 ( 925) hydrogen bonds : angle 5.40587 ( 2541) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3133.10 seconds wall clock time: 55 minutes 27.64 seconds (3327.64 seconds total)