Starting phenix.real_space_refine on Fri Jul 3 22:34:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.cif Found real_map, /net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.cif" model { file = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7a5s_11647/07_2026/7a5s_11647.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.002 sd= 0.027 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 68 5.16 5 C 10580 2.51 5 N 2748 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16608 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1634 Classifications: {'peptide': 220} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 205} Chain: "L" Number of atoms: 1694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1694 Classifications: {'peptide': 218} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 206} Chain: "A" Number of atoms: 4948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4948 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 31, 'TRANS': 592} Chain breaks: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Restraints were copied for chains: I, M, B, G Time building chain proxies: 4.67, per 1000 atoms: 0.28 Number of scatterers: 16608 At special positions: 0 Unit cell: (183.703, 190.225, 94.569, 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 68 16.00 O 3212 8.00 N 2748 7.00 C 10580 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.04 Simple disulfide: pdb=" SG CYS L 140 " - pdb=" SG CYS L 200 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 200 " distance=2.04 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 94 " distance=2.04 Simple disulfide: pdb=" SG CYS M 140 " - pdb=" SG CYS M 200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG D 1 " - " ASN A 343 " " NAG G 1 " - " ASN B 343 " Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 615.6 milliseconds 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3932 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 40 sheets defined 5.8% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'L' and resid 127 through 134 removed outlier: 3.689A pdb=" N LEU L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS L 132 " --> pdb=" O ASP L 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER L 133 " --> pdb=" O GLU L 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY L 134 " --> pdb=" O GLN L 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 134' Processing helix chain 'L' and resid 189 through 193 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.964A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 369' Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP A 442 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.690A pdb=" N LEU M 131 " --> pdb=" O SER M 127 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS M 132 " --> pdb=" O ASP M 128 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER M 133 " --> pdb=" O GLU M 129 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY M 134 " --> pdb=" O GLN M 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 127 through 134' Processing helix chain 'M' and resid 189 through 193 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 369 removed outlier: 3.965A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR B 369 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 369' Processing helix chain 'B' and resid 383 through 388 removed outlier: 4.237A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 3.759A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.783A pdb=" N ASP B 442 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 162 No H-bonds generated for 'chain 'I' and resid 160 through 162' Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU H 10 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR H 116 " --> pdb=" O GLU H 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL H 108 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.342A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 144 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER H 184 " --> pdb=" O CYS H 144 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASP H 148 " --> pdb=" O TYR H 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU L 11 " --> pdb=" O GLU L 111 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 30 through 31 removed outlier: 3.772A pdb=" N LYS L 36 " --> pdb=" O TYR L 31 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER L 120 " --> pdb=" O ASN L 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN L 143 " --> pdb=" O SER L 120 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160 removed outlier: 3.637A pdb=" N TYR L 198 " --> pdb=" O PHE L 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 277 " --> pdb=" O HIS A 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 63 through 67 removed outlier: 4.369A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.838A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 151 through 163 removed outlier: 6.522A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.837A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.223A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.569A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.761A pdb=" N VAL A 539 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR A 553 " --> pdb=" O ASP A 586 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP A 586 " --> pdb=" O THR A 553 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AC1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AC2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.263A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AC4, first strand: chain 'M' and resid 10 through 13 removed outlier: 6.247A pdb=" N LEU M 11 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TRP M 41 " --> pdb=" O LEU M 53 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 30 through 31 removed outlier: 3.773A pdb=" N LYS M 36 " --> pdb=" O TYR M 31 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 120 through 124 removed outlier: 3.879A pdb=" N SER M 120 " --> pdb=" O ASN M 143 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN M 143 " --> pdb=" O SER M 120 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 159 through 160 removed outlier: 3.637A pdb=" N TYR M 198 " --> pdb=" O PHE M 215 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.512A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN B 271 " --> pdb=" O PHE B 55 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 63 through 67 removed outlier: 4.368A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.838A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 151 through 163 removed outlier: 6.522A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 11.347A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.838A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.224A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 311 through 313 removed outlier: 3.569A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 324 through 328 removed outlier: 3.761A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.912A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA B 435 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD8, first strand: chain 'B' and resid 664 through 667 removed outlier: 6.264A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AE1, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.749A pdb=" N GLU I 10 " --> pdb=" O THR I 114 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR I 116 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N VAL I 108 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 124 through 128 removed outlier: 4.343A pdb=" N GLY I 143 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS I 144 " --> pdb=" O SER I 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER I 184 " --> pdb=" O CYS I 144 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP I 148 " --> pdb=" O TYR I 180 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N TYR I 180 " --> pdb=" O ASP I 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 155 through 158 removed outlier: 4.747A pdb=" N TYR I 198 " --> pdb=" O VAL I 215 " (cutoff:3.500A) 528 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.94 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4594 1.33 - 1.46: 3725 1.46 - 1.58: 8629 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 17028 Sorted by residual: bond pdb=" N VAL B 595 " pdb=" CA VAL B 595 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.25e+01 bond pdb=" N VAL A 595 " pdb=" CA VAL A 595 " ideal model delta sigma weight residual 1.456 1.497 -0.040 1.14e-02 7.69e+03 1.24e+01 bond pdb=" N VAL A 534 " pdb=" CA VAL A 534 " ideal model delta sigma weight residual 1.456 1.494 -0.039 1.15e-02 7.56e+03 1.13e+01 bond pdb=" N VAL B 534 " pdb=" CA VAL B 534 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL B 551 " pdb=" CA VAL B 551 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.22e-02 6.72e+03 1.07e+01 ... (remaining 17023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 21616 1.74 - 3.49: 1281 3.49 - 5.23: 231 5.23 - 6.98: 30 6.98 - 8.72: 14 Bond angle restraints: 23172 Sorted by residual: angle pdb=" N PRO A 217 " pdb=" CA PRO A 217 " pdb=" C PRO A 217 " ideal model delta sigma weight residual 111.22 116.86 -5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" N PRO B 217 " pdb=" CA PRO B 217 " pdb=" C PRO B 217 " ideal model delta sigma weight residual 111.22 116.86 -5.64 1.40e+00 5.10e-01 1.62e+01 angle pdb=" N ASN B 536 " pdb=" CA ASN B 536 " pdb=" C ASN B 536 " ideal model delta sigma weight residual 111.74 117.02 -5.28 1.35e+00 5.49e-01 1.53e+01 angle pdb=" N ASN A 536 " pdb=" CA ASN A 536 " pdb=" C ASN A 536 " ideal model delta sigma weight residual 111.74 117.02 -5.28 1.35e+00 5.49e-01 1.53e+01 angle pdb=" CA GLY B 268 " pdb=" C GLY B 268 " pdb=" O GLY B 268 " ideal model delta sigma weight residual 121.76 117.78 3.98 1.03e+00 9.43e-01 1.49e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.03: 9207 18.03 - 36.07: 661 36.07 - 54.10: 154 54.10 - 72.14: 30 72.14 - 90.17: 10 Dihedral angle restraints: 10062 sinusoidal: 3902 harmonic: 6160 Sorted by residual: dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -176.17 90.17 1 1.00e+01 1.00e-02 9.63e+01 dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual -86.00 -176.14 90.14 1 1.00e+01 1.00e-02 9.62e+01 dihedral pdb=" C ASP A 578 " pdb=" N ASP A 578 " pdb=" CA ASP A 578 " pdb=" CB ASP A 578 " ideal model delta harmonic sigma weight residual -122.60 -133.80 11.20 0 2.50e+00 1.60e-01 2.01e+01 ... (remaining 10059 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2015 0.069 - 0.137: 474 0.137 - 0.206: 61 0.206 - 0.275: 20 0.275 - 0.343: 6 Chirality restraints: 2576 Sorted by residual: chirality pdb=" CA ASN B 536 " pdb=" N ASN B 536 " pdb=" C ASN B 536 " pdb=" CB ASN B 536 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 chirality pdb=" CA ASN A 536 " pdb=" N ASN A 536 " pdb=" C ASN A 536 " pdb=" CB ASN A 536 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ASP A 578 " pdb=" N ASP A 578 " pdb=" C ASP A 578 " pdb=" CB ASP A 578 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 2573 not shown) Planarity restraints: 2976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 548 " -0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLY B 548 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 548 " -0.023 2.00e-02 2.50e+03 pdb=" N THR B 549 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 548 " 0.018 2.00e-02 2.50e+03 3.51e-02 1.23e+01 pdb=" C GLY A 548 " -0.061 2.00e-02 2.50e+03 pdb=" O GLY A 548 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 549 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 571 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C ASP A 571 " 0.045 2.00e-02 2.50e+03 pdb=" O ASP A 571 " -0.017 2.00e-02 2.50e+03 pdb=" N THR A 572 " -0.015 2.00e-02 2.50e+03 ... (remaining 2973 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 6 1.93 - 2.67: 277 2.67 - 3.42: 20398 3.42 - 4.16: 36938 4.16 - 4.90: 65913 Nonbonded interactions: 123532 Sorted by model distance: nonbonded pdb=" NH2 ARG B 273 " pdb=" OD2 ASP B 290 " model vdw 1.188 3.120 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD2 ASP A 290 " model vdw 1.189 3.120 nonbonded pdb=" NH2 ARG A 273 " pdb=" CG ASP A 290 " model vdw 1.373 3.350 nonbonded pdb=" NH2 ARG B 273 " pdb=" CG ASP B 290 " model vdw 1.373 3.350 nonbonded pdb=" NH2 ARG A 273 " pdb=" OD1 ASP A 290 " model vdw 1.766 3.120 ... (remaining 123527 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: 0.03 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'G' } 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: 0.010 Normalize map: mean=0, sd=1: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.006 0.041 17058 Z= 0.370 Angle : 0.933 8.725 23236 Z= 0.569 Chirality : 0.062 0.343 2576 Planarity : 0.005 0.051 2974 Dihedral : 13.377 89.368 6052 Min Nonbonded Distance : 1.188 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.38 % Allowed : 6.94 % Favored : 92.68 % Rotamer: Outliers : 0.65 % Allowed : 5.66 % Favored : 93.70 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.17), residues: 2104 helix: -2.03 (0.51), residues: 88 sheet: 0.09 (0.20), residues: 698 loop : -2.23 (0.15), residues: 1318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 328 TYR 0.019 0.002 TYR B 351 PHE 0.017 0.002 PHE H 29 TRP 0.027 0.002 TRP H 83 HIS 0.010 0.001 HIS L 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.37 (17028) covalent geometry : angle 0.93115 / 0.57 (23172) SS BOND : bond 0.00542 / 0.32 ( 26) SS BOND : angle 1.21436 / 0.87 ( 52) hydrogen bonds : bond 0.14456 / 9.81 ( 520) hydrogen bonds : angle 8.38848 / 5.71 ( 1344) link_BETA1-4 : bond 0.00292 / 0.15 ( 2) link_BETA1-4 : angle 1.30212 / 0.90 ( 6) link_NAG-ASN : bond 0.00032 / 0.02 ( 2) link_NAG-ASN : angle 2.40095 / 1.86 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: -0.2022 (ttm) cc_final: -0.4005 (mtp) REVERT: B 177 MET cc_start: -0.1960 (ttm) cc_final: -0.3965 (mtp) outliers start: 12 outliers final: 2 residues processed: 208 average time/residue: 0.1378 time to fit residues: 41.0088 Evaluate side-chains 92 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 200 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 77 ASN L 6 GLN L 44 GLN L 106 GLN ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 164 ASN A 66 HIS A 115 GLN A 146 HIS A 164 ASN A 218 GLN A 239 GLN A 245 HIS A 271 GLN A 321 GLN A 370 ASN A 493 GLN A 540 ASN A 542 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN A 641 ASN A 658 ASN A 675 GLN M 6 GLN M 44 GLN M 95 GLN M 106 GLN ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 164 ASN B 66 HIS B 115 GLN B 146 HIS B 164 ASN B 218 GLN B 239 GLN B 245 HIS B 271 GLN B 321 GLN B 370 ASN B 493 GLN B 540 ASN B 542 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 641 ASN B 658 ASN B 675 GLN I 39 GLN I 77 ASN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.103930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.075560 restraints weight = 55399.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.072080 restraints weight = 53246.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.073109 restraints weight = 51324.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.073376 restraints weight = 35511.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.073831 restraints weight = 33284.249| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 17058 Z= 0.244 Angle : 0.744 8.594 23236 Z= 0.390 Chirality : 0.048 0.149 2576 Planarity : 0.005 0.049 2974 Dihedral : 5.417 49.243 2296 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.94 % Allowed : 10.88 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.17), residues: 2104 helix: -2.31 (0.55), residues: 86 sheet: 0.33 (0.19), residues: 754 loop : -2.12 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 646 TYR 0.033 0.002 TYR B 612 PHE 0.025 0.002 PHE A 55 TRP 0.024 0.002 TRP I 83 HIS 0.005 0.001 HIS I 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00580 / 0.24 (17028) covalent geometry : angle 0.73993 / 0.39 (23172) SS BOND : bond 0.00456 / 0.27 ( 26) SS BOND : angle 1.59803 / 1.12 ( 52) hydrogen bonds : bond 0.04741 / 3.01 ( 520) hydrogen bonds : angle 7.03784 / 4.78 ( 1344) link_BETA1-4 : bond 0.00435 / 0.22 ( 2) link_BETA1-4 : angle 1.31089 / 0.87 ( 6) link_NAG-ASN : bond 0.00145 / 0.08 ( 2) link_NAG-ASN : angle 1.82643 / 1.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.449 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: H 149 TYR cc_start: 0.8665 (p90) cc_final: 0.8427 (p90) REVERT: A 106 PHE cc_start: 0.8465 (m-80) cc_final: 0.8257 (m-10) REVERT: A 153 MET cc_start: 0.7282 (ppp) cc_final: 0.7050 (ppp) REVERT: A 177 MET cc_start: -0.3010 (ttm) cc_final: -0.3638 (mtp) REVERT: B 153 MET cc_start: 0.7389 (ppp) cc_final: 0.7134 (ppp) REVERT: B 177 MET cc_start: -0.2841 (ttm) cc_final: -0.3201 (mmm) REVERT: B 471 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6390 (tp30) REVERT: I 2 MET cc_start: 0.7785 (ppp) cc_final: 0.7112 (ppp) outliers start: 36 outliers final: 22 residues processed: 128 average time/residue: 0.1055 time to fit residues: 21.8468 Evaluate side-chains 103 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 212 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain M residue 195 HIS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 199 ILE Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 192 optimal weight: 0.8980 chunk 162 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 165 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 63 optimal weight: 6.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 216 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 95 GLN ** M 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 216 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.104455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075500 restraints weight = 56141.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.074010 restraints weight = 45993.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.074211 restraints weight = 60510.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.074728 restraints weight = 38528.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075031 restraints weight = 32250.999| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17058 Z= 0.139 Angle : 0.614 7.691 23236 Z= 0.320 Chirality : 0.045 0.145 2576 Planarity : 0.004 0.040 2974 Dihedral : 5.054 49.215 2296 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.67 % Allowed : 12.88 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.17), residues: 2104 helix: -2.35 (0.51), residues: 100 sheet: 0.53 (0.19), residues: 750 loop : -1.85 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 18 TYR 0.013 0.001 TYR A 204 PHE 0.022 0.001 PHE A 135 TRP 0.018 0.001 TRP I 83 HIS 0.006 0.001 HIS M 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (17028) covalent geometry : angle 0.61233 / 0.32 (23172) SS BOND : bond 0.00360 / 0.23 ( 26) SS BOND : angle 0.92561 / 0.67 ( 52) hydrogen bonds : bond 0.03936 / 2.50 ( 520) hydrogen bonds : angle 6.52035 / 4.43 ( 1344) link_BETA1-4 : bond 0.00156 / 0.08 ( 2) link_BETA1-4 : angle 0.91310 / 0.64 ( 6) link_NAG-ASN : bond 0.00113 / 0.06 ( 2) link_NAG-ASN : angle 1.39688 / 1.03 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 89 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.7364 (ppp) cc_final: 0.7083 (ttp) REVERT: A 128 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 153 MET cc_start: 0.7563 (ppp) cc_final: 0.6105 (pmm) REVERT: A 177 MET cc_start: -0.3176 (ttm) cc_final: -0.4258 (mpp) REVERT: B 128 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8832 (tp) REVERT: B 153 MET cc_start: 0.7514 (ppp) cc_final: 0.5941 (pmm) REVERT: B 177 MET cc_start: -0.3132 (ttm) cc_final: -0.4511 (mpp) REVERT: B 471 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6335 (tp30) REVERT: I 2 MET cc_start: 0.7752 (ppp) cc_final: 0.7068 (ppp) outliers start: 31 outliers final: 21 residues processed: 111 average time/residue: 0.1014 time to fit residues: 18.4304 Evaluate side-chains 100 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 199 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 197 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.100886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.072146 restraints weight = 56098.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.069217 restraints weight = 45852.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069943 restraints weight = 60636.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.070044 restraints weight = 37431.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.070753 restraints weight = 32281.719| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17058 Z= 0.185 Angle : 0.615 8.138 23236 Z= 0.323 Chirality : 0.045 0.146 2576 Planarity : 0.004 0.042 2974 Dihedral : 4.989 48.690 2296 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.91 % Allowed : 13.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.17), residues: 2104 helix: -2.29 (0.55), residues: 88 sheet: 0.55 (0.19), residues: 716 loop : -1.85 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 59 TYR 0.020 0.002 TYR I 180 PHE 0.012 0.002 PHE L 215 TRP 0.016 0.002 TRP I 83 HIS 0.005 0.001 HIS L 195 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (17028) covalent geometry : angle 0.61386 / 0.32 (23172) SS BOND : bond 0.00362 / 0.22 ( 26) SS BOND : angle 0.98704 / 0.69 ( 52) hydrogen bonds : bond 0.04044 / 2.57 ( 520) hydrogen bonds : angle 6.34703 / 4.32 ( 1344) link_BETA1-4 : bond 0.00099 / 0.05 ( 2) link_BETA1-4 : angle 1.03823 / 0.65 ( 6) link_NAG-ASN : bond 0.00051 / 0.03 ( 2) link_NAG-ASN : angle 1.41101 / 1.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 84 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 1 GLN cc_start: 0.7119 (tm-30) cc_final: 0.6891 (tm-30) REVERT: H 106 MET cc_start: 0.8878 (mtm) cc_final: 0.8438 (mtt) REVERT: L 31 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7424 (t80) REVERT: A 153 MET cc_start: 0.7903 (ppp) cc_final: 0.6604 (pmm) REVERT: A 353 TRP cc_start: 0.8865 (OUTLIER) cc_final: 0.7880 (p-90) REVERT: M 31 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.7039 (t80) REVERT: B 153 MET cc_start: 0.7881 (ppp) cc_final: 0.6514 (pmm) REVERT: B 353 TRP cc_start: 0.8849 (OUTLIER) cc_final: 0.7853 (p-90) REVERT: B 471 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.6265 (tp30) REVERT: I 185 VAL cc_start: 0.9115 (OUTLIER) cc_final: 0.8874 (m) outliers start: 54 outliers final: 32 residues processed: 123 average time/residue: 0.1044 time to fit residues: 21.0552 Evaluate side-chains 110 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 72 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 145 LEU Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 131 LEU Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 89 optimal weight: 0.0970 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 158 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 8.9990 chunk 119 optimal weight: 0.5980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 1 GLN ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.101088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.067294 restraints weight = 54510.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.066553 restraints weight = 37349.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.066843 restraints weight = 26980.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.067129 restraints weight = 26942.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.067421 restraints weight = 22419.001| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17058 Z= 0.109 Angle : 0.558 7.356 23236 Z= 0.292 Chirality : 0.044 0.168 2576 Planarity : 0.004 0.039 2974 Dihedral : 4.761 50.278 2296 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.37 % Allowed : 15.09 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.18), residues: 2104 helix: -2.42 (0.49), residues: 100 sheet: 0.63 (0.19), residues: 752 loop : -1.73 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 59 TYR 0.016 0.001 TYR B 204 PHE 0.017 0.001 PHE A 135 TRP 0.015 0.001 TRP H 83 HIS 0.003 0.000 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (17028) covalent geometry : angle 0.55720 / 0.29 (23172) SS BOND : bond 0.00306 / 0.19 ( 26) SS BOND : angle 0.72973 / 0.52 ( 52) hydrogen bonds : bond 0.03469 / 2.20 ( 520) hydrogen bonds : angle 6.06826 / 4.15 ( 1344) link_BETA1-4 : bond 0.00209 / 0.11 ( 2) link_BETA1-4 : angle 0.89446 / 0.57 ( 6) link_NAG-ASN : bond 0.00164 / 0.08 ( 2) link_NAG-ASN : angle 1.17618 / 0.87 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 79 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 106 MET cc_start: 0.8730 (mtm) cc_final: 0.8315 (mtm) REVERT: L 31 TYR cc_start: 0.8605 (OUTLIER) cc_final: 0.7289 (t80) REVERT: A 153 MET cc_start: 0.8183 (ppp) cc_final: 0.7026 (pmm) REVERT: A 353 TRP cc_start: 0.8923 (OUTLIER) cc_final: 0.7886 (p-90) REVERT: M 31 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.6985 (t80) REVERT: B 153 MET cc_start: 0.8171 (ppp) cc_final: 0.6953 (pmm) REVERT: B 353 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.7805 (p-90) REVERT: B 471 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.6163 (tp30) REVERT: I 106 MET cc_start: 0.8601 (mtm) cc_final: 0.8307 (mtm) outliers start: 44 outliers final: 23 residues processed: 116 average time/residue: 0.0934 time to fit residues: 17.9191 Evaluate side-chains 102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 650 LEU Chi-restraints excluded: chain I residue 125 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 206 optimal weight: 0.8980 chunk 167 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 129 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 130 GLN ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 196 GLN ** I 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.101925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.072225 restraints weight = 55570.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.069592 restraints weight = 40943.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070244 restraints weight = 48873.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070343 restraints weight = 33279.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070716 restraints weight = 28216.956| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17058 Z= 0.114 Angle : 0.543 7.311 23236 Z= 0.283 Chirality : 0.044 0.152 2576 Planarity : 0.004 0.039 2974 Dihedral : 4.596 49.679 2296 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.32 % Allowed : 15.03 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.16 (0.18), residues: 2104 helix: -2.33 (0.49), residues: 100 sheet: 0.53 (0.19), residues: 780 loop : -1.58 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 18 TYR 0.018 0.001 TYR H 27 PHE 0.017 0.001 PHE B 106 TRP 0.012 0.001 TRP H 83 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.11 (17028) covalent geometry : angle 0.54195 / 0.28 (23172) SS BOND : bond 0.00313 / 0.19 ( 26) SS BOND : angle 0.76068 / 0.53 ( 52) hydrogen bonds : bond 0.03312 / 2.10 ( 520) hydrogen bonds : angle 5.80971 / 3.97 ( 1344) link_BETA1-4 : bond 0.00135 / 0.07 ( 2) link_BETA1-4 : angle 0.90287 / 0.60 ( 6) link_NAG-ASN : bond 0.00121 / 0.06 ( 2) link_NAG-ASN : angle 1.20253 / 0.89 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 31 TYR cc_start: 0.8611 (OUTLIER) cc_final: 0.7111 (t80) REVERT: A 153 MET cc_start: 0.7960 (ppp) cc_final: 0.6795 (pmm) REVERT: A 353 TRP cc_start: 0.8877 (OUTLIER) cc_final: 0.7790 (p-90) REVERT: M 31 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.6996 (t80) REVERT: B 153 MET cc_start: 0.7925 (ppp) cc_final: 0.6666 (pmm) REVERT: B 353 TRP cc_start: 0.8873 (OUTLIER) cc_final: 0.7789 (p-90) REVERT: B 471 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.6232 (tp30) outliers start: 43 outliers final: 25 residues processed: 115 average time/residue: 0.0931 time to fit residues: 18.0289 Evaluate side-chains 102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 72 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 642 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 114 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 137 optimal weight: 30.0000 chunk 96 optimal weight: 9.9990 chunk 17 optimal weight: 0.2980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.099195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065321 restraints weight = 53901.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.064214 restraints weight = 36089.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.064363 restraints weight = 27782.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.064726 restraints weight = 26578.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.064841 restraints weight = 22883.294| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17058 Z= 0.179 Angle : 0.591 7.038 23236 Z= 0.309 Chirality : 0.045 0.148 2576 Planarity : 0.004 0.039 2974 Dihedral : 4.770 47.811 2296 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.59 % Allowed : 15.03 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.17), residues: 2104 helix: -2.24 (0.51), residues: 88 sheet: 0.55 (0.19), residues: 738 loop : -1.68 (0.16), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.013 0.002 TYR L 55 PHE 0.020 0.002 PHE A 168 TRP 0.015 0.001 TRP I 83 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (17028) covalent geometry : angle 0.58931 / 0.31 (23172) SS BOND : bond 0.00365 / 0.22 ( 26) SS BOND : angle 1.01126 / 0.67 ( 52) hydrogen bonds : bond 0.03838 / 2.42 ( 520) hydrogen bonds : angle 5.94017 / 4.06 ( 1344) link_BETA1-4 : bond 0.00047 / 0.02 ( 2) link_BETA1-4 : angle 1.09376 / 0.64 ( 6) link_NAG-ASN : bond 0.00019 / 0.01 ( 2) link_NAG-ASN : angle 1.33311 / 0.95 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 75 time to evaluate : 0.512 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: L 31 TYR cc_start: 0.8741 (OUTLIER) cc_final: 0.7032 (t80) REVERT: A 153 MET cc_start: 0.8239 (ppp) cc_final: 0.7149 (pmm) REVERT: A 168 PHE cc_start: 0.7822 (t80) cc_final: 0.6881 (t80) REVERT: A 177 MET cc_start: -0.1691 (mmm) cc_final: -0.2682 (mpp) REVERT: A 229 LEU cc_start: 0.9521 (mt) cc_final: 0.9287 (mt) REVERT: A 353 TRP cc_start: 0.9013 (OUTLIER) cc_final: 0.8151 (p-90) REVERT: M 31 TYR cc_start: 0.8721 (OUTLIER) cc_final: 0.6930 (t80) REVERT: B 153 MET cc_start: 0.8091 (ppp) cc_final: 0.7082 (pmm) REVERT: B 353 TRP cc_start: 0.9010 (OUTLIER) cc_final: 0.8143 (p-90) REVERT: I 107 ASP cc_start: 0.8936 (OUTLIER) cc_final: 0.8564 (p0) outliers start: 48 outliers final: 33 residues processed: 114 average time/residue: 0.1052 time to fit residues: 19.1325 Evaluate side-chains 106 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 68 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain L residue 217 ARG Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 650 LEU Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 179 LEU Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 172 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 153 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 170 optimal weight: 2.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.099126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.070373 restraints weight = 55821.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.068936 restraints weight = 49471.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.069264 restraints weight = 62421.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.070020 restraints weight = 37271.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.070371 restraints weight = 31794.724| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17058 Z= 0.193 Angle : 0.596 6.888 23236 Z= 0.312 Chirality : 0.045 0.148 2576 Planarity : 0.004 0.036 2974 Dihedral : 4.648 16.764 2294 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 2.26 % Allowed : 15.52 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.17), residues: 2104 helix: -2.31 (0.46), residues: 100 sheet: 0.48 (0.18), residues: 746 loop : -1.73 (0.16), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 217 TYR 0.013 0.002 TYR H 27 PHE 0.016 0.002 PHE A 168 TRP 0.015 0.001 TRP H 83 HIS 0.002 0.001 HIS I 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.19 (17028) covalent geometry : angle 0.59402 / 0.31 (23172) SS BOND : bond 0.00476 / 0.28 ( 26) SS BOND : angle 1.11572 / 0.76 ( 52) hydrogen bonds : bond 0.03775 / 2.37 ( 520) hydrogen bonds : angle 5.91412 / 4.06 ( 1344) link_BETA1-4 : bond 0.00157 / 0.08 ( 2) link_BETA1-4 : angle 1.17067 / 0.72 ( 6) link_NAG-ASN : bond 0.00094 / 0.05 ( 2) link_NAG-ASN : angle 1.23987 / 0.90 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 69 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 31 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7060 (t80) REVERT: A 153 MET cc_start: 0.7788 (ppp) cc_final: 0.6799 (pmm) REVERT: A 168 PHE cc_start: 0.7453 (t80) cc_final: 0.6354 (t80) REVERT: A 229 LEU cc_start: 0.9166 (mt) cc_final: 0.8921 (mt) REVERT: A 353 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.8004 (p-90) REVERT: M 31 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.6995 (t80) REVERT: B 153 MET cc_start: 0.7653 (ppp) cc_final: 0.6584 (pmm) REVERT: B 168 PHE cc_start: 0.7401 (t80) cc_final: 0.7027 (t80) REVERT: B 353 TRP cc_start: 0.8882 (OUTLIER) cc_final: 0.7994 (p-90) REVERT: I 107 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8496 (p0) REVERT: I 185 VAL cc_start: 0.9167 (OUTLIER) cc_final: 0.8921 (m) outliers start: 42 outliers final: 30 residues processed: 106 average time/residue: 0.1039 time to fit residues: 17.6545 Evaluate side-chains 102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 41 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 170 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.098283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.069682 restraints weight = 56181.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.067539 restraints weight = 46428.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068116 restraints weight = 40438.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.068352 restraints weight = 32269.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.068638 restraints weight = 30806.946| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 17058 Z= 0.230 Angle : 0.624 6.770 23236 Z= 0.328 Chirality : 0.046 0.144 2576 Planarity : 0.004 0.040 2974 Dihedral : 4.759 16.800 2294 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.32 % Allowed : 15.41 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.17), residues: 2104 helix: -2.47 (0.43), residues: 100 sheet: 0.38 (0.18), residues: 776 loop : -1.79 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.013 0.002 TYR L 55 PHE 0.015 0.002 PHE A 168 TRP 0.015 0.002 TRP I 83 HIS 0.003 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (17028) covalent geometry : angle 0.62129 / 0.33 (23172) SS BOND : bond 0.00403 / 0.25 ( 26) SS BOND : angle 1.21435 / 0.82 ( 52) hydrogen bonds : bond 0.04040 / 2.53 ( 520) hydrogen bonds : angle 6.00272 / 4.12 ( 1344) link_BETA1-4 : bond 0.00042 / 0.02 ( 2) link_BETA1-4 : angle 1.21404 / 0.70 ( 6) link_NAG-ASN : bond 0.00020 / 0.01 ( 2) link_NAG-ASN : angle 1.34302 / 0.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 64 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.8577 (ppp) cc_final: 0.7428 (ppp) REVERT: L 31 TYR cc_start: 0.8626 (OUTLIER) cc_final: 0.6917 (t80) REVERT: A 153 MET cc_start: 0.7686 (ppp) cc_final: 0.6682 (pmm) REVERT: A 168 PHE cc_start: 0.7567 (t80) cc_final: 0.6469 (t80) REVERT: A 177 MET cc_start: -0.1597 (mmm) cc_final: -0.2339 (mpp) REVERT: A 229 LEU cc_start: 0.9212 (mt) cc_final: 0.8997 (mt) REVERT: A 353 TRP cc_start: 0.8927 (OUTLIER) cc_final: 0.8139 (p-90) REVERT: M 31 TYR cc_start: 0.8711 (OUTLIER) cc_final: 0.6985 (t80) REVERT: B 153 MET cc_start: 0.7659 (ppp) cc_final: 0.6565 (pmm) REVERT: B 168 PHE cc_start: 0.7614 (t80) cc_final: 0.7211 (t80) REVERT: B 177 MET cc_start: -0.1481 (mmm) cc_final: -0.2218 (mpp) REVERT: B 353 TRP cc_start: 0.8929 (OUTLIER) cc_final: 0.8144 (p-90) REVERT: I 2 MET cc_start: 0.8683 (ppp) cc_final: 0.7442 (ppp) REVERT: I 106 MET cc_start: 0.8745 (mtm) cc_final: 0.8510 (mtm) REVERT: I 107 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8536 (p0) REVERT: I 185 VAL cc_start: 0.9184 (OUTLIER) cc_final: 0.8944 (m) outliers start: 43 outliers final: 34 residues processed: 103 average time/residue: 0.1189 time to fit residues: 20.0855 Evaluate side-chains 102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 62 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 191 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 655 HIS Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 655 HIS Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 0.9990 chunk 140 optimal weight: 9.9990 chunk 177 optimal weight: 10.0000 chunk 195 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 96 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 188 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.098209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069110 restraints weight = 55884.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.066905 restraints weight = 46648.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.067069 restraints weight = 50744.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.067664 restraints weight = 34141.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.067750 restraints weight = 29960.582| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.4957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17058 Z= 0.203 Angle : 0.603 6.938 23236 Z= 0.318 Chirality : 0.046 0.147 2576 Planarity : 0.004 0.042 2974 Dihedral : 4.725 16.721 2294 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 2.10 % Allowed : 15.89 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.17), residues: 2104 helix: -2.50 (0.43), residues: 100 sheet: 0.29 (0.18), residues: 778 loop : -1.80 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.013 0.002 TYR L 55 PHE 0.015 0.002 PHE A 106 TRP 0.020 0.002 TRP M 154 HIS 0.003 0.001 HIS I 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (17028) covalent geometry : angle 0.59977 / 0.32 (23172) SS BOND : bond 0.00382 / 0.23 ( 26) SS BOND : angle 1.37161 / 0.92 ( 52) hydrogen bonds : bond 0.03861 / 2.42 ( 520) hydrogen bonds : angle 5.92610 / 4.07 ( 1344) link_BETA1-4 : bond 0.00103 / 0.05 ( 2) link_BETA1-4 : angle 1.06952 / 0.63 ( 6) link_NAG-ASN : bond 0.00012 / 0.01 ( 2) link_NAG-ASN : angle 1.26761 / 0.93 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4208 Ramachandran restraints generated. 2104 Oldfield, 0 Emsley, 2104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 63 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 2 MET cc_start: 0.8671 (ppp) cc_final: 0.7618 (ppp) REVERT: L 31 TYR cc_start: 0.8610 (OUTLIER) cc_final: 0.6893 (t80) REVERT: A 153 MET cc_start: 0.8047 (ppp) cc_final: 0.7133 (pmm) REVERT: A 168 PHE cc_start: 0.7905 (t80) cc_final: 0.7452 (t80) REVERT: A 177 MET cc_start: -0.1514 (mmm) cc_final: -0.2209 (mpp) REVERT: A 353 TRP cc_start: 0.8931 (OUTLIER) cc_final: 0.8019 (p-90) REVERT: A 650 LEU cc_start: 0.8958 (tp) cc_final: 0.8596 (pp) REVERT: M 31 TYR cc_start: 0.8681 (OUTLIER) cc_final: 0.6921 (t80) REVERT: B 153 MET cc_start: 0.7992 (ppp) cc_final: 0.6990 (pmm) REVERT: B 168 PHE cc_start: 0.8015 (t80) cc_final: 0.7600 (t80) REVERT: B 177 MET cc_start: -0.2027 (mmm) cc_final: -0.2944 (mpp) REVERT: B 353 TRP cc_start: 0.8941 (OUTLIER) cc_final: 0.8041 (p-90) REVERT: I 2 MET cc_start: 0.8637 (ppp) cc_final: 0.7551 (ppp) REVERT: I 106 MET cc_start: 0.8751 (mtm) cc_final: 0.8536 (mtm) REVERT: I 107 ASP cc_start: 0.8916 (OUTLIER) cc_final: 0.8499 (p0) REVERT: I 185 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8927 (m) outliers start: 39 outliers final: 28 residues processed: 98 average time/residue: 0.1122 time to fit residues: 18.3345 Evaluate side-chains 95 residues out of total 1856 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 61 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 173 VAL Chi-restraints excluded: chain H residue 179 LEU Chi-restraints excluded: chain H residue 183 SER Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 31 TYR Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 192 PHE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 353 TRP Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain M residue 31 TYR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 216 ASN Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 353 TRP Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain I residue 107 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 173 VAL Chi-restraints excluded: chain I residue 183 SER Chi-restraints excluded: chain I residue 185 VAL Chi-restraints excluded: chain I residue 201 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.1425 > 50: distance: 67 - 69: 5.592 distance: 69 - 70: 3.866 distance: 70 - 71: 8.780 distance: 70 - 73: 5.934 distance: 71 - 72: 8.368 distance: 71 - 78: 13.119 distance: 72 - 99: 9.755 distance: 73 - 74: 5.611 distance: 74 - 75: 7.717 distance: 75 - 76: 8.584 distance: 76 - 77: 8.719 distance: 78 - 79: 4.980 distance: 79 - 80: 13.181 distance: 79 - 82: 5.898 distance: 80 - 81: 4.301 distance: 80 - 86: 12.452 distance: 81 - 111: 21.888 distance: 82 - 83: 15.850 distance: 82 - 84: 12.793 distance: 83 - 85: 17.241 distance: 86 - 87: 8.161 distance: 87 - 88: 12.250 distance: 87 - 90: 25.565 distance: 88 - 89: 21.340 distance: 88 - 91: 14.260 distance: 91 - 92: 10.092 distance: 92 - 93: 27.105 distance: 92 - 95: 34.182 distance: 93 - 94: 32.423 distance: 93 - 99: 37.686 distance: 95 - 96: 18.713 distance: 96 - 97: 13.384 distance: 96 - 98: 9.927 distance: 99 - 100: 16.459 distance: 100 - 101: 23.912 distance: 100 - 103: 14.326 distance: 101 - 102: 18.585 distance: 101 - 111: 19.075 distance: 103 - 104: 9.767 distance: 104 - 105: 13.136 distance: 104 - 106: 11.081 distance: 105 - 107: 14.749 distance: 106 - 108: 6.281 distance: 107 - 109: 11.685 distance: 108 - 109: 8.025 distance: 109 - 110: 3.550 distance: 111 - 112: 13.799 distance: 112 - 113: 32.669 distance: 112 - 115: 13.656 distance: 113 - 114: 24.692 distance: 113 - 119: 47.826 distance: 115 - 116: 5.490 distance: 116 - 117: 35.487 distance: 116 - 118: 30.655 distance: 119 - 120: 13.635 distance: 120 - 121: 17.439 distance: 120 - 123: 11.916 distance: 121 - 122: 17.431 distance: 121 - 131: 30.317 distance: 123 - 124: 5.669 distance: 124 - 125: 17.306 distance: 124 - 126: 17.000 distance: 125 - 127: 22.493 distance: 126 - 128: 13.272 distance: 127 - 129: 8.982 distance: 128 - 129: 15.138 distance: 129 - 130: 10.699 distance: 131 - 132: 7.048 distance: 132 - 133: 24.878 distance: 132 - 135: 22.382 distance: 133 - 134: 23.848 distance: 133 - 140: 13.216 distance: 135 - 136: 46.546 distance: 136 - 137: 29.826 distance: 137 - 138: 14.485 distance: 138 - 139: 22.766 distance: 140 - 141: 21.190 distance: 141 - 142: 43.556 distance: 141 - 144: 52.143 distance: 142 - 143: 21.508 distance: 142 - 148: 17.488 distance: 144 - 145: 37.696 distance: 145 - 146: 11.329 distance: 145 - 147: 11.930 distance: 148 - 149: 3.531 distance: 148 - 154: 12.957 distance: 149 - 150: 17.023 distance: 149 - 152: 13.053 distance: 150 - 151: 8.339 distance: 150 - 155: 10.394 distance: 152 - 153: 6.867 distance: 153 - 154: 20.644