Starting phenix.real_space_refine on Sun Oct 12 05:51:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.map" model { file = "/net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x2f_38008/10_2025/8x2f_38008.cif" } resolution = 2.62 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11609 atoms to isotropic. 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 66 5.16 5 C 7599 2.51 5 N 2064 2.21 5 O 2383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12112 Number of models: 1 Model: "" Number of chains: 12 Chain: "B" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3923 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3916 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3923 Classifications: {'peptide': 491} Link IDs: {'PTRANS': 19, 'TRANS': 471} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "C" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "G" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'FUC': 1, 'GAL': 1, 'NAG': 1, 'SIA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Chain: "I" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.94, per 1000 atoms: 0.24 Number of scatterers: 12112 At special positions: 0 Unit cell: (89.7, 89.7, 152.49, 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 66 16.00 O 2383 8.00 N 2064 7.00 C 7599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 466 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 67 " distance=2.04 Simple disulfide: pdb=" SG CYS B 90 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 473 " - pdb=" SG CYS B 477 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS E 466 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 274 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 67 " distance=2.03 Simple disulfide: pdb=" SG CYS E 90 " - pdb=" SG CYS E 135 " distance=2.03 Simple disulfide: pdb=" SG CYS E 278 " - pdb=" SG CYS E 302 " distance=2.03 Simple disulfide: pdb=" SG CYS E 473 " - pdb=" SG CYS E 477 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 466 " distance=2.06 Simple disulfide: pdb=" SG CYS F 42 " - pdb=" SG CYS F 274 " distance=2.02 Simple disulfide: pdb=" SG CYS F 55 " - pdb=" SG CYS F 67 " distance=2.03 Simple disulfide: pdb=" SG CYS F 90 " - pdb=" SG CYS F 135 " distance=2.03 Simple disulfide: pdb=" SG CYS F 278 " - pdb=" SG CYS F 302 " distance=2.03 Simple disulfide: pdb=" SG CYS F 473 " - pdb=" SG CYS F 477 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG A 1 " - " FUC A 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG D 1 " - " FUC D 4 " " NAG H 1 " - " FUC H 4 " BETA1-4 " NAG A 1 " - " GAL A 2 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " GAL D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " GAL H 2 " " NAG I 1 " - " NAG I 2 " BETA2-3 " GAL A 2 " - " SIA A 3 " ~> Even though SIA is an alpha isomer, a beta linkage is required... " GAL D 2 " - " SIA D 3 " " GAL H 2 " - " SIA H 3 " NAG-ASN " NAG B 601 " - " ASN B 23 " " NAG B 602 " - " ASN B 286 " " NAG B 603 " - " ASN B 483 " " NAG C 1 " - " ASN B 165 " " NAG E 601 " - " ASN E 23 " " NAG E 602 " - " ASN E 286 " " NAG F 601 " - " ASN F 23 " " NAG F 602 " - " ASN F 286 " " NAG G 1 " - " ASN E 165 " " NAG I 1 " - " ASN F 165 " Time building additional restraints: 1.11 Conformation dependent library (CDL) restraints added in 550.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 34 sheets defined 25.3% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'B' and resid 56 through 62 Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 118 through 122 removed outlier: 3.580A pdb=" N TRP B 122 " --> pdb=" O LYS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 191 Processing helix chain 'B' and resid 369 through 388 removed outlier: 3.699A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 456 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 487 through 500 removed outlier: 3.994A pdb=" N TYR B 491 " --> pdb=" O ASP B 487 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU B 493 " --> pdb=" O PRO B 489 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N GLU B 494 " --> pdb=" O GLN B 490 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU B 497 " --> pdb=" O GLU B 493 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LYS B 498 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU B 500 " --> pdb=" O ARG B 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 97 through 105 Processing helix chain 'E' and resid 118 through 122 removed outlier: 3.582A pdb=" N TRP E 122 " --> pdb=" O LYS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 191 Processing helix chain 'E' and resid 366 through 388 removed outlier: 3.623A pdb=" N ILE E 385 " --> pdb=" O VAL E 381 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N MET E 388 " --> pdb=" O ILE E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 455 removed outlier: 3.596A pdb=" N LEU E 437 " --> pdb=" O ASN E 433 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E 444 " --> pdb=" O HIS E 440 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN E 454 " --> pdb=" O LYS E 450 " (cutoff:3.500A) Processing helix chain 'E' and resid 474 through 484 removed outlier: 4.132A pdb=" N MET E 478 " --> pdb=" O ASP E 474 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLU E 479 " --> pdb=" O ASN E 475 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER E 480 " --> pdb=" O GLU E 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 62 Processing helix chain 'F' and resid 67 through 71 removed outlier: 3.841A pdb=" N PHE F 70 " --> pdb=" O CYS F 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE F 71 " --> pdb=" O ASP F 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 67 through 71' Processing helix chain 'F' and resid 97 through 106 Processing helix chain 'F' and resid 118 through 122 Processing helix chain 'F' and resid 183 through 191 removed outlier: 3.506A pdb=" N ASN F 189 " --> pdb=" O GLU F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 388 removed outlier: 3.516A pdb=" N MET F 388 " --> pdb=" O ILE F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 403 through 455 removed outlier: 3.501A pdb=" N GLU F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU F 418 " --> pdb=" O GLU F 414 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU F 434 " --> pdb=" O LEU F 430 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS F 450 " --> pdb=" O ASN F 446 " (cutoff:3.500A) Processing helix chain 'F' and resid 478 through 482 removed outlier: 3.576A pdb=" N VAL F 481 " --> pdb=" O MET F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 488 through 490 No H-bonds generated for 'chain 'F' and resid 488 through 490' Processing helix chain 'F' and resid 491 through 498 Processing sheet with id=AA1, first strand: chain 'B' and resid 362 through 365 Processing sheet with id=AA2, first strand: chain 'B' and resid 15 through 16 Processing sheet with id=AA3, first strand: chain 'B' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'B' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'B' and resid 41 through 44 removed outlier: 6.957A pdb=" N LEU B 41 " --> pdb=" O GLY B 272 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS B 274 " --> pdb=" O LEU B 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 51 removed outlier: 6.659A pdb=" N LEU B 50 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.636A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N LEU B 175 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TYR B 252 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL B 257 " --> pdb=" O HIS B 110 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS B 110 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LYS B 259 " --> pdb=" O ILE B 108 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 108 " --> pdb=" O LYS B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 95 removed outlier: 3.636A pdb=" N ARG B 225 " --> pdb=" O HIS B 180 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N LEU B 175 " --> pdb=" O PRO B 250 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 132 through 136 Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AB2, first strand: chain 'B' and resid 283 through 284 Processing sheet with id=AB3, first strand: chain 'E' and resid 361 through 365 removed outlier: 3.876A pdb=" N GLY E 362 " --> pdb=" O HIS E 355 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS E 355 " --> pdb=" O GLY E 362 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 14 through 16 removed outlier: 4.111A pdb=" N GLU E 14 " --> pdb=" O VAL E 26 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AB6, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AB7, first strand: chain 'E' and resid 41 through 44 removed outlier: 6.990A pdb=" N LEU E 41 " --> pdb=" O GLY E 272 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N CYS E 274 " --> pdb=" O LEU E 41 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 50 through 51 removed outlier: 6.794A pdb=" N LEU E 50 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.543A pdb=" N ARG E 225 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N LEU E 175 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N TYR E 252 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 257 " --> pdb=" O HIS E 110 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS E 110 " --> pdb=" O VAL E 257 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS E 259 " --> pdb=" O ILE E 108 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE E 108 " --> pdb=" O LYS E 259 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 93 through 95 removed outlier: 3.543A pdb=" N ARG E 225 " --> pdb=" O HIS E 180 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU E 175 " --> pdb=" O PRO E 250 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 132 through 136 Processing sheet with id=AC3, first strand: chain 'E' and resid 160 through 165 removed outlier: 3.516A pdb=" N ILE E 162 " --> pdb=" O PHE E 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 283 through 284 Processing sheet with id=AC5, first strand: chain 'F' and resid 2 through 3 removed outlier: 3.519A pdb=" N ILE F 3 " --> pdb=" O PHE F 467 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE F 467 " --> pdb=" O ILE F 3 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 5 through 7 removed outlier: 3.505A pdb=" N GLY F 352 " --> pdb=" O GLY F 6 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 14 through 16 removed outlier: 4.133A pdb=" N GLU F 14 " --> pdb=" O VAL F 26 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 29 through 31 Processing sheet with id=AC9, first strand: chain 'F' and resid 33 through 34 Processing sheet with id=AD1, first strand: chain 'F' and resid 41 through 43 removed outlier: 5.360A pdb=" N LEU F 41 " --> pdb=" O GLY F 272 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N CYS F 274 " --> pdb=" O LEU F 41 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 50 through 51 removed outlier: 6.788A pdb=" N LEU F 50 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.573A pdb=" N ARG F 225 " --> pdb=" O HIS F 180 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LEU F 175 " --> pdb=" O TYR F 252 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR F 252 " --> pdb=" O LEU F 175 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 257 " --> pdb=" O HIS F 110 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N HIS F 110 " --> pdb=" O VAL F 257 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS F 259 " --> pdb=" O ILE F 108 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE F 108 " --> pdb=" O LYS F 259 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 93 through 95 removed outlier: 3.573A pdb=" N ARG F 225 " --> pdb=" O HIS F 180 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N LEU F 175 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 125 through 126 Processing sheet with id=AD6, first strand: chain 'F' and resid 160 through 165 Processing sheet with id=AD7, first strand: chain 'F' and resid 284 through 285 removed outlier: 3.542A pdb=" N ILE F 285 " --> pdb=" O CYS F 278 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS F 278 " --> pdb=" O ILE F 285 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1305 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: 2.01 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3965 1.34 - 1.48: 3094 1.48 - 1.62: 5227 1.62 - 1.75: 0 1.75 - 1.89: 96 Bond restraints: 12382 Sorted by residual: bond pdb=" C1 SIA H 3 " pdb=" C2 SIA H 3 " ideal model delta sigma weight residual 1.585 1.516 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C1 SIA D 3 " pdb=" C2 SIA D 3 " ideal model delta sigma weight residual 1.585 1.517 0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C4 NAG C 1 " pdb=" O4 NAG C 1 " ideal model delta sigma weight residual 1.409 1.473 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C1 SIA D 3 " pdb=" O1A SIA D 3 " ideal model delta sigma weight residual 1.262 1.201 0.061 2.00e-02 2.50e+03 9.35e+00 bond pdb=" C1 SIA A 3 " pdb=" C2 SIA A 3 " ideal model delta sigma weight residual 1.585 1.524 0.061 2.00e-02 2.50e+03 9.26e+00 ... (remaining 12377 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 16562 2.73 - 5.45: 182 5.45 - 8.18: 21 8.18 - 10.91: 5 10.91 - 13.64: 4 Bond angle restraints: 16774 Sorted by residual: angle pdb=" C TYR F 137 " pdb=" CA TYR F 137 " pdb=" CB TYR F 137 " ideal model delta sigma weight residual 116.54 110.34 6.20 1.15e+00 7.56e-01 2.91e+01 angle pdb=" N CYS F 466 " pdb=" CA CYS F 466 " pdb=" C CYS F 466 " ideal model delta sigma weight residual 109.52 116.81 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" C1 SIA D 3 " pdb=" C2 SIA D 3 " pdb=" C3 SIA D 3 " ideal model delta sigma weight residual 115.48 101.84 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" C1 SIA H 3 " pdb=" C2 SIA H 3 " pdb=" O6 SIA H 3 " ideal model delta sigma weight residual 109.00 96.28 12.72 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C1 SIA H 3 " pdb=" C2 SIA H 3 " pdb=" C3 SIA H 3 " ideal model delta sigma weight residual 115.48 103.28 12.20 3.00e+00 1.11e-01 1.65e+01 ... (remaining 16769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 7182 22.12 - 44.24: 470 44.24 - 66.36: 80 66.36 - 88.48: 19 88.48 - 110.60: 28 Dihedral angle restraints: 7779 sinusoidal: 3511 harmonic: 4268 Sorted by residual: dihedral pdb=" CB CYS E 473 " pdb=" SG CYS E 473 " pdb=" SG CYS E 477 " pdb=" CB CYS E 477 " ideal model delta sinusoidal sigma weight residual -86.00 -160.70 74.70 1 1.00e+01 1.00e-02 7.07e+01 dihedral pdb=" CB CYS E 42 " pdb=" SG CYS E 42 " pdb=" SG CYS E 274 " pdb=" CB CYS E 274 " ideal model delta sinusoidal sigma weight residual -86.00 -16.35 -69.65 1 1.00e+01 1.00e-02 6.26e+01 dihedral pdb=" CB CYS E 55 " pdb=" SG CYS E 55 " pdb=" SG CYS E 67 " pdb=" CB CYS E 67 " ideal model delta sinusoidal sigma weight residual 93.00 162.41 -69.41 1 1.00e+01 1.00e-02 6.22e+01 ... (remaining 7776 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 1829 0.125 - 0.251: 28 0.251 - 0.376: 4 0.376 - 0.502: 1 0.502 - 0.627: 2 Chirality restraints: 1864 Sorted by residual: chirality pdb=" C2 SIA D 3 " pdb=" O3 GAL D 2 " pdb=" C1 SIA D 3 " pdb=" O6 SIA D 3 " both_signs ideal model delta sigma weight residual False -2.50 -3.13 0.63 2.00e-02 2.50e+03 9.84e+02 chirality pdb=" C2 SIA H 3 " pdb=" O3 GAL H 2 " pdb=" C1 SIA H 3 " pdb=" O6 SIA H 3 " both_signs ideal model delta sigma weight residual False -2.50 -3.01 0.51 2.00e-02 2.50e+03 6.44e+02 chirality pdb=" C2 SIA A 3 " pdb=" O3 GAL A 2 " pdb=" C1 SIA A 3 " pdb=" O6 SIA A 3 " both_signs ideal model delta sigma weight residual False -2.50 -2.99 0.49 2.00e-02 2.50e+03 5.93e+02 ... (remaining 1861 not shown) Planarity restraints: 2167 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 1 " 0.241 2.00e-02 2.50e+03 2.00e-01 5.02e+02 pdb=" C7 NAG C 1 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG C 1 " 0.167 2.00e-02 2.50e+03 pdb=" N2 NAG C 1 " -0.333 2.00e-02 2.50e+03 pdb=" O7 NAG C 1 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.185 2.00e-02 2.50e+03 1.53e-01 2.91e+02 pdb=" C7 NAG I 1 " 0.052 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.136 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.246 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.135 2.00e-02 2.50e+03 1.15e-01 1.65e+02 pdb=" C7 NAG A 1 " -0.028 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.032 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.184 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.109 2.00e-02 2.50e+03 ... (remaining 2164 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2766 2.79 - 3.32: 10436 3.32 - 3.84: 18649 3.84 - 4.37: 22488 4.37 - 4.90: 39041 Nonbonded interactions: 93380 Sorted by model distance: nonbonded pdb=" ND1 HIS F 355 " pdb=" OE1 GLU F 479 " model vdw 2.260 3.120 nonbonded pdb=" N GLU F 270 " pdb=" OE1 GLU F 270 " model vdw 2.262 3.120 nonbonded pdb=" O TYR B 488 " pdb=" OG SER B 492 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR F 448 " pdb=" OE2 GLU F 461 " model vdw 2.295 3.040 nonbonded pdb=" N GLU B 340 " pdb=" OE1 GLU B 340 " model vdw 2.323 3.120 ... (remaining 93375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'B' and (resid 1 through 320 or (resid 331 and (name N or name CA or name \ C or name O or name CB )) or resid 332 through 602)) selection = chain 'E' selection = (chain 'F' and (resid 1 through 320 or (resid 331 and (name N or name CA or name \ C or name O or name CB )) or resid 332 through 602)) } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'I' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.970 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.020 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:8.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 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 : 0.004 0.085 12422 Z= 0.219 Angle : 0.814 14.761 16876 Z= 0.381 Chirality : 0.054 0.627 1864 Planarity : 0.008 0.200 2157 Dihedral : 16.399 110.602 4989 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.39 % Allowed : 13.31 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.20), residues: 1460 helix: 0.40 (0.26), residues: 370 sheet: 0.03 (0.29), residues: 298 loop : -1.66 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.027 0.001 TYR F 491 PHE 0.009 0.001 PHE F 467 TRP 0.009 0.001 TRP F 122 HIS 0.009 0.001 HIS F 355 Details of bonding type rmsd covalent geometry : bond 0.00431 (12382) covalent geometry : angle 0.72140 (16774) SS BOND : bond 0.00795 ( 18) SS BOND : angle 1.78986 ( 36) hydrogen bonds : bond 0.29220 ( 433) hydrogen bonds : angle 7.52238 ( 1305) link_BETA1-3 : bond 0.00454 ( 3) link_BETA1-3 : angle 2.26434 ( 9) link_BETA1-4 : bond 0.01970 ( 6) link_BETA1-4 : angle 3.96716 ( 18) link_BETA2-3 : bond 0.06257 ( 3) link_BETA2-3 : angle 9.31116 ( 9) link_NAG-ASN : bond 0.01093 ( 10) link_NAG-ASN : angle 6.38361 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 388 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7545 (mmm) REVERT: F 449 ASP cc_start: 0.8524 (m-30) cc_final: 0.8201 (p0) outliers start: 18 outliers final: 15 residues processed: 69 average time/residue: 0.5543 time to fit residues: 42.1793 Evaluate side-chains 68 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 52 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 77 SER Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 3 ILE Chi-restraints excluded: chain F residue 43 ASP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 483 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 ASN B 146 ASN B 166 ASN B 240 HIS B 246 ASN B 371 GLN B 391 GLN B 424 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 11 ASN E 30 GLN E 222 GLN E 391 GLN E 408 ASN E 410 ASN F 30 GLN F 87 ASN F 109 ASN F 138 GLN F 154 ASN F 279 GLN F 292 HIS ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 ASN F 391 GLN F 401 ASN ** F 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.067918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.045719 restraints weight = 32406.095| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.18 r_work: 0.2523 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12422 Z= 0.179 Angle : 0.650 9.410 16876 Z= 0.331 Chirality : 0.045 0.240 1864 Planarity : 0.004 0.043 2157 Dihedral : 12.587 90.091 2168 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.32 % Allowed : 11.15 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.20), residues: 1460 helix: 1.69 (0.27), residues: 372 sheet: 0.39 (0.30), residues: 296 loop : -1.71 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 496 TYR 0.017 0.001 TYR F 353 PHE 0.017 0.001 PHE F 338 TRP 0.011 0.001 TRP B 421 HIS 0.009 0.001 HIS F 355 Details of bonding type rmsd covalent geometry : bond 0.00391 (12382) covalent geometry : angle 0.62862 (16774) SS BOND : bond 0.00346 ( 18) SS BOND : angle 1.14092 ( 36) hydrogen bonds : bond 0.09681 ( 433) hydrogen bonds : angle 5.20320 ( 1305) link_BETA1-3 : bond 0.01147 ( 3) link_BETA1-3 : angle 2.01567 ( 9) link_BETA1-4 : bond 0.01103 ( 6) link_BETA1-4 : angle 2.77014 ( 18) link_BETA2-3 : bond 0.01053 ( 3) link_BETA2-3 : angle 4.09583 ( 9) link_NAG-ASN : bond 0.00292 ( 10) link_NAG-ASN : angle 2.00710 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: E 462 LEU cc_start: 0.8903 (mm) cc_final: 0.8568 (mp) outliers start: 30 outliers final: 10 residues processed: 89 average time/residue: 0.5397 time to fit residues: 53.0196 Evaluate side-chains 62 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 353 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 61 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 25 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 HIS ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN F 207 GLN ** F 355 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 471 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.066476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.043936 restraints weight = 33123.351| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 3.23 r_work: 0.2461 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12422 Z= 0.251 Angle : 0.678 9.293 16876 Z= 0.342 Chirality : 0.046 0.213 1864 Planarity : 0.004 0.047 2157 Dihedral : 10.893 94.072 2152 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.71 % Allowed : 11.61 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.21), residues: 1460 helix: 1.90 (0.27), residues: 371 sheet: 0.46 (0.30), residues: 296 loop : -1.81 (0.18), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 496 TYR 0.015 0.001 TYR F 353 PHE 0.020 0.002 PHE F 338 TRP 0.011 0.001 TRP B 421 HIS 0.007 0.001 HIS F 355 Details of bonding type rmsd covalent geometry : bond 0.00592 (12382) covalent geometry : angle 0.65597 (16774) SS BOND : bond 0.00629 ( 18) SS BOND : angle 1.26135 ( 36) hydrogen bonds : bond 0.09595 ( 433) hydrogen bonds : angle 5.06059 ( 1305) link_BETA1-3 : bond 0.00915 ( 3) link_BETA1-3 : angle 2.20981 ( 9) link_BETA1-4 : bond 0.00805 ( 6) link_BETA1-4 : angle 2.74297 ( 18) link_BETA2-3 : bond 0.01405 ( 3) link_BETA2-3 : angle 4.64834 ( 9) link_NAG-ASN : bond 0.00232 ( 10) link_NAG-ASN : angle 1.81538 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 60 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: B 335 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7537 (mp) REVERT: E 462 LEU cc_start: 0.8952 (mm) cc_final: 0.8675 (mt) outliers start: 35 outliers final: 13 residues processed: 86 average time/residue: 0.5270 time to fit residues: 50.1481 Evaluate side-chains 67 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 338 PHE Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 451 VAL Chi-restraints excluded: chain F residue 462 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 143 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 141 optimal weight: 4.9990 chunk 70 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 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 = 0.3197 r_free = 0.3197 target = 0.067563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.045218 restraints weight = 32906.261| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.21 r_work: 0.2513 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12422 Z= 0.173 Angle : 0.611 9.393 16876 Z= 0.308 Chirality : 0.043 0.224 1864 Planarity : 0.004 0.043 2157 Dihedral : 9.652 97.801 2152 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.32 % Allowed : 12.93 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.21), residues: 1460 helix: 2.15 (0.27), residues: 367 sheet: 0.66 (0.31), residues: 278 loop : -1.67 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 72 TYR 0.012 0.001 TYR E 353 PHE 0.017 0.001 PHE F 338 TRP 0.010 0.001 TRP B 421 HIS 0.003 0.001 HIS B 8 Details of bonding type rmsd covalent geometry : bond 0.00390 (12382) covalent geometry : angle 0.59061 (16774) SS BOND : bond 0.00459 ( 18) SS BOND : angle 1.38645 ( 36) hydrogen bonds : bond 0.08509 ( 433) hydrogen bonds : angle 4.84036 ( 1305) link_BETA1-3 : bond 0.00922 ( 3) link_BETA1-3 : angle 1.99797 ( 9) link_BETA1-4 : bond 0.00907 ( 6) link_BETA1-4 : angle 2.71028 ( 18) link_BETA2-3 : bond 0.00891 ( 3) link_BETA2-3 : angle 4.06933 ( 9) link_NAG-ASN : bond 0.00166 ( 10) link_NAG-ASN : angle 1.54621 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: B 335 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7530 (mp) REVERT: E 462 LEU cc_start: 0.8988 (mm) cc_final: 0.8701 (mt) REVERT: E 470 TYR cc_start: 0.9243 (m-80) cc_final: 0.9008 (m-80) REVERT: F 491 TYR cc_start: 0.7727 (OUTLIER) cc_final: 0.7236 (t80) outliers start: 30 outliers final: 13 residues processed: 85 average time/residue: 0.5072 time to fit residues: 47.7607 Evaluate side-chains 70 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 462 LEU Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 86 optimal weight: 9.9990 chunk 55 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 111 optimal weight: 0.0670 chunk 131 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 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 = 0.3224 r_free = 0.3224 target = 0.068934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.046401 restraints weight = 32922.705| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.23 r_work: 0.2545 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12422 Z= 0.124 Angle : 0.570 9.460 16876 Z= 0.288 Chirality : 0.042 0.210 1864 Planarity : 0.003 0.037 2157 Dihedral : 8.685 101.534 2150 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.40 % Allowed : 13.31 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.21), residues: 1460 helix: 2.30 (0.28), residues: 367 sheet: 0.85 (0.31), residues: 286 loop : -1.56 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 72 TYR 0.011 0.001 TYR E 353 PHE 0.029 0.001 PHE F 338 TRP 0.010 0.001 TRP E 421 HIS 0.004 0.000 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00245 (12382) covalent geometry : angle 0.55118 (16774) SS BOND : bond 0.00284 ( 18) SS BOND : angle 1.01057 ( 36) hydrogen bonds : bond 0.07636 ( 433) hydrogen bonds : angle 4.64716 ( 1305) link_BETA1-3 : bond 0.00941 ( 3) link_BETA1-3 : angle 1.83566 ( 9) link_BETA1-4 : bond 0.00887 ( 6) link_BETA1-4 : angle 2.71510 ( 18) link_BETA2-3 : bond 0.00584 ( 3) link_BETA2-3 : angle 3.71513 ( 9) link_NAG-ASN : bond 0.00204 ( 10) link_NAG-ASN : angle 1.40215 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 61 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 ILE cc_start: 0.7798 (OUTLIER) cc_final: 0.7492 (mp) REVERT: E 462 LEU cc_start: 0.9027 (mm) cc_final: 0.8724 (mt) REVERT: E 470 TYR cc_start: 0.9282 (m-80) cc_final: 0.9043 (m-80) REVERT: F 367 LYS cc_start: 0.9269 (mmtt) cc_final: 0.9019 (mmpt) outliers start: 31 outliers final: 14 residues processed: 89 average time/residue: 0.5097 time to fit residues: 50.3060 Evaluate side-chains 66 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ASP Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 63 optimal weight: 1.9990 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 0.8980 chunk 73 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 146 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 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 = 0.3203 r_free = 0.3203 target = 0.067922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.045575 restraints weight = 32636.533| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.20 r_work: 0.2525 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12422 Z= 0.164 Angle : 0.590 8.857 16876 Z= 0.296 Chirality : 0.043 0.172 1864 Planarity : 0.003 0.039 2157 Dihedral : 8.181 107.461 2150 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.09 % Allowed : 14.24 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.21), residues: 1460 helix: 2.34 (0.28), residues: 367 sheet: 0.81 (0.31), residues: 278 loop : -1.54 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.015 0.001 TYR B 491 PHE 0.040 0.001 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.004 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00377 (12382) covalent geometry : angle 0.56969 (16774) SS BOND : bond 0.00336 ( 18) SS BOND : angle 1.31428 ( 36) hydrogen bonds : bond 0.07776 ( 433) hydrogen bonds : angle 4.58772 ( 1305) link_BETA1-3 : bond 0.00900 ( 3) link_BETA1-3 : angle 1.96029 ( 9) link_BETA1-4 : bond 0.00767 ( 6) link_BETA1-4 : angle 2.82672 ( 18) link_BETA2-3 : bond 0.00915 ( 3) link_BETA2-3 : angle 3.81977 ( 9) link_NAG-ASN : bond 0.00170 ( 10) link_NAG-ASN : angle 1.49560 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7524 (mp) REVERT: E 462 LEU cc_start: 0.9050 (mm) cc_final: 0.8734 (mt) REVERT: E 470 TYR cc_start: 0.9276 (m-80) cc_final: 0.9024 (m-80) REVERT: F 274 CYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5803 (p) outliers start: 27 outliers final: 13 residues processed: 80 average time/residue: 0.4863 time to fit residues: 43.1360 Evaluate side-chains 67 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain B residue 455 LEU Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 105 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 143 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.068258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.046036 restraints weight = 32596.985| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.17 r_work: 0.2534 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12422 Z= 0.148 Angle : 0.582 8.761 16876 Z= 0.293 Chirality : 0.042 0.173 1864 Planarity : 0.003 0.045 2157 Dihedral : 7.749 113.071 2148 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.09 % Allowed : 14.24 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.21), residues: 1460 helix: 2.41 (0.28), residues: 367 sheet: 0.86 (0.31), residues: 278 loop : -1.52 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 496 TYR 0.010 0.001 TYR E 353 PHE 0.035 0.001 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.004 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00333 (12382) covalent geometry : angle 0.56294 (16774) SS BOND : bond 0.00331 ( 18) SS BOND : angle 1.23316 ( 36) hydrogen bonds : bond 0.07545 ( 433) hydrogen bonds : angle 4.50813 ( 1305) link_BETA1-3 : bond 0.00952 ( 3) link_BETA1-3 : angle 1.94240 ( 9) link_BETA1-4 : bond 0.00757 ( 6) link_BETA1-4 : angle 2.74781 ( 18) link_BETA2-3 : bond 0.00693 ( 3) link_BETA2-3 : angle 3.57768 ( 9) link_NAG-ASN : bond 0.00164 ( 10) link_NAG-ASN : angle 1.47422 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 335 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7513 (mp) REVERT: E 462 LEU cc_start: 0.9067 (mm) cc_final: 0.8729 (mt) REVERT: E 470 TYR cc_start: 0.9280 (m-80) cc_final: 0.9018 (m-80) REVERT: F 274 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5775 (p) REVERT: F 478 MET cc_start: 0.8121 (pp-130) cc_final: 0.7904 (ppp) outliers start: 27 outliers final: 11 residues processed: 79 average time/residue: 0.4908 time to fit residues: 43.1167 Evaluate side-chains 67 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 59 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.067797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.045548 restraints weight = 32465.617| |-----------------------------------------------------------------------------| r_work (start): 0.2659 rms_B_bonded: 3.18 r_work: 0.2520 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12422 Z= 0.169 Angle : 0.600 9.242 16876 Z= 0.302 Chirality : 0.043 0.161 1864 Planarity : 0.004 0.065 2157 Dihedral : 7.650 116.620 2148 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.47 % Allowed : 15.17 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.21), residues: 1460 helix: 2.26 (0.28), residues: 367 sheet: 0.86 (0.32), residues: 278 loop : -1.58 (0.19), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 496 TYR 0.012 0.001 TYR B 491 PHE 0.042 0.001 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.004 0.001 HIS F 471 Details of bonding type rmsd covalent geometry : bond 0.00392 (12382) covalent geometry : angle 0.57926 (16774) SS BOND : bond 0.00339 ( 18) SS BOND : angle 1.53566 ( 36) hydrogen bonds : bond 0.07659 ( 433) hydrogen bonds : angle 4.61289 ( 1305) link_BETA1-3 : bond 0.00873 ( 3) link_BETA1-3 : angle 1.99954 ( 9) link_BETA1-4 : bond 0.00777 ( 6) link_BETA1-4 : angle 2.74099 ( 18) link_BETA2-3 : bond 0.00824 ( 3) link_BETA2-3 : angle 3.58598 ( 9) link_NAG-ASN : bond 0.00148 ( 10) link_NAG-ASN : angle 1.54127 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 55 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.9232 (OUTLIER) cc_final: 0.8599 (mmm) REVERT: B 335 ILE cc_start: 0.7851 (OUTLIER) cc_final: 0.7560 (mp) REVERT: E 462 LEU cc_start: 0.9083 (mm) cc_final: 0.8754 (mt) REVERT: E 470 TYR cc_start: 0.9281 (m-80) cc_final: 0.9034 (m-80) REVERT: F 274 CYS cc_start: 0.5973 (OUTLIER) cc_final: 0.5751 (p) outliers start: 19 outliers final: 14 residues processed: 71 average time/residue: 0.5277 time to fit residues: 41.3651 Evaluate side-chains 70 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 111 PHE Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 124 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 ASN ** B 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.045133 restraints weight = 32655.584| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.18 r_work: 0.2501 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 12422 Z= 0.198 Angle : 0.630 9.502 16876 Z= 0.317 Chirality : 0.043 0.223 1864 Planarity : 0.004 0.072 2157 Dihedral : 7.638 117.478 2148 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.78 % Allowed : 14.71 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.21), residues: 1460 helix: 2.16 (0.28), residues: 367 sheet: 0.83 (0.32), residues: 278 loop : -1.61 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 456 TYR 0.010 0.001 TYR E 353 PHE 0.041 0.001 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.003 0.001 HIS F 471 Details of bonding type rmsd covalent geometry : bond 0.00469 (12382) covalent geometry : angle 0.61015 (16774) SS BOND : bond 0.00333 ( 18) SS BOND : angle 1.44312 ( 36) hydrogen bonds : bond 0.07825 ( 433) hydrogen bonds : angle 4.65611 ( 1305) link_BETA1-3 : bond 0.00870 ( 3) link_BETA1-3 : angle 2.05536 ( 9) link_BETA1-4 : bond 0.00769 ( 6) link_BETA1-4 : angle 2.70216 ( 18) link_BETA2-3 : bond 0.00891 ( 3) link_BETA2-3 : angle 3.70577 ( 9) link_NAG-ASN : bond 0.00151 ( 10) link_NAG-ASN : angle 1.59621 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 53 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8612 (mmm) REVERT: B 335 ILE cc_start: 0.7840 (OUTLIER) cc_final: 0.7561 (mp) REVERT: E 462 LEU cc_start: 0.9089 (mm) cc_final: 0.8762 (mt) REVERT: E 470 TYR cc_start: 0.9300 (m-80) cc_final: 0.9052 (m-80) REVERT: F 274 CYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5714 (p) outliers start: 23 outliers final: 13 residues processed: 74 average time/residue: 0.4816 time to fit residues: 39.5963 Evaluate side-chains 69 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 299 ILE Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 116 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 125 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 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 = 0.3191 r_free = 0.3191 target = 0.067282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.045087 restraints weight = 32792.156| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.19 r_work: 0.2501 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12422 Z= 0.189 Angle : 0.628 9.685 16876 Z= 0.317 Chirality : 0.043 0.144 1864 Planarity : 0.004 0.076 2157 Dihedral : 7.629 118.051 2148 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.32 % Allowed : 15.09 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.21), residues: 1460 helix: 2.15 (0.28), residues: 367 sheet: 0.82 (0.32), residues: 278 loop : -1.63 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 456 TYR 0.010 0.001 TYR E 353 PHE 0.040 0.002 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.003 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00443 (12382) covalent geometry : angle 0.60887 (16774) SS BOND : bond 0.00319 ( 18) SS BOND : angle 1.39392 ( 36) hydrogen bonds : bond 0.07852 ( 433) hydrogen bonds : angle 4.67457 ( 1305) link_BETA1-3 : bond 0.00854 ( 3) link_BETA1-3 : angle 2.07396 ( 9) link_BETA1-4 : bond 0.00768 ( 6) link_BETA1-4 : angle 2.63878 ( 18) link_BETA2-3 : bond 0.00742 ( 3) link_BETA2-3 : angle 3.72893 ( 9) link_NAG-ASN : bond 0.00136 ( 10) link_NAG-ASN : angle 1.63344 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2920 Ramachandran restraints generated. 1460 Oldfield, 0 Emsley, 1460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.8617 (mmm) REVERT: B 335 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7527 (mp) REVERT: E 462 LEU cc_start: 0.9101 (mm) cc_final: 0.8778 (mt) REVERT: E 470 TYR cc_start: 0.9311 (m-80) cc_final: 0.9086 (m-80) REVERT: F 274 CYS cc_start: 0.5933 (OUTLIER) cc_final: 0.5711 (p) REVERT: F 289 MET cc_start: 0.9092 (mmm) cc_final: 0.7948 (mtm) outliers start: 17 outliers final: 12 residues processed: 68 average time/residue: 0.5024 time to fit residues: 37.9887 Evaluate side-chains 68 residues out of total 1293 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 111 PHE Chi-restraints excluded: chain B residue 289 MET Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 335 ILE Chi-restraints excluded: chain B residue 353 TYR Chi-restraints excluded: chain E residue 8 HIS Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 384 ILE Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 274 CYS Chi-restraints excluded: chain F residue 353 TYR Chi-restraints excluded: chain F residue 477 CYS Chi-restraints excluded: chain F residue 491 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 17 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 54 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 454 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 = 0.3207 r_free = 0.3207 target = 0.068024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.045569 restraints weight = 32649.615| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.20 r_work: 0.2533 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12422 Z= 0.145 Angle : 0.597 10.722 16876 Z= 0.300 Chirality : 0.042 0.142 1864 Planarity : 0.004 0.081 2157 Dihedral : 7.496 116.823 2148 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.39 % Allowed : 15.09 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1460 helix: 2.22 (0.28), residues: 367 sheet: 0.92 (0.32), residues: 278 loop : -1.56 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 72 TYR 0.010 0.001 TYR E 353 PHE 0.038 0.001 PHE F 338 TRP 0.009 0.001 TRP B 421 HIS 0.004 0.001 HIS E 273 Details of bonding type rmsd covalent geometry : bond 0.00327 (12382) covalent geometry : angle 0.57893 (16774) SS BOND : bond 0.00278 ( 18) SS BOND : angle 1.27088 ( 36) hydrogen bonds : bond 0.07380 ( 433) hydrogen bonds : angle 4.53583 ( 1305) link_BETA1-3 : bond 0.00871 ( 3) link_BETA1-3 : angle 1.93121 ( 9) link_BETA1-4 : bond 0.00819 ( 6) link_BETA1-4 : angle 2.49663 ( 18) link_BETA2-3 : bond 0.00446 ( 3) link_BETA2-3 : angle 3.47921 ( 9) link_NAG-ASN : bond 0.00136 ( 10) link_NAG-ASN : angle 1.57077 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3492.07 seconds wall clock time: 60 minutes 25.45 seconds (3625.45 seconds total)