Starting phenix.real_space_refine on Sat Aug 23 16:43:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7t_28910/08_2025/8f7t_28910.map" } resolution = 4.1 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= 0.001 sd= 0.011 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 108 5.16 5 C 8376 2.51 5 N 2280 2.21 5 O 2562 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13326 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "C" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 971 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 1, 'TRANS': 119} Chain breaks: 1 Chain: "E" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 Chain: "G" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3373 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 24, 'TRANS': 401} Chain breaks: 5 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: "K" 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: "L" 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: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "G" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.11, per 1000 atoms: 0.23 Number of scatterers: 13326 At special positions: 0 Unit cell: (119.52, 127.82, 114.54, 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 108 16.00 O 2562 8.00 N 2280 7.00 C 8376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 598 " - pdb=" SG CYS A 604 " distance=2.03 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS C 501 " distance=1.91 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS B 605 " - pdb=" SG CYS G 501 " distance=2.05 Simple disulfide: pdb=" SG CYS C 56 " - pdb=" SG CYS C 76 " distance=2.04 Simple disulfide: pdb=" SG CYS C 121 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 159 " distance=2.04 Simple disulfide: pdb=" SG CYS C 203 " - pdb=" SG CYS C 433 " distance=2.02 Simple disulfide: pdb=" SG CYS C 220 " - pdb=" SG CYS C 249 " distance=2.03 Simple disulfide: pdb=" SG CYS C 230 " - pdb=" SG CYS C 241 " distance=2.03 Simple disulfide: pdb=" SG CYS C 298 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 56 " - pdb=" SG CYS E 76 " distance=2.04 Simple disulfide: pdb=" SG CYS E 121 " - pdb=" SG CYS E 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 128 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 159 " distance=2.04 Simple disulfide: pdb=" SG CYS E 203 " - pdb=" SG CYS E 433 " distance=2.02 Simple disulfide: pdb=" SG CYS E 220 " - pdb=" SG CYS E 249 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 241 " distance=2.03 Simple disulfide: pdb=" SG CYS E 298 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 56 " - pdb=" SG CYS G 76 " distance=2.04 Simple disulfide: pdb=" SG CYS G 121 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 128 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 159 " distance=2.04 Simple disulfide: pdb=" SG CYS G 203 " - pdb=" SG CYS G 433 " distance=2.02 Simple disulfide: pdb=" SG CYS G 220 " - pdb=" SG CYS G 249 " distance=2.03 Simple disulfide: pdb=" SG CYS G 230 " - pdb=" SG CYS G 241 " distance=2.03 Simple disulfide: pdb=" SG CYS G 298 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.03 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " 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 BETA1-6 " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG C 601 " - " ASN C 291 " " NAG C 602 " - " ASN C 332 " " NAG C 603 " - " ASN C 132 " " NAG C 604 " - " ASN C 162 " " NAG E 601 " - " ASN E 291 " " NAG E 602 " - " ASN E 332 " " NAG E 603 " - " ASN E 132 " " NAG E 604 " - " ASN E 162 " " NAG G 601 " - " ASN G 291 " " NAG G 602 " - " ASN G 332 " " NAG G 603 " - " ASN G 132 " " NAG G 604 " - " ASN G 162 " " NAG I 1 " - " ASN C 448 " " NAG K 1 " - " ASN E 448 " " NAG L 1 " - " ASN G 448 " Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 517.4 milliseconds Enol-peptide restraints added in 1.2 microseconds 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3102 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 30 sheets defined 25.9% alpha, 23.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.145A pdb=" N GLY A 527 " --> pdb=" O GLY A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 Processing helix chain 'A' and resid 537 through 543 removed outlier: 3.503A pdb=" N ALA A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 595 removed outlier: 3.579A pdb=" N ILE A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 615 removed outlier: 3.821A pdb=" N TRP A 614 " --> pdb=" O ASN A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 626 removed outlier: 4.263A pdb=" N MET A 626 " --> pdb=" O ILE A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 636 Processing helix chain 'A' and resid 638 through 658 Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.079A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 537 through 543 Processing helix chain 'B' and resid 571 through 595 removed outlier: 3.521A pdb=" N ILE B 583 " --> pdb=" O ARG B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 615 removed outlier: 3.645A pdb=" N TRP B 614 " --> pdb=" O ASN B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.288A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 658 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP C 104 " --> pdb=" O ASN C 100 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 352 Processing helix chain 'C' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS C 485 " --> pdb=" O GLU C 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR C 486 " --> pdb=" O LEU C 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 482 through 486' Processing helix chain 'D' and resid 524 through 528 removed outlier: 4.128A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 537 through 543 removed outlier: 3.678A pdb=" N ALA D 541 " --> pdb=" O LEU D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 571 through 595 Processing helix chain 'D' and resid 611 through 615 removed outlier: 3.817A pdb=" N TRP D 614 " --> pdb=" O ASN D 611 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.853A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 636 Processing helix chain 'D' and resid 638 through 658 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP E 104 " --> pdb=" O ASN E 100 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 352 Processing helix chain 'E' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS E 485 " --> pdb=" O GLU E 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR E 486 " --> pdb=" O LEU E 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 482 through 486' Processing helix chain 'G' and resid 72 through 76 Processing helix chain 'G' and resid 100 through 118 removed outlier: 4.214A pdb=" N ASP G 104 " --> pdb=" O ASN G 100 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 352 Processing helix chain 'G' and resid 475 through 481 removed outlier: 3.989A pdb=" N TRP G 479 " --> pdb=" O MET G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 482 through 486 removed outlier: 4.347A pdb=" N LYS G 485 " --> pdb=" O GLU G 482 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR G 486 " --> pdb=" O LEU G 483 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 482 through 486' Processing sheet with id=AA1, first strand: chain 'C' and resid 37 through 42 Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 58 Processing sheet with id=AA3, first strand: chain 'C' and resid 86 through 88 removed outlier: 4.362A pdb=" N VAL C 244 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 93 through 96 removed outlier: 4.018A pdb=" N GLU C 93 " --> pdb=" O CYS C 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 156 through 159 Processing sheet with id=AA6, first strand: chain 'C' and resid 183 through 184 Processing sheet with id=AA7, first strand: chain 'C' and resid 262 through 263 removed outlier: 6.187A pdb=" N LEU C 262 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 443 " --> pdb=" O ARG C 300 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY C 451 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU C 453 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU C 290 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR C 455 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 286 through 300 current: chain 'C' and resid 359 through 361 Processing sheet with id=AA8, first strand: chain 'C' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL C 288 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR C 455 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU C 290 " --> pdb=" O LEU C 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU C 453 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU C 292 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY C 451 " --> pdb=" O GLU C 292 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE C 443 " --> pdb=" O ARG C 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 443 through 456 current: chain 'C' and resid 413 through 421 removed outlier: 4.239A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS C 385 " --> pdb=" O HIS C 374 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR C 305 " --> pdb=" O GLY C 321 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 423 through 424 Processing sheet with id=AB2, first strand: chain 'E' and resid 37 through 42 Processing sheet with id=AB3, first strand: chain 'E' and resid 57 through 58 Processing sheet with id=AB4, first strand: chain 'E' and resid 86 through 88 removed outlier: 4.361A pdb=" N VAL E 244 " --> pdb=" O LEU E 88 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 93 through 96 removed outlier: 4.019A pdb=" N GLU E 93 " --> pdb=" O CYS E 241 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 156 through 159 Processing sheet with id=AB7, first strand: chain 'E' and resid 183 through 184 Processing sheet with id=AB8, first strand: chain 'E' and resid 262 through 263 removed outlier: 6.188A pdb=" N LEU E 262 " --> pdb=" O THR E 450 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 443 " --> pdb=" O ARG E 300 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY E 451 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU E 292 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU E 453 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU E 290 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N THR E 455 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL E 288 " --> pdb=" O THR E 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 286 through 300 current: chain 'E' and resid 359 through 361 Processing sheet with id=AB9, first strand: chain 'E' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL E 288 " --> pdb=" O THR E 455 " (cutoff:3.500A) removed outlier: 10.744A pdb=" N THR E 455 " --> pdb=" O VAL E 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU E 290 " --> pdb=" O LEU E 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU E 453 " --> pdb=" O LEU E 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU E 292 " --> pdb=" O GLY E 451 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N GLY E 451 " --> pdb=" O GLU E 292 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE E 443 " --> pdb=" O ARG E 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 443 through 456 current: chain 'E' and resid 413 through 421 removed outlier: 4.240A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS E 385 " --> pdb=" O HIS E 374 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR E 305 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 423 through 424 Processing sheet with id=AC3, first strand: chain 'G' and resid 37 through 42 Processing sheet with id=AC4, first strand: chain 'G' and resid 57 through 58 Processing sheet with id=AC5, first strand: chain 'G' and resid 86 through 88 removed outlier: 4.361A pdb=" N VAL G 244 " --> pdb=" O LEU G 88 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 93 through 96 removed outlier: 4.018A pdb=" N GLU G 93 " --> pdb=" O CYS G 241 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 156 through 159 Processing sheet with id=AC8, first strand: chain 'G' and resid 183 through 184 Processing sheet with id=AC9, first strand: chain 'G' and resid 262 through 263 removed outlier: 6.187A pdb=" N LEU G 262 " --> pdb=" O THR G 450 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 443 " --> pdb=" O ARG G 300 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY G 451 " --> pdb=" O GLU G 292 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU G 292 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU G 453 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU G 290 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR G 455 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N VAL G 288 " --> pdb=" O THR G 455 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 286 through 300 current: chain 'G' and resid 359 through 361 Processing sheet with id=AD1, first strand: chain 'G' and resid 274 through 276 removed outlier: 11.112A pdb=" N VAL G 288 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 10.743A pdb=" N THR G 455 " --> pdb=" O VAL G 288 " (cutoff:3.500A) removed outlier: 12.360A pdb=" N LEU G 290 " --> pdb=" O LEU G 453 " (cutoff:3.500A) removed outlier: 12.249A pdb=" N LEU G 453 " --> pdb=" O LEU G 290 " (cutoff:3.500A) removed outlier: 10.775A pdb=" N GLU G 292 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N GLY G 451 " --> pdb=" O GLU G 292 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G 443 " --> pdb=" O ARG G 300 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 443 through 456 current: chain 'G' and resid 413 through 421 removed outlier: 4.240A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS G 385 " --> pdb=" O HIS G 374 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 304 through 310 removed outlier: 6.035A pdb=" N THR G 305 " --> pdb=" O GLY G 321 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 423 through 424 424 hydrogen bonds defined for protein. 1173 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: 1.63 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2202 1.30 - 1.43: 3362 1.43 - 1.56: 7876 1.56 - 1.69: 6 1.69 - 1.82: 144 Bond restraints: 13590 Sorted by residual: bond pdb=" C GLN C 315 " pdb=" O GLN C 315 " ideal model delta sigma weight residual 1.235 1.166 0.070 1.28e-02 6.10e+03 2.96e+01 bond pdb=" CA ILE C 311 " pdb=" CB ILE C 311 " ideal model delta sigma weight residual 1.540 1.488 0.052 1.36e-02 5.41e+03 1.48e+01 bond pdb=" N ARG C 310 " pdb=" CA ARG C 310 " ideal model delta sigma weight residual 1.453 1.410 0.044 1.22e-02 6.72e+03 1.29e+01 bond pdb=" CB ILE C 311 " pdb=" CG1 ILE C 311 " ideal model delta sigma weight residual 1.530 1.459 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ILE C 311 " pdb=" CA ILE C 311 " ideal model delta sigma weight residual 1.459 1.417 0.042 1.25e-02 6.40e+03 1.13e+01 ... (remaining 13585 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 17897 2.39 - 4.77: 471 4.77 - 7.16: 61 7.16 - 9.54: 8 9.54 - 11.93: 4 Bond angle restraints: 18441 Sorted by residual: angle pdb=" N THR G 163 " pdb=" CA THR G 163 " pdb=" C THR G 163 " ideal model delta sigma weight residual 109.24 118.85 -9.61 1.63e+00 3.76e-01 3.48e+01 angle pdb=" N THR C 163 " pdb=" CA THR C 163 " pdb=" C THR C 163 " ideal model delta sigma weight residual 109.24 118.84 -9.60 1.63e+00 3.76e-01 3.47e+01 angle pdb=" N THR E 163 " pdb=" CA THR E 163 " pdb=" C THR E 163 " ideal model delta sigma weight residual 109.24 118.82 -9.58 1.63e+00 3.76e-01 3.45e+01 angle pdb=" N ILE C 311 " pdb=" CA ILE C 311 " pdb=" C ILE C 311 " ideal model delta sigma weight residual 109.34 97.41 11.93 2.08e+00 2.31e-01 3.29e+01 angle pdb=" C GLY C 312 " pdb=" N PRO C 313 " pdb=" CA PRO C 313 " ideal model delta sigma weight residual 119.84 126.69 -6.85 1.25e+00 6.40e-01 3.00e+01 ... (remaining 18436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.09: 7627 25.09 - 50.18: 714 50.18 - 75.27: 114 75.27 - 100.36: 51 100.36 - 125.45: 38 Dihedral angle restraints: 8544 sinusoidal: 3780 harmonic: 4764 Sorted by residual: dihedral pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " pdb=" SG CYS C 241 " pdb=" CB CYS C 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS G 230 " pdb=" SG CYS G 230 " pdb=" SG CYS G 241 " pdb=" CB CYS G 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.74 -75.74 1 1.00e+01 1.00e-02 7.24e+01 dihedral pdb=" CB CYS E 230 " pdb=" SG CYS E 230 " pdb=" SG CYS E 241 " pdb=" CB CYS E 241 " ideal model delta sinusoidal sigma weight residual 93.00 168.73 -75.73 1 1.00e+01 1.00e-02 7.23e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1780 0.067 - 0.135: 333 0.135 - 0.202: 28 0.202 - 0.269: 3 0.269 - 0.336: 1 Chirality restraints: 2145 Sorted by residual: chirality pdb=" CA ILE C 311 " pdb=" N ILE C 311 " pdb=" C ILE C 311 " pdb=" CB ILE C 311 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE E 311 " pdb=" N ILE E 311 " pdb=" C ILE E 311 " pdb=" CB ILE E 311 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" CA ILE G 311 " pdb=" N ILE G 311 " pdb=" C ILE G 311 " pdb=" CB ILE G 311 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2142 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG G 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG G 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG G 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG G 604 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG C 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 604 " 0.360 2.00e-02 2.50e+03 3.07e-01 1.18e+03 pdb=" C7 NAG E 604 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG E 604 " 0.151 2.00e-02 2.50e+03 pdb=" N2 NAG E 604 " -0.544 2.00e-02 2.50e+03 pdb=" O7 NAG E 604 " 0.123 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 66 2.45 - 3.06: 8768 3.06 - 3.67: 19308 3.67 - 4.29: 27190 4.29 - 4.90: 45239 Nonbonded interactions: 100571 Sorted by model distance: nonbonded pdb=" CG PRO C 329 " pdb=" O CYS C 418 " model vdw 1.835 3.440 nonbonded pdb=" CG PRO G 329 " pdb=" O CYS G 418 " model vdw 1.874 3.440 nonbonded pdb=" CG PRO E 329 " pdb=" O CYS E 418 " model vdw 1.981 3.440 nonbonded pdb=" O ILE G 311 " pdb=" CB GLN G 315 " model vdw 2.095 3.440 nonbonded pdb=" OG1 THR A 606 " pdb=" O VAL C 38 " model vdw 2.114 3.040 ... (remaining 100566 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 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.150 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 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 0.121 13644 Z= 0.299 Angle : 0.895 11.931 18567 Z= 0.485 Chirality : 0.051 0.336 2145 Planarity : 0.013 0.307 2325 Dihedral : 21.491 125.448 5334 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.63 % Allowed : 10.42 % Favored : 88.95 % Rotamer: Outliers : 1.36 % Allowed : 29.13 % Favored : 69.51 % Cbeta Deviations : 0.06 % 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: -2.43 (0.20), residues: 1593 helix: 0.05 (0.27), residues: 381 sheet: -1.28 (0.24), residues: 396 loop : -2.68 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 306 TYR 0.016 0.002 TYR G 484 PHE 0.022 0.003 PHE C 161 TRP 0.023 0.002 TRP B 610 HIS 0.004 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00635 (13590) covalent geometry : angle 0.87799 (18441) SS BOND : bond 0.02077 ( 36) SS BOND : angle 1.87363 ( 72) hydrogen bonds : bond 0.19636 ( 403) hydrogen bonds : angle 6.73139 ( 1173) link_BETA1-6 : bond 0.00207 ( 3) link_BETA1-6 : angle 0.91290 ( 9) link_NAG-ASN : bond 0.01024 ( 15) link_NAG-ASN : angle 3.01647 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 354 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 592 LEU cc_start: 0.9079 (mt) cc_final: 0.8811 (mm) REVERT: D 591 GLN cc_start: 0.8450 (tp40) cc_final: 0.8221 (tp-100) REVERT: G 118 LEU cc_start: 0.8402 (tp) cc_final: 0.8049 (tp) outliers start: 20 outliers final: 4 residues processed: 370 average time/residue: 0.1077 time to fit residues: 55.5154 Evaluate side-chains 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 GLN B 616 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 650 GLN C 105 GLN ** C 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 105 GLN E 205 GLN G 105 GLN G 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.058310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.047079 restraints weight = 75539.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.048718 restraints weight = 42779.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.049920 restraints weight = 28870.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.050784 restraints weight = 21659.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.051437 restraints weight = 17435.136| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13644 Z= 0.216 Angle : 0.834 9.481 18567 Z= 0.413 Chirality : 0.051 0.269 2145 Planarity : 0.005 0.053 2325 Dihedral : 16.866 119.395 2169 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.66 % Favored : 90.96 % Rotamer: Outliers : 0.75 % Allowed : 5.69 % Favored : 93.56 % 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: -2.29 (0.20), residues: 1593 helix: 0.25 (0.27), residues: 384 sheet: -1.35 (0.22), residues: 450 loop : -2.62 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 542 TYR 0.041 0.002 TYR D 643 PHE 0.019 0.002 PHE D 573 TRP 0.040 0.003 TRP G 47 HIS 0.004 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00489 (13590) covalent geometry : angle 0.81432 (18441) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.51423 ( 72) hydrogen bonds : bond 0.04838 ( 403) hydrogen bonds : angle 5.61108 ( 1173) link_BETA1-6 : bond 0.00659 ( 3) link_BETA1-6 : angle 1.98492 ( 9) link_NAG-ASN : bond 0.00631 ( 15) link_NAG-ASN : angle 3.33440 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 278 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.8852 (mmm) cc_final: 0.8000 (mmm) REVERT: A 539 VAL cc_start: 0.8767 (t) cc_final: 0.8528 (p) REVERT: A 629 MET cc_start: 0.9469 (mmm) cc_final: 0.8629 (mmm) REVERT: B 530 MET cc_start: 0.8666 (mmt) cc_final: 0.7886 (mmm) REVERT: B 629 MET cc_start: 0.9684 (mtt) cc_final: 0.9098 (mmt) REVERT: C 102 MET cc_start: 0.9399 (mtm) cc_final: 0.9150 (mpp) REVERT: C 113 LEU cc_start: 0.9422 (mt) cc_final: 0.9172 (mt) REVERT: C 261 LEU cc_start: 0.9523 (mt) cc_final: 0.9291 (mt) REVERT: D 530 MET cc_start: 0.9254 (tpp) cc_final: 0.9014 (mmm) REVERT: D 601 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7528 (ptpp) REVERT: D 611 ASN cc_start: 0.7360 (OUTLIER) cc_final: 0.7079 (p0) REVERT: D 626 MET cc_start: 0.8787 (tpt) cc_final: 0.8407 (tpt) REVERT: G 40 VAL cc_start: 0.9540 (t) cc_final: 0.9211 (p) REVERT: G 88 LEU cc_start: 0.9488 (mt) cc_final: 0.9013 (mp) REVERT: G 102 MET cc_start: 0.9249 (mtm) cc_final: 0.8784 (mpp) REVERT: G 261 LEU cc_start: 0.9513 (mt) cc_final: 0.9245 (mt) REVERT: G 315 GLN cc_start: 0.9547 (mp10) cc_final: 0.9216 (mp10) outliers start: 11 outliers final: 5 residues processed: 287 average time/residue: 0.1197 time to fit residues: 48.4122 Evaluate side-chains 191 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 185 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 99 optimal weight: 0.9980 chunk 65 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 630 GLN C 352 HIS ** D 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.056085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.044907 restraints weight = 79085.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.046534 restraints weight = 44858.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.047648 restraints weight = 30355.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.048483 restraints weight = 22977.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.049080 restraints weight = 18550.619| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13644 Z= 0.220 Angle : 0.776 9.087 18567 Z= 0.385 Chirality : 0.048 0.285 2145 Planarity : 0.005 0.042 2325 Dihedral : 13.276 113.241 2169 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.60 % Favored : 90.02 % Rotamer: Outliers : 0.14 % Allowed : 6.37 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.32 (0.19), residues: 1593 helix: 0.04 (0.25), residues: 387 sheet: -1.36 (0.23), residues: 432 loop : -2.51 (0.20), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 644 TYR 0.013 0.002 TYR B 643 PHE 0.020 0.002 PHE E 391 TRP 0.020 0.002 TRP G 47 HIS 0.005 0.001 HIS E 352 Details of bonding type rmsd covalent geometry : bond 0.00490 (13590) covalent geometry : angle 0.76036 (18441) SS BOND : bond 0.00394 ( 36) SS BOND : angle 1.16100 ( 72) hydrogen bonds : bond 0.04496 ( 403) hydrogen bonds : angle 5.34547 ( 1173) link_BETA1-6 : bond 0.00355 ( 3) link_BETA1-6 : angle 1.75072 ( 9) link_NAG-ASN : bond 0.00526 ( 15) link_NAG-ASN : angle 2.97620 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 239 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9003 (mmm) cc_final: 0.8298 (mmm) REVERT: A 537 LEU cc_start: 0.9430 (mt) cc_final: 0.9099 (mp) REVERT: A 598 CYS cc_start: 0.8131 (m) cc_final: 0.7794 (m) REVERT: A 629 MET cc_start: 0.9474 (mmm) cc_final: 0.9220 (mmm) REVERT: B 530 MET cc_start: 0.8907 (mmt) cc_final: 0.7900 (mmm) REVERT: B 630 GLN cc_start: 0.9656 (OUTLIER) cc_final: 0.9446 (pm20) REVERT: C 102 MET cc_start: 0.9424 (mtm) cc_final: 0.9134 (mtm) REVERT: C 118 LEU cc_start: 0.9600 (tp) cc_final: 0.9299 (pp) REVERT: D 537 LEU cc_start: 0.8913 (mt) cc_final: 0.8546 (mp) REVERT: D 624 ASP cc_start: 0.9521 (m-30) cc_final: 0.9308 (m-30) REVERT: D 626 MET cc_start: 0.8976 (tpt) cc_final: 0.8545 (tpt) REVERT: D 643 TYR cc_start: 0.9683 (m-80) cc_final: 0.9390 (m-80) REVERT: E 99 LYS cc_start: 0.9352 (mmpt) cc_final: 0.9150 (mmmt) REVERT: E 492 LYS cc_start: 0.9579 (mttt) cc_final: 0.9356 (mtmt) REVERT: G 102 MET cc_start: 0.9311 (mtm) cc_final: 0.8737 (mpp) REVERT: G 118 LEU cc_start: 0.9571 (tp) cc_final: 0.9360 (pp) REVERT: G 261 LEU cc_start: 0.9493 (mt) cc_final: 0.9291 (mt) REVERT: G 434 MET cc_start: 0.9147 (mtm) cc_final: 0.8499 (mpp) outliers start: 2 outliers final: 0 residues processed: 241 average time/residue: 0.1253 time to fit residues: 41.9410 Evaluate side-chains 171 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 90 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 8.9990 chunk 153 optimal weight: 0.5980 chunk 158 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 630 GLN A 653 GLN C 205 GLN D 650 GLN D 653 GLN G 205 GLN G 260 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.057083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.045800 restraints weight = 77791.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.047452 restraints weight = 43636.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.048584 restraints weight = 29497.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.049430 restraints weight = 22278.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.050025 restraints weight = 17987.401| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13644 Z= 0.135 Angle : 0.732 9.396 18567 Z= 0.356 Chirality : 0.047 0.274 2145 Planarity : 0.004 0.033 2325 Dihedral : 10.298 76.259 2169 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.85 % Favored : 91.78 % Rotamer: Outliers : 0.27 % Allowed : 4.20 % Favored : 95.53 % 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: -2.10 (0.20), residues: 1593 helix: 0.13 (0.26), residues: 387 sheet: -1.03 (0.24), residues: 420 loop : -2.44 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 644 TYR 0.014 0.001 TYR C 219 PHE 0.025 0.002 PHE D 573 TRP 0.027 0.002 TRP B 571 HIS 0.004 0.001 HIS C 218 Details of bonding type rmsd covalent geometry : bond 0.00310 (13590) covalent geometry : angle 0.71837 (18441) SS BOND : bond 0.00229 ( 36) SS BOND : angle 0.99629 ( 72) hydrogen bonds : bond 0.04135 ( 403) hydrogen bonds : angle 5.06636 ( 1173) link_BETA1-6 : bond 0.00192 ( 3) link_BETA1-6 : angle 1.69480 ( 9) link_NAG-ASN : bond 0.00380 ( 15) link_NAG-ASN : angle 2.72324 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 239 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9111 (mmm) cc_final: 0.8425 (mmm) REVERT: A 537 LEU cc_start: 0.9380 (mt) cc_final: 0.9079 (mp) REVERT: A 598 CYS cc_start: 0.8031 (m) cc_final: 0.7611 (m) REVERT: A 630 GLN cc_start: 0.9646 (OUTLIER) cc_final: 0.9405 (pm20) REVERT: B 530 MET cc_start: 0.8805 (mmt) cc_final: 0.8102 (mmm) REVERT: B 629 MET cc_start: 0.8877 (mtt) cc_final: 0.8624 (mmt) REVERT: B 633 ARG cc_start: 0.9256 (ptp-110) cc_final: 0.9050 (ptt-90) REVERT: B 657 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8105 (pm20) REVERT: C 102 MET cc_start: 0.9411 (mtm) cc_final: 0.9073 (mtp) REVERT: C 118 LEU cc_start: 0.9580 (tp) cc_final: 0.9330 (pp) REVERT: C 123 LYS cc_start: 0.9024 (tptt) cc_final: 0.8798 (tptp) REVERT: C 261 LEU cc_start: 0.9443 (mt) cc_final: 0.9243 (mt) REVERT: D 537 LEU cc_start: 0.8857 (mt) cc_final: 0.8514 (mp) REVERT: D 601 LYS cc_start: 0.8315 (mtpt) cc_final: 0.7726 (ptmt) REVERT: D 624 ASP cc_start: 0.9514 (m-30) cc_final: 0.9278 (m-30) REVERT: D 626 MET cc_start: 0.9187 (tpt) cc_final: 0.8811 (tpp) REVERT: D 645 LEU cc_start: 0.9754 (mt) cc_final: 0.9554 (pp) REVERT: E 70 VAL cc_start: 0.9622 (m) cc_final: 0.9186 (p) REVERT: E 102 MET cc_start: 0.9240 (mtm) cc_final: 0.8763 (mpp) REVERT: E 492 LYS cc_start: 0.9557 (mttt) cc_final: 0.9312 (mtmt) REVERT: G 70 VAL cc_start: 0.9588 (m) cc_final: 0.9186 (p) REVERT: G 86 MET cc_start: 0.8773 (tmm) cc_final: 0.8406 (tmm) REVERT: G 88 LEU cc_start: 0.9440 (mp) cc_final: 0.8799 (mp) REVERT: G 100 ASN cc_start: 0.8840 (t0) cc_final: 0.8183 (t0) REVERT: G 106 MET cc_start: 0.9378 (tmm) cc_final: 0.8838 (tmm) REVERT: G 261 LEU cc_start: 0.9505 (mt) cc_final: 0.9263 (mt) REVERT: G 434 MET cc_start: 0.9054 (mtm) cc_final: 0.8503 (mpp) outliers start: 4 outliers final: 0 residues processed: 243 average time/residue: 0.1188 time to fit residues: 40.3607 Evaluate side-chains 177 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 175 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 147 optimal weight: 0.0870 chunk 47 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 1 optimal weight: 30.0000 chunk 5 optimal weight: 4.9990 chunk 160 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 205 GLN C 422 GLN ** D 653 GLN ** 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 = 0.3237 r_free = 0.3237 target = 0.057173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.045968 restraints weight = 79464.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.047621 restraints weight = 44873.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.048803 restraints weight = 30245.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.049647 restraints weight = 22729.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.050260 restraints weight = 18284.201| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13644 Z= 0.136 Angle : 0.719 9.594 18567 Z= 0.356 Chirality : 0.048 0.273 2145 Planarity : 0.004 0.040 2325 Dihedral : 9.463 73.657 2169 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.66 % Favored : 90.96 % Rotamer: Outliers : 0.07 % Allowed : 3.25 % Favored : 96.68 % 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: -1.96 (0.20), residues: 1593 helix: 0.08 (0.26), residues: 390 sheet: -0.80 (0.24), residues: 420 loop : -2.37 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 633 TYR 0.014 0.001 TYR G 219 PHE 0.023 0.002 PHE D 573 TRP 0.033 0.002 TRP G 47 HIS 0.003 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00313 (13590) covalent geometry : angle 0.70433 (18441) SS BOND : bond 0.00273 ( 36) SS BOND : angle 1.11457 ( 72) hydrogen bonds : bond 0.04001 ( 403) hydrogen bonds : angle 5.00796 ( 1173) link_BETA1-6 : bond 0.00161 ( 3) link_BETA1-6 : angle 1.63060 ( 9) link_NAG-ASN : bond 0.00404 ( 15) link_NAG-ASN : angle 2.72308 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 230 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9209 (mmm) cc_final: 0.8602 (mmm) REVERT: A 537 LEU cc_start: 0.9374 (mt) cc_final: 0.9092 (mp) REVERT: A 591 GLN cc_start: 0.9439 (tt0) cc_final: 0.8999 (tm-30) REVERT: A 595 ILE cc_start: 0.9592 (tt) cc_final: 0.9341 (tt) REVERT: A 598 CYS cc_start: 0.8013 (m) cc_final: 0.7619 (m) REVERT: A 629 MET cc_start: 0.9305 (mmm) cc_final: 0.9022 (mmm) REVERT: B 530 MET cc_start: 0.8912 (mmt) cc_final: 0.8189 (mmm) REVERT: B 629 MET cc_start: 0.9368 (mtt) cc_final: 0.8905 (mmt) REVERT: C 70 VAL cc_start: 0.9452 (m) cc_final: 0.9053 (p) REVERT: C 102 MET cc_start: 0.9385 (mtm) cc_final: 0.9076 (mtp) REVERT: C 118 LEU cc_start: 0.9593 (tp) cc_final: 0.9300 (pp) REVERT: C 123 LYS cc_start: 0.9193 (tptt) cc_final: 0.8893 (tptp) REVERT: C 261 LEU cc_start: 0.9427 (mt) cc_final: 0.9201 (mt) REVERT: D 537 LEU cc_start: 0.8904 (mt) cc_final: 0.8571 (mp) REVERT: D 624 ASP cc_start: 0.9485 (m-30) cc_final: 0.9239 (m-30) REVERT: D 626 MET cc_start: 0.9141 (tpt) cc_final: 0.8919 (tpt) REVERT: D 643 TYR cc_start: 0.9617 (m-80) cc_final: 0.8860 (m-80) REVERT: E 40 VAL cc_start: 0.9450 (t) cc_final: 0.9151 (p) REVERT: E 70 VAL cc_start: 0.9330 (m) cc_final: 0.8991 (p) REVERT: E 102 MET cc_start: 0.9249 (mtm) cc_final: 0.8957 (mtt) REVERT: E 196 ILE cc_start: 0.9155 (mm) cc_final: 0.8883 (mm) REVERT: G 70 VAL cc_start: 0.9426 (m) cc_final: 0.8946 (p) REVERT: G 88 LEU cc_start: 0.9324 (mp) cc_final: 0.8983 (mp) REVERT: G 100 ASN cc_start: 0.8797 (t0) cc_final: 0.7987 (t0) REVERT: G 108 GLU cc_start: 0.9431 (pm20) cc_final: 0.9230 (pm20) REVERT: G 261 LEU cc_start: 0.9489 (mt) cc_final: 0.9265 (mt) REVERT: G 434 MET cc_start: 0.9051 (mtm) cc_final: 0.8447 (mpp) outliers start: 1 outliers final: 1 residues processed: 231 average time/residue: 0.1145 time to fit residues: 37.3099 Evaluate side-chains 168 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 167 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 29 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 126 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 138 optimal weight: 7.9990 chunk 49 optimal weight: 0.2980 chunk 78 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 12 optimal weight: 10.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.046280 restraints weight = 79057.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047929 restraints weight = 44881.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.049101 restraints weight = 30299.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049957 restraints weight = 22819.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050573 restraints weight = 18401.881| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13644 Z= 0.124 Angle : 0.697 9.467 18567 Z= 0.345 Chirality : 0.047 0.261 2145 Planarity : 0.004 0.037 2325 Dihedral : 9.023 70.425 2169 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.72 % Favored : 91.90 % Rotamer: Outliers : 0.20 % Allowed : 3.12 % Favored : 96.68 % 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: -1.87 (0.20), residues: 1593 helix: 0.09 (0.26), residues: 390 sheet: -0.54 (0.26), residues: 390 loop : -2.34 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 644 TYR 0.011 0.001 TYR E 219 PHE 0.018 0.001 PHE D 573 TRP 0.020 0.002 TRP G 47 HIS 0.002 0.001 HIS E 218 Details of bonding type rmsd covalent geometry : bond 0.00284 (13590) covalent geometry : angle 0.68439 (18441) SS BOND : bond 0.00246 ( 36) SS BOND : angle 0.87500 ( 72) hydrogen bonds : bond 0.03828 ( 403) hydrogen bonds : angle 4.97105 ( 1173) link_BETA1-6 : bond 0.00251 ( 3) link_BETA1-6 : angle 1.61502 ( 9) link_NAG-ASN : bond 0.00329 ( 15) link_NAG-ASN : angle 2.56012 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 229 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9244 (mmm) cc_final: 0.8656 (mmm) REVERT: A 537 LEU cc_start: 0.9366 (mt) cc_final: 0.9087 (mp) REVERT: A 584 GLU cc_start: 0.9319 (pt0) cc_final: 0.9092 (pt0) REVERT: A 598 CYS cc_start: 0.8010 (m) cc_final: 0.7591 (m) REVERT: A 629 MET cc_start: 0.9374 (mmm) cc_final: 0.9020 (mmm) REVERT: A 643 TYR cc_start: 0.9684 (m-80) cc_final: 0.9396 (m-80) REVERT: B 530 MET cc_start: 0.8984 (mmt) cc_final: 0.8311 (mmm) REVERT: B 643 TYR cc_start: 0.9684 (m-80) cc_final: 0.9383 (m-80) REVERT: C 70 VAL cc_start: 0.9437 (m) cc_final: 0.8993 (p) REVERT: C 102 MET cc_start: 0.9422 (mtm) cc_final: 0.9083 (mtp) REVERT: C 115 ASP cc_start: 0.9259 (t0) cc_final: 0.9047 (t0) REVERT: C 118 LEU cc_start: 0.9504 (tp) cc_final: 0.9281 (pp) REVERT: C 123 LYS cc_start: 0.9213 (tptt) cc_final: 0.8848 (tptp) REVERT: C 261 LEU cc_start: 0.9410 (mt) cc_final: 0.9179 (mt) REVERT: D 537 LEU cc_start: 0.8879 (mt) cc_final: 0.8556 (mp) REVERT: D 585 ARG cc_start: 0.9640 (tpp80) cc_final: 0.9426 (tpp80) REVERT: D 601 LYS cc_start: 0.8511 (mtpt) cc_final: 0.7967 (ptmt) REVERT: D 624 ASP cc_start: 0.9521 (m-30) cc_final: 0.9274 (m-30) REVERT: D 626 MET cc_start: 0.9161 (tpt) cc_final: 0.8823 (tpp) REVERT: D 633 ARG cc_start: 0.9731 (ttm110) cc_final: 0.9528 (mtp-110) REVERT: D 643 TYR cc_start: 0.9602 (m-80) cc_final: 0.8866 (m-80) REVERT: E 102 MET cc_start: 0.9264 (mtm) cc_final: 0.8992 (mtt) REVERT: G 70 VAL cc_start: 0.9448 (m) cc_final: 0.9062 (p) REVERT: G 88 LEU cc_start: 0.9270 (mp) cc_final: 0.9031 (mp) REVERT: G 102 MET cc_start: 0.9368 (mtm) cc_final: 0.9014 (mtt) REVERT: G 261 LEU cc_start: 0.9479 (mt) cc_final: 0.9255 (mt) REVERT: G 434 MET cc_start: 0.8591 (mpp) cc_final: 0.8370 (mpp) REVERT: G 490 GLU cc_start: 0.9237 (pt0) cc_final: 0.9017 (pt0) outliers start: 3 outliers final: 3 residues processed: 231 average time/residue: 0.1187 time to fit residues: 38.7001 Evaluate side-chains 163 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 160 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 94 optimal weight: 0.0980 chunk 8 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN A 616 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN D 653 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.057331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.046194 restraints weight = 77324.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.047778 restraints weight = 44352.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.048938 restraints weight = 30207.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.049761 restraints weight = 22714.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.050353 restraints weight = 18343.636| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.5126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13644 Z= 0.138 Angle : 0.716 9.451 18567 Z= 0.357 Chirality : 0.047 0.261 2145 Planarity : 0.004 0.042 2325 Dihedral : 8.753 67.870 2169 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.16 % Favored : 91.46 % Rotamer: Outliers : 0.20 % Allowed : 1.36 % Favored : 98.44 % 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: -1.76 (0.20), residues: 1593 helix: 0.49 (0.27), residues: 375 sheet: -0.44 (0.26), residues: 384 loop : -2.41 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 633 TYR 0.009 0.001 TYR G 219 PHE 0.019 0.002 PHE B 573 TRP 0.052 0.003 TRP B 610 HIS 0.002 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00310 (13590) covalent geometry : angle 0.70243 (18441) SS BOND : bond 0.00244 ( 36) SS BOND : angle 1.16089 ( 72) hydrogen bonds : bond 0.03917 ( 403) hydrogen bonds : angle 4.97461 ( 1173) link_BETA1-6 : bond 0.00180 ( 3) link_BETA1-6 : angle 1.57252 ( 9) link_NAG-ASN : bond 0.00317 ( 15) link_NAG-ASN : angle 2.57886 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9284 (mmm) cc_final: 0.8876 (mmm) REVERT: A 537 LEU cc_start: 0.9412 (mt) cc_final: 0.9155 (mp) REVERT: A 584 GLU cc_start: 0.9176 (pt0) cc_final: 0.8954 (pt0) REVERT: A 629 MET cc_start: 0.9123 (mmm) cc_final: 0.8796 (mmm) REVERT: A 643 TYR cc_start: 0.9654 (m-80) cc_final: 0.8974 (m-80) REVERT: B 530 MET cc_start: 0.9021 (mmt) cc_final: 0.8246 (mmm) REVERT: B 579 ARG cc_start: 0.9042 (ptm160) cc_final: 0.8656 (ptm160) REVERT: B 659 ASP cc_start: 0.7515 (p0) cc_final: 0.7303 (p0) REVERT: C 70 VAL cc_start: 0.9462 (m) cc_final: 0.9089 (p) REVERT: C 102 MET cc_start: 0.9405 (mtm) cc_final: 0.9048 (mtp) REVERT: C 115 ASP cc_start: 0.9252 (t0) cc_final: 0.9024 (t0) REVERT: C 118 LEU cc_start: 0.9510 (tp) cc_final: 0.9239 (pp) REVERT: C 261 LEU cc_start: 0.9417 (mt) cc_final: 0.9181 (mt) REVERT: C 434 MET cc_start: 0.8903 (mpp) cc_final: 0.8692 (mpp) REVERT: D 585 ARG cc_start: 0.9653 (tpp80) cc_final: 0.9450 (tpp80) REVERT: D 601 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8112 (ptmt) REVERT: D 611 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.7118 (p0) REVERT: D 624 ASP cc_start: 0.9499 (m-30) cc_final: 0.9241 (m-30) REVERT: D 626 MET cc_start: 0.9040 (tpt) cc_final: 0.8729 (tpp) REVERT: D 643 TYR cc_start: 0.9592 (m-80) cc_final: 0.8861 (m-80) REVERT: E 70 VAL cc_start: 0.9343 (m) cc_final: 0.8916 (p) REVERT: E 102 MET cc_start: 0.9244 (mtm) cc_final: 0.8970 (mtt) REVERT: G 70 VAL cc_start: 0.9326 (m) cc_final: 0.9063 (p) REVERT: G 88 LEU cc_start: 0.9279 (mp) cc_final: 0.9027 (mp) REVERT: G 261 LEU cc_start: 0.9489 (mt) cc_final: 0.9246 (mt) REVERT: G 434 MET cc_start: 0.8742 (mpp) cc_final: 0.8494 (mpp) outliers start: 3 outliers final: 0 residues processed: 222 average time/residue: 0.1241 time to fit residues: 38.7583 Evaluate side-chains 165 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 164 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 611 ASN ** D 653 GLN ** 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 = 0.3236 r_free = 0.3236 target = 0.056460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045381 restraints weight = 78961.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.046933 restraints weight = 45637.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.048057 restraints weight = 31056.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.048852 restraints weight = 23525.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.049438 restraints weight = 19137.856| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13644 Z= 0.144 Angle : 0.722 9.410 18567 Z= 0.361 Chirality : 0.047 0.250 2145 Planarity : 0.004 0.045 2325 Dihedral : 8.488 64.892 2169 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.85 % Favored : 91.78 % Rotamer: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.10 % 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: -1.70 (0.20), residues: 1593 helix: 0.23 (0.26), residues: 393 sheet: -0.69 (0.25), residues: 420 loop : -2.13 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 644 TYR 0.008 0.001 TYR E 219 PHE 0.018 0.002 PHE D 573 TRP 0.044 0.002 TRP B 571 HIS 0.003 0.001 HIS G 74 Details of bonding type rmsd covalent geometry : bond 0.00327 (13590) covalent geometry : angle 0.70742 (18441) SS BOND : bond 0.00247 ( 36) SS BOND : angle 1.22240 ( 72) hydrogen bonds : bond 0.03912 ( 403) hydrogen bonds : angle 5.01850 ( 1173) link_BETA1-6 : bond 0.00254 ( 3) link_BETA1-6 : angle 1.60517 ( 9) link_NAG-ASN : bond 0.00326 ( 15) link_NAG-ASN : angle 2.63709 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 217 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9284 (mmm) cc_final: 0.8865 (mmm) REVERT: A 643 TYR cc_start: 0.9669 (m-80) cc_final: 0.8993 (m-80) REVERT: B 530 MET cc_start: 0.9115 (mmt) cc_final: 0.8399 (mmm) REVERT: B 643 TYR cc_start: 0.9646 (m-80) cc_final: 0.9401 (m-80) REVERT: B 659 ASP cc_start: 0.7484 (p0) cc_final: 0.7273 (p0) REVERT: C 70 VAL cc_start: 0.9511 (m) cc_final: 0.9125 (p) REVERT: C 102 MET cc_start: 0.9436 (mtm) cc_final: 0.9052 (mtp) REVERT: C 109 ASP cc_start: 0.9563 (m-30) cc_final: 0.9297 (m-30) REVERT: C 115 ASP cc_start: 0.9289 (t0) cc_final: 0.9017 (t0) REVERT: C 118 LEU cc_start: 0.9523 (tp) cc_final: 0.9206 (pp) REVERT: C 261 LEU cc_start: 0.9403 (mt) cc_final: 0.9155 (mt) REVERT: C 304 MET cc_start: 0.8967 (mmm) cc_final: 0.8297 (mmp) REVERT: D 624 ASP cc_start: 0.9493 (m-30) cc_final: 0.9221 (m-30) REVERT: D 626 MET cc_start: 0.9098 (tpt) cc_final: 0.8764 (tpp) REVERT: D 643 TYR cc_start: 0.9595 (m-80) cc_final: 0.8940 (m-80) REVERT: E 70 VAL cc_start: 0.9476 (m) cc_final: 0.9112 (p) REVERT: E 100 ASN cc_start: 0.8724 (t0) cc_final: 0.8038 (t0) REVERT: E 108 GLU cc_start: 0.9328 (pp20) cc_final: 0.8733 (pp20) REVERT: E 434 MET cc_start: 0.8973 (mpp) cc_final: 0.8565 (mpp) REVERT: G 115 ASP cc_start: 0.9310 (t70) cc_final: 0.9104 (t0) REVERT: G 434 MET cc_start: 0.8818 (mpp) cc_final: 0.8459 (mpp) outliers start: 2 outliers final: 0 residues processed: 219 average time/residue: 0.1242 time to fit residues: 38.0507 Evaluate side-chains 158 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 1 optimal weight: 9.9990 chunk 133 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN D 577 GLN D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.054340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.043437 restraints weight = 82330.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.044966 restraints weight = 46771.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.046060 restraints weight = 31735.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046840 restraints weight = 23975.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.047358 restraints weight = 19486.356| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.5465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13644 Z= 0.228 Angle : 0.787 11.521 18567 Z= 0.392 Chirality : 0.048 0.253 2145 Planarity : 0.005 0.056 2325 Dihedral : 8.519 63.584 2169 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.35 % Favored : 90.27 % Rotamer: Outliers : 0.20 % Allowed : 1.08 % Favored : 98.71 % 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: -1.76 (0.20), residues: 1593 helix: 0.13 (0.26), residues: 393 sheet: -0.46 (0.26), residues: 384 loop : -2.26 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 644 TYR 0.011 0.002 TYR C 318 PHE 0.015 0.002 PHE E 391 TRP 0.033 0.002 TRP B 571 HIS 0.004 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00499 (13590) covalent geometry : angle 0.76967 (18441) SS BOND : bond 0.00480 ( 36) SS BOND : angle 1.46532 ( 72) hydrogen bonds : bond 0.04141 ( 403) hydrogen bonds : angle 5.26466 ( 1173) link_BETA1-6 : bond 0.00127 ( 3) link_BETA1-6 : angle 1.62949 ( 9) link_NAG-ASN : bond 0.00522 ( 15) link_NAG-ASN : angle 2.99781 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9406 (mmm) cc_final: 0.8929 (mmm) REVERT: A 643 TYR cc_start: 0.9704 (m-80) cc_final: 0.9025 (m-80) REVERT: B 530 MET cc_start: 0.9245 (mmt) cc_final: 0.8430 (mmm) REVERT: B 571 TRP cc_start: 0.8746 (m100) cc_final: 0.7685 (m-10) REVERT: B 643 TYR cc_start: 0.9614 (m-80) cc_final: 0.9073 (m-80) REVERT: B 659 ASP cc_start: 0.7512 (p0) cc_final: 0.7308 (p0) REVERT: C 102 MET cc_start: 0.9491 (mtm) cc_final: 0.9056 (mtp) REVERT: C 115 ASP cc_start: 0.9377 (t0) cc_final: 0.9072 (t0) REVERT: C 118 LEU cc_start: 0.9619 (tp) cc_final: 0.9242 (pp) REVERT: D 611 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7228 (p0) REVERT: D 624 ASP cc_start: 0.9523 (m-30) cc_final: 0.9232 (m-30) REVERT: D 626 MET cc_start: 0.9192 (tpt) cc_final: 0.8828 (tpp) REVERT: D 629 MET cc_start: 0.9274 (mmm) cc_final: 0.8825 (mmm) REVERT: D 632 ASP cc_start: 0.9746 (t70) cc_final: 0.9027 (t0) REVERT: D 643 TYR cc_start: 0.9626 (m-80) cc_final: 0.9016 (m-80) REVERT: E 102 MET cc_start: 0.9399 (mtm) cc_final: 0.9088 (mtt) REVERT: E 434 MET cc_start: 0.8970 (mpp) cc_final: 0.8541 (mpp) REVERT: G 70 VAL cc_start: 0.9493 (m) cc_final: 0.9120 (p) REVERT: G 102 MET cc_start: 0.9407 (mtm) cc_final: 0.8921 (mtt) REVERT: G 109 ASP cc_start: 0.9631 (m-30) cc_final: 0.9387 (m-30) REVERT: G 434 MET cc_start: 0.8850 (mpp) cc_final: 0.8504 (mpp) outliers start: 3 outliers final: 1 residues processed: 197 average time/residue: 0.1320 time to fit residues: 35.9983 Evaluate side-chains 148 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 146 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 139 optimal weight: 9.9990 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 137 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 653 GLN ** 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 = 0.3201 r_free = 0.3201 target = 0.054945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.044039 restraints weight = 80325.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045573 restraints weight = 45579.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.046668 restraints weight = 30979.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.047467 restraints weight = 23364.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.048029 restraints weight = 18893.744| |-----------------------------------------------------------------------------| r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13644 Z= 0.158 Angle : 0.757 12.613 18567 Z= 0.374 Chirality : 0.048 0.254 2145 Planarity : 0.004 0.047 2325 Dihedral : 8.390 61.734 2169 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.38 % Allowed : 7.91 % Favored : 91.71 % Rotamer: Outliers : 0.20 % Allowed : 0.27 % Favored : 99.53 % 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: -1.76 (0.20), residues: 1593 helix: 0.02 (0.26), residues: 393 sheet: -0.43 (0.26), residues: 384 loop : -2.20 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 633 TYR 0.010 0.001 TYR A 638 PHE 0.016 0.002 PHE C 391 TRP 0.053 0.002 TRP A 571 HIS 0.004 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00357 (13590) covalent geometry : angle 0.74175 (18441) SS BOND : bond 0.00270 ( 36) SS BOND : angle 1.27853 ( 72) hydrogen bonds : bond 0.04010 ( 403) hydrogen bonds : angle 5.18404 ( 1173) link_BETA1-6 : bond 0.00148 ( 3) link_BETA1-6 : angle 1.67631 ( 9) link_NAG-ASN : bond 0.00333 ( 15) link_NAG-ASN : angle 2.82837 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3186 Ramachandran restraints generated. 1593 Oldfield, 0 Emsley, 1593 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 204 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 MET cc_start: 0.9434 (mmm) cc_final: 0.8934 (mmm) REVERT: A 571 TRP cc_start: 0.8334 (m100) cc_final: 0.7667 (m-10) REVERT: B 530 MET cc_start: 0.9265 (mmt) cc_final: 0.8517 (mmm) REVERT: B 571 TRP cc_start: 0.8607 (m100) cc_final: 0.7476 (m-10) REVERT: B 659 ASP cc_start: 0.7432 (p0) cc_final: 0.7222 (p0) REVERT: C 70 VAL cc_start: 0.9309 (m) cc_final: 0.8896 (p) REVERT: C 102 MET cc_start: 0.9495 (mtm) cc_final: 0.9073 (mtp) REVERT: C 109 ASP cc_start: 0.9626 (m-30) cc_final: 0.9305 (m-30) REVERT: C 114 TRP cc_start: 0.9589 (m100) cc_final: 0.9257 (t-100) REVERT: C 115 ASP cc_start: 0.9362 (t0) cc_final: 0.9084 (t0) REVERT: C 118 LEU cc_start: 0.9598 (tp) cc_final: 0.9377 (pp) REVERT: C 304 MET cc_start: 0.8796 (mmm) cc_final: 0.8159 (mmp) REVERT: C 434 MET cc_start: 0.8935 (mpp) cc_final: 0.8263 (mpp) REVERT: D 611 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.7260 (p0) REVERT: D 626 MET cc_start: 0.9235 (tpt) cc_final: 0.8863 (tpp) REVERT: D 643 TYR cc_start: 0.9654 (m-80) cc_final: 0.8975 (m-80) REVERT: E 70 VAL cc_start: 0.9531 (m) cc_final: 0.9165 (p) REVERT: E 100 ASN cc_start: 0.9079 (t0) cc_final: 0.8250 (t0) REVERT: E 434 MET cc_start: 0.8969 (mpp) cc_final: 0.8533 (mpp) REVERT: G 100 ASN cc_start: 0.9160 (t0) cc_final: 0.8483 (t0) REVERT: G 115 ASP cc_start: 0.9353 (t70) cc_final: 0.9124 (t0) REVERT: G 434 MET cc_start: 0.8873 (mpp) cc_final: 0.8515 (mpp) REVERT: G 478 ASN cc_start: 0.8958 (m110) cc_final: 0.8576 (m110) outliers start: 3 outliers final: 1 residues processed: 207 average time/residue: 0.1390 time to fit residues: 39.8102 Evaluate side-chains 156 residues out of total 1476 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 49 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 611 ASN ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 611 ASN ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 611 ASN ** D 653 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.043497 restraints weight = 81539.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.045004 restraints weight = 46236.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.046089 restraints weight = 31375.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.046872 restraints weight = 23692.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.047418 restraints weight = 19233.265| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13644 Z= 0.180 Angle : 0.769 12.685 18567 Z= 0.385 Chirality : 0.048 0.255 2145 Planarity : 0.004 0.052 2325 Dihedral : 8.332 60.939 2169 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.44 % Allowed : 8.85 % Favored : 90.71 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % Favored : 99.59 % 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: -1.74 (0.20), residues: 1593 helix: 0.01 (0.26), residues: 393 sheet: -0.66 (0.25), residues: 414 loop : -2.07 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 633 TYR 0.024 0.002 TYR A 643 PHE 0.016 0.002 PHE C 391 TRP 0.040 0.002 TRP A 571 HIS 0.003 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00404 (13590) covalent geometry : angle 0.75280 (18441) SS BOND : bond 0.00293 ( 36) SS BOND : angle 1.28012 ( 72) hydrogen bonds : bond 0.04212 ( 403) hydrogen bonds : angle 5.24437 ( 1173) link_BETA1-6 : bond 0.00107 ( 3) link_BETA1-6 : angle 1.65476 ( 9) link_NAG-ASN : bond 0.00399 ( 15) link_NAG-ASN : angle 2.91388 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.25 seconds wall clock time: 33 minutes 48.82 seconds (2028.82 seconds total)