Starting phenix.real_space_refine on Sat Aug 23 23:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw7_40810/08_2025/8sw7_40810.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 102 5.16 5 C 9437 2.51 5 N 2600 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 15133 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3424 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3365 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 18, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" 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: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 4.01, per 1000 atoms: 0.26 Number of scatterers: 15133 At special positions: 0 Unit cell: (128.875, 136.092, 120.627, 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 102 16.00 O 2994 8.00 N 2600 7.00 C 9437 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.02 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.04 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.01 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.05 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.02 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.10 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.04 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.03 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.02 Simple disulfide: pdb=" SG CYS F 228 " - pdb=" SG CYS F 239 " distance=2.03 Simple disulfide: pdb=" SG CYS F 296 " - pdb=" SG CYS F 331 " distance=2.03 Simple disulfide: pdb=" SG CYS F 378 " - pdb=" SG CYS F 445 " distance=2.06 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 133 " " NAG A 603 " - " ASN A 137 " " NAG A 604 " - " ASN A 156 " " NAG A 605 " - " ASN A 160 " " NAG A 606 " - " ASN A 197 " " NAG A 607 " - " ASN A 234 " " NAG A 608 " - " ASN A 241 " " NAG A 609 " - " ASN A 276 " " NAG A 610 " - " ASN A 289 " " NAG A 611 " - " ASN A 301 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 392 " " NAG A 614 " - " ASN A 448 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 133 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 234 " " NAG C 606 " - " ASN C 241 " " NAG C 607 " - " ASN C 289 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 332 " " NAG C 611 " - " ASN C 392 " " NAG C 612 " - " ASN C 448 " " NAG C 613 " - " ASN C 386 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 701 " - " ASN E 611 " " NAG E 702 " - " ASN E 618 " " NAG E 703 " - " ASN E 637 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 133 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 160 " " NAG F 605 " - " ASN F 234 " " NAG F 606 " - " ASN F 241 " " NAG F 607 " - " ASN F 276 " " NAG F 608 " - " ASN F 289 " " NAG F 609 " - " ASN F 295 " " NAG F 610 " - " ASN F 301 " " NAG F 611 " - " ASN F 332 " " NAG F 612 " - " ASN F 386 " " NAG F 613 " - " ASN F 392 " " NAG F 614 " - " ASN F 448 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN C 262 " " NAG J 1 " - " ASN F 262 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 599.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3578 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 34 sheets defined 26.6% alpha, 37.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.111A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 removed outlier: 3.858A pdb=" N ARG A 151 " --> pdb=" O ASP A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 354 removed outlier: 4.123A pdb=" N LYS A 351 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N HIS A 352 " --> pdb=" O GLN A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.687A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.383A 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 536 through 542 Processing helix chain 'B' and resid 573 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'C' and resid 98 through 116 removed outlier: 3.627A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 475 through 484 removed outlier: 3.861A pdb=" N TRP C 479 " --> pdb=" O MET C 475 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 633 removed outlier: 3.529A pdb=" N LYS D 633 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 634 through 637 removed outlier: 5.637A pdb=" N ASN D 637 " --> pdb=" O GLU D 634 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 634 through 637' Processing helix chain 'D' and resid 638 through 663 Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.178A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 535 Processing helix chain 'E' and resid 536 through 543 Processing helix chain 'E' and resid 572 through 595 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 662 Processing helix chain 'F' and resid 98 through 117 removed outlier: 4.233A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 167 removed outlier: 3.902A pdb=" N ARG F 166 " --> pdb=" O THR F 163 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP F 167 " --> pdb=" O GLU F 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 163 through 167' Processing helix chain 'F' and resid 335 through 351 removed outlier: 4.073A pdb=" N LYS F 351 " --> pdb=" O LYS F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 476 through 484 removed outlier: 4.239A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.747A pdb=" N UNK H 32 " --> pdb=" O UNK H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 66 No H-bonds generated for 'chain 'H' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.334A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 4.199A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.706A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.615A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.655A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.712A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 273 removed outlier: 10.712A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.377A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.655A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.108A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.178A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'C' and resid 172 through 177 Processing sheet with id=AB6, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.721A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 259 through 261 removed outlier: 10.342A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.971A pdb=" N THR C 450 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N GLU C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.565A pdb=" N ASN C 448 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.418A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.579A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.127A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.871A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.212A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.342A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 304 through 312 removed outlier: 6.417A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.143A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 45 through 47 removed outlier: 4.653A pdb=" N VAL F 242 " --> pdb=" O LEU F 86 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC4, first strand: chain 'F' and resid 91 through 94 removed outlier: 3.877A pdb=" N GLU F 91 " --> pdb=" O CYS F 239 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 170 through 177 removed outlier: 3.651A pdb=" N GLN F 130 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.547A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU F 260 " --> pdb=" O THR F 450 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA F 329 " --> pdb=" O CYS F 418 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N PHE F 382 " --> pdb=" O LYS F 421 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 271 through 273 removed outlier: 6.922A pdb=" N THR F 450 " --> pdb=" O LEU F 288 " (cutoff:3.500A) removed outlier: 10.192A pdb=" N GLU F 290 " --> pdb=" O ASN F 448 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N ASN F 448 " --> pdb=" O GLU F 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N VAL F 292 " --> pdb=" O VAL F 446 " (cutoff:3.500A) removed outlier: 9.858A pdb=" N VAL F 446 " --> pdb=" O VAL F 292 " (cutoff:3.500A) removed outlier: 11.263A pdb=" N ILE F 294 " --> pdb=" O ARG F 444 " (cutoff:3.500A) removed outlier: 9.985A pdb=" N ARG F 444 " --> pdb=" O ILE F 294 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 301 through 312 removed outlier: 4.081A pdb=" N ASN F 301 " --> pdb=" O ILE F 323A" (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR F 303 " --> pdb=" O ASP F 322 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ASP F 322 " --> pdb=" O THR F 303 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYS F 305 " --> pdb=" O THR F 320 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N THR F 320 " --> pdb=" O LYS F 305 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ILE F 307 " --> pdb=" O TYR F 318 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR F 318 " --> pdb=" O ILE F 307 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ILE F 309 " --> pdb=" O TRP F 316 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N TRP F 316 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 7 through 8 Processing sheet with id=AD2, first strand: chain 'H' and resid 12 through 13 removed outlier: 6.569A pdb=" N UNK H 12 " --> pdb=" O UNK H 124 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N UNK H 96 " --> pdb=" O UNK H 115 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N UNK H 115 " --> pdb=" O UNK H 96 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N UNK H 98 " --> pdb=" O UNK H 113 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 59 through 60 removed outlier: 6.357A pdb=" N UNK H 45 " --> pdb=" O UNK H 40 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N UNK H 40 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N UNK H 34 " --> pdb=" O UNK H 51 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD6, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.546A pdb=" N UNK L 11 " --> pdb=" O UNK L 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'L' and resid 45 through 48 removed outlier: 6.269A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1596 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 3792 1.33 - 1.48: 5118 1.48 - 1.63: 6341 1.63 - 1.78: 52 1.78 - 1.94: 86 Bond restraints: 15389 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.24e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" CD2 TRP E 571 " pdb=" CE3 TRP E 571 " ideal model delta sigma weight residual 1.398 1.504 -0.106 1.60e-02 3.91e+03 4.36e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.500 -0.102 1.60e-02 3.91e+03 4.07e+01 bond pdb=" CZ2 TRP E 571 " pdb=" CH2 TRP E 571 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.03e+01 ... (remaining 15384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17546 2.22 - 4.43: 2810 4.43 - 6.65: 475 6.65 - 8.87: 86 8.87 - 11.08: 9 Bond angle restraints: 20926 Sorted by residual: angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.58 100.83 9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N ARG F 476 " pdb=" CA ARG F 476 " pdb=" C ARG F 476 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.25 -7.69 1.01e+00 9.80e-01 5.79e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" N PRO F 437 " pdb=" CA PRO F 437 " pdb=" C PRO F 437 " ideal model delta sigma weight residual 110.58 102.50 8.08 1.07e+00 8.73e-01 5.71e+01 ... (remaining 20921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9708 21.13 - 42.27: 204 42.27 - 63.40: 70 63.40 - 84.54: 32 84.54 - 105.67: 15 Dihedral angle restraints: 10029 sinusoidal: 4537 harmonic: 5492 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.08 -47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.29 43.29 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 10026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1757 0.102 - 0.203: 526 0.203 - 0.304: 170 0.304 - 0.406: 97 0.406 - 0.507: 34 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.84e+01 ... (remaining 2581 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.099 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN D 611 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.095 2.00e-02 2.50e+03 9.81e-02 1.20e+02 pdb=" CG ASN A 234 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " 0.076 2.00e-02 2.50e+03 7.89e-02 7.77e+01 pdb=" CG ASN C 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.096 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1886 2.73 - 3.27: 14014 3.27 - 3.82: 23448 3.82 - 4.36: 29523 4.36 - 4.90: 47925 Nonbonded interactions: 116796 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.188 3.040 nonbonded pdb=" N UNK H 51 " pdb=" N UNK H 52 " model vdw 2.394 2.560 nonbonded pdb=" NZ LYS C 231 " pdb=" OE1 GLU C 267 " model vdw 2.418 3.120 nonbonded pdb=" N LEU F 125 " pdb=" O LEU F 125 " model vdw 2.419 2.496 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.423 2.496 ... (remaining 116791 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' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 457 or resid 463 through 503 or resid 603 through 614)) selection = (chain 'C' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 612)) selection = (chain 'F' and (resid 32 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and resid 522 through 702) selection = chain 'D' selection = (chain 'E' and resid 522 through 702) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.400 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.023 0.145 15480 Z= 1.196 Angle : 1.741 12.204 21166 Z= 1.111 Chirality : 0.133 0.507 2584 Planarity : 0.009 0.052 2613 Dihedral : 11.373 105.669 6352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.20), residues: 1622 helix: 0.55 (0.26), residues: 376 sheet: 1.10 (0.25), residues: 398 loop : 0.33 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 617 TYR 0.038 0.007 TYR B 643 PHE 0.029 0.006 PHE A 353 TRP 0.045 0.009 TRP F 35 HIS 0.010 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02220 (15389) covalent geometry : angle 1.71843 (20926) SS BOND : bond 0.01589 ( 33) SS BOND : angle 3.60500 ( 66) hydrogen bonds : bond 0.15922 ( 555) hydrogen bonds : angle 7.89529 ( 1596) link_BETA1-4 : bond 0.07521 ( 6) link_BETA1-4 : angle 4.80451 ( 18) link_NAG-ASN : bond 0.08112 ( 52) link_NAG-ASN : angle 2.67185 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 599 time to evaluate : 0.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 477 ASP cc_start: 0.7926 (m-30) cc_final: 0.7700 (m-30) REVERT: B 627 THR cc_start: 0.8679 (p) cc_final: 0.8453 (t) REVERT: F 474 ASP cc_start: 0.7602 (t70) cc_final: 0.7090 (t70) outliers start: 2 outliers final: 0 residues processed: 601 average time/residue: 0.1354 time to fit residues: 117.4622 Evaluate side-chains 364 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 103 GLN A 195 ASN A 203 GLN A 422 GLN A 425 ASN C 130 GLN C 287 GLN D 607 ASN E 575 GLN E 591 GLN F 203 GLN F 283 ASN F 428 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.165687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.139791 restraints weight = 22857.886| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.53 r_work: 0.3561 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15480 Z= 0.175 Angle : 0.796 16.340 21166 Z= 0.392 Chirality : 0.049 0.244 2584 Planarity : 0.004 0.074 2613 Dihedral : 7.681 65.043 3206 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.11 % Allowed : 12.59 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.21), residues: 1622 helix: 1.77 (0.28), residues: 360 sheet: 0.72 (0.24), residues: 421 loop : -0.25 (0.21), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 298 TYR 0.042 0.002 TYR E 643 PHE 0.031 0.002 PHE F 53 TRP 0.023 0.002 TRP C 479 HIS 0.005 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00383 (15389) covalent geometry : angle 0.73927 (20926) SS BOND : bond 0.00362 ( 33) SS BOND : angle 1.44286 ( 66) hydrogen bonds : bond 0.06079 ( 555) hydrogen bonds : angle 5.98465 ( 1596) link_BETA1-4 : bond 0.00625 ( 6) link_BETA1-4 : angle 3.86511 ( 18) link_NAG-ASN : bond 0.00395 ( 52) link_NAG-ASN : angle 3.18684 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 435 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8936 (m100) cc_final: 0.7943 (m100) REVERT: A 150 MET cc_start: 0.8222 (mmp) cc_final: 0.7600 (mmt) REVERT: A 258 GLN cc_start: 0.9015 (mt0) cc_final: 0.8711 (mt0) REVERT: A 269 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8351 (mm-30) REVERT: A 275 GLU cc_start: 0.8750 (tt0) cc_final: 0.8421 (tt0) REVERT: A 440 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7829 (pm20) REVERT: A 452 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8162 (pp) REVERT: B 616 ASN cc_start: 0.8332 (t0) cc_final: 0.8032 (t0) REVERT: B 627 THR cc_start: 0.8828 (p) cc_final: 0.8626 (t) REVERT: C 178 ARG cc_start: 0.8269 (ptm-80) cc_final: 0.7954 (ptm-80) REVERT: C 192 ARG cc_start: 0.8037 (ttm170) cc_final: 0.7722 (tpp-160) REVERT: C 492 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8205 (mt-10) REVERT: D 638 TYR cc_start: 0.8332 (m-80) cc_final: 0.8100 (m-80) REVERT: D 651 ASN cc_start: 0.8710 (t0) cc_final: 0.8503 (t0) REVERT: E 542 ARG cc_start: 0.8771 (ttm170) cc_final: 0.8378 (ttm170) REVERT: E 634 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8043 (tm-30) REVERT: E 645 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8612 (mt) REVERT: F 46 LYS cc_start: 0.9005 (mttm) cc_final: 0.8715 (mttp) REVERT: F 153 GLU cc_start: 0.8336 (tp30) cc_final: 0.8076 (tp30) REVERT: F 192 ARG cc_start: 0.7372 (ptt180) cc_final: 0.6823 (ptt180) REVERT: F 368 ASP cc_start: 0.7900 (m-30) cc_final: 0.7619 (p0) outliers start: 46 outliers final: 25 residues processed: 456 average time/residue: 0.1229 time to fit residues: 83.7342 Evaluate side-chains 402 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 374 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain E residue 645 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 147 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 64 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 132 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 302 ASN A 374 HIS ** C 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN F 374 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.154655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.129182 restraints weight = 23761.981| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.50 r_work: 0.3426 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 15480 Z= 0.351 Angle : 0.906 16.914 21166 Z= 0.444 Chirality : 0.053 0.277 2584 Planarity : 0.005 0.045 2613 Dihedral : 7.509 53.530 3206 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 5.28 % Allowed : 13.07 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.20), residues: 1622 helix: 1.15 (0.27), residues: 372 sheet: 0.15 (0.24), residues: 420 loop : -0.87 (0.20), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 504 TYR 0.021 0.003 TYR F 191 PHE 0.027 0.003 PHE A 468 TRP 0.024 0.002 TRP C 96 HIS 0.009 0.002 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00813 (15389) covalent geometry : angle 0.85432 (20926) SS BOND : bond 0.00780 ( 33) SS BOND : angle 2.12686 ( 66) hydrogen bonds : bond 0.06299 ( 555) hydrogen bonds : angle 5.97266 ( 1596) link_BETA1-4 : bond 0.00982 ( 6) link_BETA1-4 : angle 2.90073 ( 18) link_NAG-ASN : bond 0.00604 ( 52) link_NAG-ASN : angle 3.26195 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 396 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9165 (m100) cc_final: 0.8232 (m100) REVERT: A 51 THR cc_start: 0.9285 (m) cc_final: 0.8998 (p) REVERT: A 269 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8427 (mm-30) REVERT: A 440 GLN cc_start: 0.8478 (pt0) cc_final: 0.8194 (pm20) REVERT: B 616 ASN cc_start: 0.8444 (t0) cc_final: 0.8220 (t0) REVERT: C 104 MET cc_start: 0.9353 (ttt) cc_final: 0.9083 (ttt) REVERT: C 178 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.7997 (ptm-80) REVERT: C 190 GLU cc_start: 0.5393 (pm20) cc_final: 0.4925 (pm20) REVERT: C 191 TYR cc_start: 0.8145 (m-80) cc_final: 0.7768 (m-10) REVERT: C 283 ASN cc_start: 0.8830 (m-40) cc_final: 0.8566 (m-40) REVERT: C 394 THR cc_start: 0.7868 (m) cc_final: 0.7619 (t) REVERT: C 484 TYR cc_start: 0.8212 (p90) cc_final: 0.7884 (p90) REVERT: D 530 MET cc_start: 0.6950 (mtt) cc_final: 0.6261 (mtt) REVERT: D 599 SER cc_start: 0.9452 (t) cc_final: 0.9086 (p) REVERT: E 542 ARG cc_start: 0.8831 (ttm170) cc_final: 0.8316 (ttm170) REVERT: E 571 TRP cc_start: 0.5586 (OUTLIER) cc_final: 0.5190 (p-90) REVERT: E 588 ARG cc_start: 0.7204 (mtt180) cc_final: 0.6947 (tmm-80) REVERT: E 634 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8208 (tm-30) REVERT: E 655 LYS cc_start: 0.8608 (mmtp) cc_final: 0.7943 (mtpp) REVERT: F 107 ASP cc_start: 0.8741 (m-30) cc_final: 0.8338 (m-30) REVERT: F 153 GLU cc_start: 0.8514 (tp30) cc_final: 0.8218 (tp30) REVERT: F 241 ASN cc_start: 0.6996 (m-40) cc_final: 0.6738 (t0) REVERT: F 368 ASP cc_start: 0.8030 (m-30) cc_final: 0.7706 (p0) REVERT: F 377 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7956 (t0) REVERT: F 502 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8495 (ttmt) outliers start: 78 outliers final: 62 residues processed: 439 average time/residue: 0.1201 time to fit residues: 79.2595 Evaluate side-chains 424 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 359 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 194 ILE Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 288 LEU Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 649 SER Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 369 LEU Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 423 ILE Chi-restraints excluded: chain F residue 439 ILE Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 502 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN E 653 GLN F 283 ASN F 478 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.159394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133901 restraints weight = 23342.977| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 3.53 r_work: 0.3487 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15480 Z= 0.149 Angle : 0.688 16.148 21166 Z= 0.334 Chirality : 0.046 0.228 2584 Planarity : 0.003 0.032 2613 Dihedral : 6.161 42.728 3206 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.72 % Allowed : 16.45 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.21), residues: 1622 helix: 1.66 (0.28), residues: 363 sheet: 0.14 (0.24), residues: 443 loop : -0.81 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 504 TYR 0.017 0.002 TYR F 484 PHE 0.020 0.002 PHE F 53 TRP 0.013 0.001 TRP D 623 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00337 (15389) covalent geometry : angle 0.63756 (20926) SS BOND : bond 0.00414 ( 33) SS BOND : angle 1.67830 ( 66) hydrogen bonds : bond 0.04989 ( 555) hydrogen bonds : angle 5.54728 ( 1596) link_BETA1-4 : bond 0.00590 ( 6) link_BETA1-4 : angle 2.57668 ( 18) link_NAG-ASN : bond 0.00381 ( 52) link_NAG-ASN : angle 2.77181 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 381 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: A 35 TRP cc_start: 0.9089 (m100) cc_final: 0.8132 (m100) REVERT: A 102 GLU cc_start: 0.8468 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 440 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8232 (pm20) REVERT: B 540 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.6306 (mp10) REVERT: B 616 ASN cc_start: 0.8408 (t0) cc_final: 0.8095 (t0) REVERT: C 104 MET cc_start: 0.9348 (ttt) cc_final: 0.9077 (ttt) REVERT: C 150 MET cc_start: 0.7953 (mtp) cc_final: 0.7441 (mtm) REVERT: C 178 ARG cc_start: 0.8297 (ptm-80) cc_final: 0.8061 (ptm-80) REVERT: C 190 GLU cc_start: 0.5397 (pm20) cc_final: 0.4975 (pm20) REVERT: C 191 TYR cc_start: 0.8122 (m-80) cc_final: 0.7899 (m-10) REVERT: C 192 ARG cc_start: 0.8104 (ttm170) cc_final: 0.7552 (tpt170) REVERT: C 394 THR cc_start: 0.7783 (m) cc_final: 0.7404 (t) REVERT: C 484 TYR cc_start: 0.8234 (p90) cc_final: 0.7915 (p90) REVERT: D 530 MET cc_start: 0.6935 (mtt) cc_final: 0.6213 (mtt) REVERT: E 542 ARG cc_start: 0.8767 (ttm170) cc_final: 0.8158 (ttm170) REVERT: E 571 TRP cc_start: 0.5230 (OUTLIER) cc_final: 0.4964 (p-90) REVERT: E 634 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8184 (tm-30) REVERT: F 107 ASP cc_start: 0.8666 (m-30) cc_final: 0.8248 (m-30) REVERT: F 112 TRP cc_start: 0.8305 (t-100) cc_final: 0.7879 (t-100) REVERT: F 153 GLU cc_start: 0.8365 (tp30) cc_final: 0.8123 (tp30) REVERT: F 274 SER cc_start: 0.8971 (t) cc_final: 0.8695 (p) REVERT: F 377 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7941 (t0) REVERT: F 502 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8292 (tttp) outliers start: 55 outliers final: 36 residues processed: 410 average time/residue: 0.1223 time to fit residues: 75.0458 Evaluate side-chains 391 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 350 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 502 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 14 optimal weight: 4.9990 chunk 185 optimal weight: 9.9990 chunk 106 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 147 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN E 543 ASN F 283 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.161178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135714 restraints weight = 23762.927| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.51 r_work: 0.3530 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15480 Z= 0.167 Angle : 0.667 15.514 21166 Z= 0.324 Chirality : 0.045 0.228 2584 Planarity : 0.003 0.032 2613 Dihedral : 5.707 40.137 3206 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.20 % Allowed : 16.38 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.21), residues: 1622 helix: 1.72 (0.28), residues: 364 sheet: 0.05 (0.23), residues: 435 loop : -0.86 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 419 TYR 0.022 0.002 TYR C 318 PHE 0.015 0.002 PHE A 376 TRP 0.010 0.001 TRP E 571 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd covalent geometry : bond 0.00386 (15389) covalent geometry : angle 0.62634 (20926) SS BOND : bond 0.00414 ( 33) SS BOND : angle 1.45021 ( 66) hydrogen bonds : bond 0.04718 ( 555) hydrogen bonds : angle 5.45247 ( 1596) link_BETA1-4 : bond 0.00654 ( 6) link_BETA1-4 : angle 2.25106 ( 18) link_NAG-ASN : bond 0.00293 ( 52) link_NAG-ASN : angle 2.49812 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 371 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9118 (m100) cc_final: 0.8257 (m100) REVERT: A 51 THR cc_start: 0.9246 (m) cc_final: 0.8901 (p) REVERT: A 428 GLN cc_start: 0.8659 (mt0) cc_final: 0.8379 (mm110) REVERT: A 440 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: B 540 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.6462 (mp10) REVERT: B 616 ASN cc_start: 0.8362 (t0) cc_final: 0.8055 (t0) REVERT: C 104 MET cc_start: 0.9402 (ttt) cc_final: 0.9135 (ttt) REVERT: C 178 ARG cc_start: 0.8291 (ptm-80) cc_final: 0.8052 (ptm-80) REVERT: C 394 THR cc_start: 0.7735 (m) cc_final: 0.7386 (t) REVERT: D 530 MET cc_start: 0.6986 (mtt) cc_final: 0.6308 (mtt) REVERT: E 634 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8203 (tm-30) REVERT: F 107 ASP cc_start: 0.8661 (m-30) cc_final: 0.8229 (m-30) REVERT: F 112 TRP cc_start: 0.8353 (t-100) cc_final: 0.8016 (t-100) REVERT: F 502 LYS cc_start: 0.8784 (OUTLIER) cc_final: 0.8380 (tttp) outliers start: 62 outliers final: 48 residues processed: 404 average time/residue: 0.1210 time to fit residues: 73.3670 Evaluate side-chains 401 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 350 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 502 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 175 optimal weight: 8.9990 chunk 56 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 91 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 143 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 142 optimal weight: 0.3980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 425 ASN C 195 ASN C 425 ASN E 543 ASN E 630 GLN F 203 GLN F 283 ASN F 377 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.164269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138618 restraints weight = 23533.388| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.54 r_work: 0.3571 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15480 Z= 0.118 Angle : 0.627 15.037 21166 Z= 0.306 Chirality : 0.044 0.200 2584 Planarity : 0.003 0.031 2613 Dihedral : 5.219 37.787 3206 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.66 % Allowed : 18.08 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.21), residues: 1622 helix: 1.98 (0.28), residues: 365 sheet: 0.10 (0.23), residues: 440 loop : -0.90 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 178 TYR 0.030 0.001 TYR E 643 PHE 0.019 0.001 PHE C 391 TRP 0.011 0.001 TRP E 596 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00259 (15389) covalent geometry : angle 0.58676 (20926) SS BOND : bond 0.00478 ( 33) SS BOND : angle 1.62765 ( 66) hydrogen bonds : bond 0.04207 ( 555) hydrogen bonds : angle 5.28211 ( 1596) link_BETA1-4 : bond 0.00569 ( 6) link_BETA1-4 : angle 1.88886 ( 18) link_NAG-ASN : bond 0.00235 ( 52) link_NAG-ASN : angle 2.36757 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 376 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9096 (m100) cc_final: 0.8252 (m100) REVERT: A 102 GLU cc_start: 0.8464 (mm-30) cc_final: 0.8096 (mm-30) REVERT: A 440 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: B 540 GLN cc_start: 0.8031 (OUTLIER) cc_final: 0.6384 (mp10) REVERT: B 616 ASN cc_start: 0.8327 (t0) cc_final: 0.7977 (t0) REVERT: C 104 MET cc_start: 0.9376 (ttt) cc_final: 0.9113 (ttt) REVERT: C 178 ARG cc_start: 0.8266 (ptm-80) cc_final: 0.8016 (ptm-80) REVERT: C 394 THR cc_start: 0.7685 (m) cc_final: 0.7402 (t) REVERT: D 530 MET cc_start: 0.7195 (mtt) cc_final: 0.6460 (mtt) REVERT: E 530 MET cc_start: 0.8813 (mtm) cc_final: 0.8387 (mtm) REVERT: E 634 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8252 (tm-30) REVERT: F 107 ASP cc_start: 0.8650 (m-30) cc_final: 0.8208 (m-30) REVERT: F 112 TRP cc_start: 0.8329 (t-100) cc_final: 0.8027 (t-100) REVERT: F 231 LYS cc_start: 0.8063 (mttp) cc_final: 0.7688 (mttm) REVERT: F 502 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8379 (tttp) outliers start: 54 outliers final: 42 residues processed: 412 average time/residue: 0.1191 time to fit residues: 74.1570 Evaluate side-chains 384 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 339 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 502 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 30 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 0.6980 chunk 133 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 658 GLN E 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.161698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135951 restraints weight = 23722.885| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.54 r_work: 0.3534 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15480 Z= 0.182 Angle : 0.654 14.676 21166 Z= 0.319 Chirality : 0.045 0.203 2584 Planarity : 0.003 0.035 2613 Dihedral : 5.354 39.991 3206 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.40 % Allowed : 18.82 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.21), residues: 1622 helix: 1.85 (0.28), residues: 366 sheet: 0.04 (0.24), residues: 438 loop : -0.95 (0.21), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 178 TYR 0.026 0.002 TYR E 643 PHE 0.013 0.002 PHE A 376 TRP 0.011 0.001 TRP E 614 HIS 0.004 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00422 (15389) covalent geometry : angle 0.62049 (20926) SS BOND : bond 0.00482 ( 33) SS BOND : angle 1.27457 ( 66) hydrogen bonds : bond 0.04447 ( 555) hydrogen bonds : angle 5.27950 ( 1596) link_BETA1-4 : bond 0.00640 ( 6) link_BETA1-4 : angle 1.87660 ( 18) link_NAG-ASN : bond 0.00272 ( 52) link_NAG-ASN : angle 2.31753 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 346 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9145 (m100) cc_final: 0.8314 (m100) REVERT: A 51 THR cc_start: 0.9278 (m) cc_final: 0.8959 (p) REVERT: A 102 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8201 (mm-30) REVERT: A 269 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7994 (mm-30) REVERT: A 440 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8318 (pm20) REVERT: B 540 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6450 (mp10) REVERT: B 616 ASN cc_start: 0.8320 (t0) cc_final: 0.8046 (t0) REVERT: C 104 MET cc_start: 0.9374 (ttt) cc_final: 0.9117 (ttt) REVERT: C 178 ARG cc_start: 0.8296 (ptm-80) cc_final: 0.8058 (ptm-80) REVERT: C 394 THR cc_start: 0.7717 (m) cc_final: 0.7407 (t) REVERT: D 530 MET cc_start: 0.7201 (mtt) cc_final: 0.6540 (mtt) REVERT: E 530 MET cc_start: 0.8757 (mtm) cc_final: 0.8447 (mtm) REVERT: E 634 GLU cc_start: 0.8566 (mt-10) cc_final: 0.8257 (tm-30) REVERT: F 107 ASP cc_start: 0.8694 (m-30) cc_final: 0.8258 (m-30) REVERT: F 112 TRP cc_start: 0.8378 (t-100) cc_final: 0.7960 (t-100) REVERT: F 231 LYS cc_start: 0.8076 (mttp) cc_final: 0.7650 (mttm) outliers start: 65 outliers final: 55 residues processed: 388 average time/residue: 0.1140 time to fit residues: 67.5813 Evaluate side-chains 395 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 338 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 427 TRP Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 455 THR Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 93 optimal weight: 0.0980 chunk 128 optimal weight: 2.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 170 GLN E 543 ASN E 630 GLN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139070 restraints weight = 23675.537| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.55 r_work: 0.3577 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 15480 Z= 0.112 Angle : 0.602 14.358 21166 Z= 0.295 Chirality : 0.043 0.194 2584 Planarity : 0.003 0.040 2613 Dihedral : 4.982 37.574 3206 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.72 % Allowed : 19.50 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.21), residues: 1622 helix: 2.11 (0.28), residues: 365 sheet: 0.04 (0.24), residues: 462 loop : -0.91 (0.22), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.024 0.001 TYR E 643 PHE 0.013 0.001 PHE C 391 TRP 0.014 0.001 TRP E 614 HIS 0.004 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00249 (15389) covalent geometry : angle 0.57059 (20926) SS BOND : bond 0.00438 ( 33) SS BOND : angle 1.31638 ( 66) hydrogen bonds : bond 0.03990 ( 555) hydrogen bonds : angle 5.12873 ( 1596) link_BETA1-4 : bond 0.00615 ( 6) link_BETA1-4 : angle 1.63090 ( 18) link_NAG-ASN : bond 0.00245 ( 52) link_NAG-ASN : angle 2.11906 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 371 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9108 (m100) cc_final: 0.8270 (m100) REVERT: A 102 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8205 (mm-30) REVERT: A 269 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7908 (mm-30) REVERT: B 616 ASN cc_start: 0.8308 (t0) cc_final: 0.7962 (t0) REVERT: C 104 MET cc_start: 0.9355 (ttt) cc_final: 0.9114 (ttt) REVERT: C 178 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.8026 (ptm-80) REVERT: C 394 THR cc_start: 0.7661 (m) cc_final: 0.7359 (t) REVERT: D 530 MET cc_start: 0.7202 (mtt) cc_final: 0.6584 (mtt) REVERT: E 530 MET cc_start: 0.8702 (mtm) cc_final: 0.8322 (mtm) REVERT: F 107 ASP cc_start: 0.8678 (m-30) cc_final: 0.8192 (m-30) REVERT: F 112 TRP cc_start: 0.8321 (t-100) cc_final: 0.7993 (t-100) REVERT: F 192 ARG cc_start: 0.7334 (ptt180) cc_final: 0.6851 (ptt180) REVERT: F 231 LYS cc_start: 0.8042 (mttp) cc_final: 0.7614 (mttm) outliers start: 55 outliers final: 47 residues processed: 406 average time/residue: 0.1106 time to fit residues: 68.6488 Evaluate side-chains 390 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 343 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 181 VAL Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 455 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 105 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 165 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 92 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 36 optimal weight: 0.0970 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.164892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.139301 restraints weight = 23536.285| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.56 r_work: 0.3576 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15480 Z= 0.116 Angle : 0.596 14.184 21166 Z= 0.293 Chirality : 0.043 0.195 2584 Planarity : 0.003 0.040 2613 Dihedral : 4.867 37.723 3206 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.72 % Allowed : 20.04 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.21), residues: 1622 helix: 2.16 (0.28), residues: 365 sheet: 0.12 (0.24), residues: 442 loop : -0.94 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.022 0.001 TYR E 643 PHE 0.012 0.001 PHE A 53 TRP 0.011 0.001 TRP E 614 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00261 (15389) covalent geometry : angle 0.56733 (20926) SS BOND : bond 0.00387 ( 33) SS BOND : angle 1.16192 ( 66) hydrogen bonds : bond 0.03937 ( 555) hydrogen bonds : angle 5.06401 ( 1596) link_BETA1-4 : bond 0.00592 ( 6) link_BETA1-4 : angle 1.57760 ( 18) link_NAG-ASN : bond 0.00235 ( 52) link_NAG-ASN : angle 2.02181 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 358 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9089 (m100) cc_final: 0.8244 (m100) REVERT: A 51 THR cc_start: 0.9233 (m) cc_final: 0.9002 (p) REVERT: A 102 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8222 (mm-30) REVERT: A 269 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7900 (mm-30) REVERT: B 540 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6549 (mp10) REVERT: B 616 ASN cc_start: 0.8303 (t0) cc_final: 0.7951 (t0) REVERT: C 104 MET cc_start: 0.9355 (ttt) cc_final: 0.9124 (ttt) REVERT: C 178 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.7968 (ptm-80) REVERT: C 394 THR cc_start: 0.7665 (m) cc_final: 0.7379 (t) REVERT: D 530 MET cc_start: 0.7070 (mtt) cc_final: 0.6440 (mtt) REVERT: E 530 MET cc_start: 0.8678 (mtm) cc_final: 0.8421 (mtm) REVERT: F 107 ASP cc_start: 0.8681 (m-30) cc_final: 0.8193 (m-30) REVERT: F 112 TRP cc_start: 0.8372 (t-100) cc_final: 0.8002 (t-100) REVERT: F 192 ARG cc_start: 0.7373 (ptt180) cc_final: 0.6932 (ptt180) REVERT: F 231 LYS cc_start: 0.8026 (mttp) cc_final: 0.7611 (mttm) outliers start: 55 outliers final: 47 residues processed: 392 average time/residue: 0.1028 time to fit residues: 60.9224 Evaluate side-chains 403 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 355 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 124 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 165 optimal weight: 9.9990 chunk 51 optimal weight: 0.3980 chunk 126 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139631 restraints weight = 23433.265| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.55 r_work: 0.3578 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.5157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 15480 Z= 0.122 Angle : 0.626 14.357 21166 Z= 0.307 Chirality : 0.044 0.200 2584 Planarity : 0.003 0.043 2613 Dihedral : 4.862 37.622 3206 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.45 % Allowed : 21.12 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.21), residues: 1622 helix: 2.14 (0.29), residues: 365 sheet: 0.14 (0.24), residues: 444 loop : -0.96 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.021 0.001 TYR E 643 PHE 0.013 0.001 PHE A 53 TRP 0.017 0.001 TRP F 35 HIS 0.005 0.001 HIS C 352 Details of bonding type rmsd covalent geometry : bond 0.00280 (15389) covalent geometry : angle 0.59349 (20926) SS BOND : bond 0.00504 ( 33) SS BOND : angle 2.02037 ( 66) hydrogen bonds : bond 0.03937 ( 555) hydrogen bonds : angle 5.05283 ( 1596) link_BETA1-4 : bond 0.00586 ( 6) link_BETA1-4 : angle 1.54492 ( 18) link_NAG-ASN : bond 0.00248 ( 52) link_NAG-ASN : angle 1.99086 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3244 Ramachandran restraints generated. 1622 Oldfield, 0 Emsley, 1622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 365 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9093 (m100) cc_final: 0.8256 (m100) REVERT: A 51 THR cc_start: 0.9224 (m) cc_final: 0.9013 (p) REVERT: A 102 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8233 (mm-30) REVERT: A 269 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7897 (mm-30) REVERT: B 540 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.6545 (mp10) REVERT: B 616 ASN cc_start: 0.8304 (t0) cc_final: 0.8031 (t0) REVERT: C 104 MET cc_start: 0.9367 (ttt) cc_final: 0.9123 (ttt) REVERT: C 178 ARG cc_start: 0.8218 (ptm-80) cc_final: 0.7852 (ptm-80) REVERT: C 394 THR cc_start: 0.7725 (m) cc_final: 0.7413 (t) REVERT: D 530 MET cc_start: 0.7113 (mtt) cc_final: 0.6478 (mtt) REVERT: E 626 MET cc_start: 0.7594 (ttt) cc_final: 0.7030 (ttt) REVERT: F 107 ASP cc_start: 0.8657 (m-30) cc_final: 0.8177 (m-30) REVERT: F 112 TRP cc_start: 0.8427 (t-100) cc_final: 0.8038 (t-100) REVERT: F 121 LYS cc_start: 0.8244 (mttt) cc_final: 0.7811 (mtpp) REVERT: F 192 ARG cc_start: 0.7391 (ptt180) cc_final: 0.6948 (ptt180) REVERT: F 231 LYS cc_start: 0.8056 (mttp) cc_final: 0.7639 (mttm) outliers start: 51 outliers final: 47 residues processed: 396 average time/residue: 0.1171 time to fit residues: 70.2487 Evaluate side-chains 401 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 353 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 272 ILE Chi-restraints excluded: chain A residue 295 ASN Chi-restraints excluded: chain A residue 333 VAL Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 604 CYS Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 191 TYR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 203 GLN Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 455 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 146 optimal weight: 4.9990 chunk 116 optimal weight: 0.2980 chunk 127 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 141 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 178 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 GLN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.163145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137505 restraints weight = 23534.860| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.55 r_work: 0.3554 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15480 Z= 0.158 Angle : 0.646 14.361 21166 Z= 0.317 Chirality : 0.045 0.199 2584 Planarity : 0.003 0.039 2613 Dihedral : 5.068 39.494 3206 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.72 % Allowed : 20.99 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.21), residues: 1622 helix: 2.03 (0.28), residues: 366 sheet: 0.09 (0.24), residues: 441 loop : -1.02 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 178 TYR 0.021 0.001 TYR E 643 PHE 0.022 0.002 PHE A 361 TRP 0.015 0.001 TRP E 614 HIS 0.006 0.001 HIS A 72 Details of bonding type rmsd covalent geometry : bond 0.00370 (15389) covalent geometry : angle 0.61518 (20926) SS BOND : bond 0.00544 ( 33) SS BOND : angle 1.84776 ( 66) hydrogen bonds : bond 0.04145 ( 555) hydrogen bonds : angle 5.11193 ( 1596) link_BETA1-4 : bond 0.00589 ( 6) link_BETA1-4 : angle 1.59925 ( 18) link_NAG-ASN : bond 0.00251 ( 52) link_NAG-ASN : angle 2.04078 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.27 seconds wall clock time: 58 minutes 40.48 seconds (3520.48 seconds total)