Starting phenix.real_space_refine on Fri Jul 3 17:29:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_40810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw7_40810/07_2026/8sw7_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-dev-6108/lib/python3.11/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 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 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 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 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 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 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 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 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 chiralities: 14 Time building chain proxies: 3.51, per 1000 atoms: 0.23 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: 1.41 Conformation dependent library (CDL) restraints added in 663.6 milliseconds 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: 0.67 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: 3.02 Time building geometry restraints manager: 1.84 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 - 17.50: 8492 17.50 - 35.00: 215 35.00 - 52.50: 76 52.50 - 70.00: 23 70.00 - 87.50: 11 Dihedral angle restraints: 8817 sinusoidal: 3325 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 8814 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: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.420 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 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 : 10.034 87.497 5140 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 are 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/Z covalent geometry : bond 0.02220 / 1.17 (15389) covalent geometry : angle 1.71843 / 1.11 (20926) SS BOND : bond 0.01589 / 1.15 ( 33) SS BOND : angle 3.60500 / 2.69 ( 66) hydrogen bonds : bond 0.15922 / 11.24 ( 555) hydrogen bonds : angle 7.89529 / 5.56 ( 1596) link_BETA1-4 : bond 0.07521 / 4.55 ( 6) link_BETA1-4 : angle 4.80451 / 3.13 ( 18) link_NAG-ASN : bond 0.08112 / 5.13 ( 52) link_NAG-ASN : angle 2.67185 / 1.87 ( 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 : 0.562 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: 0.1311 time to fit residues: 114.3906 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 : 0.549 ------------------------------------------------------------------------------- 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... 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 = 0.3996 r_free = 0.3996 target = 0.165104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139313 restraints weight = 22848.653| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.52 r_work: 0.3552 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15480 Z= 0.186 Angle : 0.806 15.798 21166 Z= 0.399 Chirality : 0.048 0.317 2584 Planarity : 0.004 0.084 2613 Dihedral : 5.176 50.588 1994 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.98 % Allowed : 12.80 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.21), residues: 1622 helix: 1.86 (0.28), residues: 360 sheet: 0.75 (0.24), residues: 442 loop : -0.19 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 298 TYR 0.039 0.002 TYR E 643 PHE 0.030 0.002 PHE F 53 TRP 0.024 0.002 TRP C 479 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00412 / 0.19 (15389) covalent geometry : angle 0.74491 / 0.39 (20926) SS BOND : bond 0.00466 / 0.26 ( 33) SS BOND : angle 1.59608 / 1.36 ( 66) hydrogen bonds : bond 0.06421 / 4.56 ( 555) hydrogen bonds : angle 6.02994 / 4.26 ( 1596) link_BETA1-4 : bond 0.00895 / 0.57 ( 6) link_BETA1-4 : angle 3.38852 / 2.16 ( 18) link_NAG-ASN : bond 0.00557 / 0.33 ( 52) link_NAG-ASN : angle 3.37556 / 2.47 ( 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 468 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 424 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8227 (mmp) cc_final: 0.7596 (mmt) REVERT: A 258 GLN cc_start: 0.9023 (mt0) cc_final: 0.8701 (mt0) REVERT: A 269 GLU cc_start: 0.8576 (mt-10) cc_final: 0.8351 (mm-30) REVERT: A 452 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8152 (pp) REVERT: B 627 THR cc_start: 0.8807 (p) cc_final: 0.8603 (t) REVERT: C 178 ARG cc_start: 0.8249 (ptm-80) cc_final: 0.8037 (ptm-80) REVERT: C 192 ARG cc_start: 0.7996 (ttm170) cc_final: 0.7777 (tpp-160) REVERT: C 287 GLN cc_start: 0.8126 (tt0) cc_final: 0.7837 (tt0) REVERT: D 530 MET cc_start: 0.6268 (mtt) cc_final: 0.5844 (mtt) REVERT: D 651 ASN cc_start: 0.8743 (t0) cc_final: 0.8542 (t0) REVERT: E 542 ARG cc_start: 0.8707 (ttm170) cc_final: 0.8323 (ttm170) REVERT: E 630 GLN cc_start: 0.8365 (mt0) cc_final: 0.7808 (mt0) REVERT: F 46 LYS cc_start: 0.9015 (mttm) cc_final: 0.8741 (mttp) REVERT: F 153 GLU cc_start: 0.8337 (tp30) cc_final: 0.8083 (tp30) REVERT: F 192 ARG cc_start: 0.7341 (ptt180) cc_final: 0.6800 (ptt180) REVERT: F 267 GLU cc_start: 0.7757 (pm20) cc_final: 0.7554 (pm20) REVERT: F 368 ASP cc_start: 0.7909 (m-30) cc_final: 0.7643 (p0) outliers start: 44 outliers final: 24 residues processed: 442 average time/residue: 0.1194 time to fit residues: 79.5676 Evaluate side-chains 390 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 365 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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 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 364 SER Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 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 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: 7.9990 chunk 85 optimal weight: 9.9990 chunk 74 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 119 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 302 ASN C 170 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130930 restraints weight = 23667.376| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 3.49 r_work: 0.3450 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 15480 Z= 0.306 Angle : 0.826 14.872 21166 Z= 0.408 Chirality : 0.051 0.495 2584 Planarity : 0.005 0.042 2613 Dihedral : 5.242 47.995 1994 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.67 % Allowed : 13.74 % Favored : 81.58 % 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 are not related in a simple way. whole: 0.01 (0.20), residues: 1622 helix: 1.31 (0.27), residues: 370 sheet: 0.19 (0.23), residues: 473 loop : -0.70 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 504 TYR 0.019 0.003 TYR F 191 PHE 0.024 0.003 PHE A 468 TRP 0.017 0.002 TRP B 571 HIS 0.007 0.002 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.31 (15389) covalent geometry : angle 0.77792 / 0.40 (20926) SS BOND : bond 0.00713 / 0.42 ( 33) SS BOND : angle 2.34562 / 1.97 ( 66) hydrogen bonds : bond 0.06096 / 4.36 ( 555) hydrogen bonds : angle 5.87906 / 4.14 ( 1596) link_BETA1-4 : bond 0.00823 / 0.49 ( 6) link_BETA1-4 : angle 2.44487 / 1.54 ( 18) link_NAG-ASN : bond 0.00759 / 0.39 ( 52) link_NAG-ASN : angle 2.89444 / 2.11 ( 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 451 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 382 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9117 (m100) cc_final: 0.8209 (m100) REVERT: A 51 THR cc_start: 0.9272 (m) cc_final: 0.8941 (p) REVERT: A 269 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8431 (mm-30) REVERT: B 616 ASN cc_start: 0.8374 (t0) cc_final: 0.8100 (t0) REVERT: C 104 MET cc_start: 0.9394 (ttt) cc_final: 0.9152 (ttt) REVERT: C 178 ARG cc_start: 0.8215 (ptm-80) cc_final: 0.7956 (ptm-80) REVERT: C 191 TYR cc_start: 0.8129 (m-80) cc_final: 0.7709 (m-10) REVERT: C 287 GLN cc_start: 0.8409 (tt0) cc_final: 0.8142 (tt0) REVERT: D 530 MET cc_start: 0.6849 (mtt) cc_final: 0.6100 (mtt) REVERT: E 542 ARG cc_start: 0.8765 (ttm170) cc_final: 0.8308 (ttm170) REVERT: E 543 ASN cc_start: 0.8485 (m-40) cc_final: 0.8091 (m-40) REVERT: E 571 TRP cc_start: 0.5636 (OUTLIER) cc_final: 0.5329 (p-90) REVERT: E 634 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8186 (tm-30) REVERT: E 645 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8620 (mt) REVERT: E 655 LYS cc_start: 0.8650 (mmtp) cc_final: 0.7944 (mtpp) REVERT: F 107 ASP cc_start: 0.8683 (m-30) cc_final: 0.8225 (m-30) REVERT: F 153 GLU cc_start: 0.8472 (tp30) cc_final: 0.8197 (tp30) REVERT: F 241 ASN cc_start: 0.6936 (m-40) cc_final: 0.6662 (t0) REVERT: F 368 ASP cc_start: 0.8061 (m-30) cc_final: 0.7757 (p0) REVERT: F 377 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7760 (t0) REVERT: F 475 MET cc_start: 0.9003 (mmm) cc_final: 0.8757 (tpp) outliers start: 69 outliers final: 53 residues processed: 422 average time/residue: 0.1142 time to fit residues: 72.6756 Evaluate side-chains 400 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 344 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 243 SER 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 373 THR Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 450 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 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 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 D residue 544 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 645 LEU 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 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 331 CYS 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 50 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 161 optimal weight: 0.1980 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 114 GLN C 425 ASN D 616 ASN F 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.160980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.135291 restraints weight = 23242.046| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.54 r_work: 0.3506 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 15480 Z= 0.139 Angle : 0.664 15.945 21166 Z= 0.325 Chirality : 0.044 0.226 2584 Planarity : 0.003 0.032 2613 Dihedral : 4.732 28.032 1994 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.25 % Allowed : 16.52 % Favored : 80.23 % 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 are not related in a simple way. whole: 0.11 (0.21), residues: 1622 helix: 1.67 (0.28), residues: 365 sheet: 0.24 (0.23), residues: 452 loop : -0.76 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.015 0.002 TYR A 173 PHE 0.013 0.002 PHE A 53 TRP 0.018 0.001 TRP E 614 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (15389) covalent geometry : angle 0.62410 / 0.31 (20926) SS BOND : bond 0.00275 / 0.17 ( 33) SS BOND : angle 1.82941 / 1.48 ( 66) hydrogen bonds : bond 0.04887 / 3.43 ( 555) hydrogen bonds : angle 5.49649 / 3.87 ( 1596) link_BETA1-4 : bond 0.00565 / 0.32 ( 6) link_BETA1-4 : angle 1.89353 / 1.21 ( 18) link_NAG-ASN : bond 0.00419 / 0.22 ( 52) link_NAG-ASN : angle 2.38489 / 1.75 ( 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 429 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 381 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9054 (m100) cc_final: 0.8114 (m100) REVERT: A 275 GLU cc_start: 0.8698 (tt0) cc_final: 0.8339 (tt0) REVERT: A 428 GLN cc_start: 0.8666 (mt0) cc_final: 0.8299 (mm110) REVERT: B 540 GLN cc_start: 0.7790 (mt0) cc_final: 0.7479 (mp10) REVERT: B 616 ASN cc_start: 0.8493 (t0) cc_final: 0.8224 (t0) REVERT: C 100 MET cc_start: 0.9089 (mtp) cc_final: 0.8799 (mtm) REVERT: C 104 MET cc_start: 0.9338 (ttt) cc_final: 0.9068 (ttt) REVERT: C 150 MET cc_start: 0.7863 (mtp) cc_final: 0.7400 (mtm) REVERT: C 178 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7990 (ptm-80) REVERT: C 190 GLU cc_start: 0.7129 (tm-30) cc_final: 0.6505 (pm20) REVERT: C 191 TYR cc_start: 0.8115 (m-80) cc_final: 0.7691 (m-10) REVERT: C 192 ARG cc_start: 0.8008 (ttm170) cc_final: 0.7761 (tpp-160) REVERT: C 195 ASN cc_start: 0.8188 (t0) cc_final: 0.7977 (t0) REVERT: C 287 GLN cc_start: 0.8370 (tt0) cc_final: 0.8112 (tt0) REVERT: C 394 THR cc_start: 0.7853 (m) cc_final: 0.7460 (t) REVERT: D 530 MET cc_start: 0.6884 (mtt) cc_final: 0.6092 (mtt) REVERT: E 542 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8142 (ttm170) REVERT: E 634 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8177 (tm-30) REVERT: E 655 LYS cc_start: 0.8525 (mmtp) cc_final: 0.7804 (mtpp) REVERT: F 107 ASP cc_start: 0.8687 (m-30) cc_final: 0.8236 (m-30) REVERT: F 112 TRP cc_start: 0.8262 (t-100) cc_final: 0.8030 (t-100) REVERT: F 153 GLU cc_start: 0.8355 (tp30) cc_final: 0.8132 (tp30) REVERT: F 274 SER cc_start: 0.8857 (t) cc_final: 0.8617 (p) REVERT: F 368 ASP cc_start: 0.8078 (m-30) cc_final: 0.7759 (p0) REVERT: F 377 ASN cc_start: 0.8188 (OUTLIER) cc_final: 0.7904 (t0) REVERT: F 456 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7230 (mtp85) outliers start: 48 outliers final: 34 residues processed: 410 average time/residue: 0.1086 time to fit residues: 67.6373 Evaluate side-chains 380 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 345 time to evaluate : 0.565 ------------------------------------------------------------------------------- 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 170 GLN Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 440 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU 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 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 529 THR 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 292 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER 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: 10.9990 chunk 106 optimal weight: 0.5980 chunk 165 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 616 ASN C 258 GLN C 478 ASN D 616 ASN E 543 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.133412 restraints weight = 23466.612| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 3.40 r_work: 0.3503 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 15480 Z= 0.241 Angle : 0.720 16.433 21166 Z= 0.352 Chirality : 0.047 0.201 2584 Planarity : 0.004 0.034 2613 Dihedral : 4.828 25.030 1994 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.87 % Allowed : 15.71 % Favored : 79.42 % 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 are not related in a simple way. whole: -0.20 (0.21), residues: 1622 helix: 1.44 (0.28), residues: 371 sheet: 0.02 (0.24), residues: 435 loop : -0.94 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 480 TYR 0.021 0.002 TYR C 318 PHE 0.021 0.002 PHE A 376 TRP 0.011 0.002 TRP C 479 HIS 0.006 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 (15389) covalent geometry : angle 0.68650 / 0.34 (20926) SS BOND : bond 0.00474 / 0.27 ( 33) SS BOND : angle 1.59712 / 1.34 ( 66) hydrogen bonds : bond 0.05194 / 3.71 ( 555) hydrogen bonds : angle 5.55651 / 3.92 ( 1596) link_BETA1-4 : bond 0.00646 / 0.36 ( 6) link_BETA1-4 : angle 1.88192 / 1.17 ( 18) link_NAG-ASN : bond 0.00360 / 0.22 ( 52) link_NAG-ASN : angle 2.38720 / 1.73 ( 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 429 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 357 time to evaluate : 0.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9128 (m100) cc_final: 0.8242 (m100) REVERT: A 51 THR cc_start: 0.9277 (m) cc_final: 0.8923 (p) REVERT: A 102 GLU cc_start: 0.8500 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 428 GLN cc_start: 0.8663 (mt0) cc_final: 0.8371 (mm110) REVERT: A 440 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8294 (pm20) REVERT: B 540 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7473 (mt0) REVERT: C 104 MET cc_start: 0.9399 (ttt) cc_final: 0.9130 (ttt) REVERT: C 178 ARG cc_start: 0.8336 (ptm-80) cc_final: 0.8124 (ptm-80) REVERT: C 191 TYR cc_start: 0.8316 (m-80) cc_final: 0.7978 (m-10) REVERT: C 192 ARG cc_start: 0.8024 (ttm170) cc_final: 0.7475 (tpt170) REVERT: C 394 THR cc_start: 0.7739 (m) cc_final: 0.7441 (t) REVERT: C 426 MET cc_start: 0.8339 (mmm) cc_final: 0.8121 (mmm) REVERT: D 530 MET cc_start: 0.6983 (mtt) cc_final: 0.6343 (mtt) REVERT: E 542 ARG cc_start: 0.8768 (ttm170) cc_final: 0.8160 (ttm170) REVERT: E 634 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8211 (tm-30) REVERT: F 87 GLU cc_start: 0.7855 (mp0) cc_final: 0.7383 (mp0) REVERT: F 107 ASP cc_start: 0.8694 (m-30) cc_final: 0.8287 (m-30) REVERT: F 274 SER cc_start: 0.9006 (t) cc_final: 0.8777 (p) REVERT: F 377 ASN cc_start: 0.8260 (OUTLIER) cc_final: 0.8005 (t0) outliers start: 72 outliers final: 57 residues processed: 394 average time/residue: 0.1135 time to fit residues: 68.4503 Evaluate side-chains 400 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 340 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 170 GLN 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 243 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 272 ILE 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 604 CYS 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 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 C residue 442 VAL Chi-restraints excluded: chain D residue 544 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 E residue 529 THR Chi-restraints excluded: chain E residue 534 SER 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 111 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 122 LEU Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 377 ASN Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 504 ARG 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: 0.9980 chunk 153 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 GLN C 425 ASN E 543 ASN E 653 GLN F 85 HIS F 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.136510 restraints weight = 23625.135| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 3.53 r_work: 0.3538 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15480 Z= 0.143 Angle : 0.655 16.135 21166 Z= 0.318 Chirality : 0.044 0.225 2584 Planarity : 0.003 0.031 2613 Dihedral : 4.599 23.050 1994 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.20 % Allowed : 16.52 % Favored : 79.28 % 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 are not related in a simple way. whole: -0.09 (0.21), residues: 1622 helix: 1.70 (0.28), residues: 365 sheet: 0.16 (0.24), residues: 418 loop : -0.97 (0.21), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.031 0.002 TYR E 643 PHE 0.013 0.001 PHE A 376 TRP 0.011 0.001 TRP E 596 HIS 0.010 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (15389) covalent geometry : angle 0.61965 / 0.31 (20926) SS BOND : bond 0.00374 / 0.21 ( 33) SS BOND : angle 1.66757 / 1.35 ( 66) hydrogen bonds : bond 0.04591 / 3.26 ( 555) hydrogen bonds : angle 5.34381 / 3.77 ( 1596) link_BETA1-4 : bond 0.00618 / 0.34 ( 6) link_BETA1-4 : angle 1.65779 / 1.05 ( 18) link_NAG-ASN : bond 0.00283 / 0.17 ( 52) link_NAG-ASN : angle 2.27368 / 1.65 ( 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 429 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 367 time to evaluate : 0.515 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: 0.8228 (m100) REVERT: A 102 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8171 (mm-30) REVERT: A 269 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7947 (mm-30) REVERT: A 428 GLN cc_start: 0.8623 (mt0) cc_final: 0.8383 (mm110) REVERT: A 440 GLN cc_start: 0.8551 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: B 540 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7606 (mp10) REVERT: C 104 MET cc_start: 0.9389 (ttt) cc_final: 0.9128 (ttt) REVERT: C 178 ARG cc_start: 0.8316 (ptm-80) cc_final: 0.8081 (ptm-80) REVERT: C 191 TYR cc_start: 0.8261 (m-80) cc_final: 0.7966 (m-10) REVERT: C 192 ARG cc_start: 0.8000 (ttm170) cc_final: 0.7373 (tpt170) REVERT: C 394 THR cc_start: 0.7737 (m) cc_final: 0.7371 (t) REVERT: C 426 MET cc_start: 0.8379 (mmm) cc_final: 0.8163 (mmm) REVERT: D 530 MET cc_start: 0.7233 (mtt) cc_final: 0.6574 (mtt) REVERT: D 588 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8183 (ttm-80) REVERT: E 634 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8155 (tm-30) REVERT: F 107 ASP cc_start: 0.8687 (m-30) cc_final: 0.8273 (m-30) REVERT: F 112 TRP cc_start: 0.8422 (t-100) cc_final: 0.8000 (t-100) REVERT: F 231 LYS cc_start: 0.8181 (mttt) cc_final: 0.7739 (mttm) REVERT: F 274 SER cc_start: 0.8703 (t) cc_final: 0.8213 (p) REVERT: F 377 ASN cc_start: 0.8217 (p0) cc_final: 0.8015 (t0) outliers start: 62 outliers final: 49 residues processed: 403 average time/residue: 0.1060 time to fit residues: 65.2014 Evaluate side-chains 396 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 345 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 115 SER 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 243 SER 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 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 619 LEU 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 364 SER Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 573 ILE 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 111 LEU 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 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 446 VAL 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: 5.9990 chunk 50 optimal weight: 0.9990 chunk 146 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 154 optimal weight: 0.0050 chunk 133 optimal weight: 3.9990 chunk 105 optimal weight: 0.5980 chunk 70 optimal weight: 7.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 425 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 543 ASN F 203 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138282 restraints weight = 23582.298| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 3.53 r_work: 0.3564 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 15480 Z= 0.123 Angle : 0.627 15.827 21166 Z= 0.305 Chirality : 0.043 0.190 2584 Planarity : 0.003 0.029 2613 Dihedral : 4.453 28.105 1994 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.27 % Allowed : 17.13 % Favored : 78.61 % 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 are not related in a simple way. whole: 0.00 (0.21), residues: 1622 helix: 1.91 (0.29), residues: 360 sheet: 0.15 (0.24), residues: 432 loop : -0.95 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 178 TYR 0.027 0.002 TYR E 643 PHE 0.013 0.001 PHE A 53 TRP 0.011 0.001 TRP E 623 HIS 0.010 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (15389) covalent geometry : angle 0.59808 / 0.30 (20926) SS BOND : bond 0.00393 / 0.21 ( 33) SS BOND : angle 1.64737 / 1.38 ( 66) hydrogen bonds : bond 0.04289 / 3.05 ( 555) hydrogen bonds : angle 5.23369 / 3.70 ( 1596) link_BETA1-4 : bond 0.00599 / 0.33 ( 6) link_BETA1-4 : angle 1.55676 / 0.99 ( 18) link_NAG-ASN : bond 0.00304 / 0.18 ( 52) link_NAG-ASN : angle 1.97718 / 1.44 ( 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 425 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 362 time to evaluate : 0.446 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: 0.8234 (m100) REVERT: A 190 GLU cc_start: 0.7756 (mp0) cc_final: 0.7078 (mp0) REVERT: A 269 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7888 (mm-30) REVERT: A 428 GLN cc_start: 0.8566 (mt0) cc_final: 0.8349 (mm110) REVERT: A 440 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8301 (pm20) REVERT: B 540 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7540 (mp10) REVERT: C 104 MET cc_start: 0.9362 (ttt) cc_final: 0.9113 (ttt) REVERT: C 178 ARG cc_start: 0.8283 (ptm-80) cc_final: 0.8038 (ptm-80) REVERT: C 191 TYR cc_start: 0.8268 (m-80) cc_final: 0.7985 (m-10) REVERT: C 192 ARG cc_start: 0.7852 (ttm170) cc_final: 0.7241 (tpt170) REVERT: C 394 THR cc_start: 0.7770 (m) cc_final: 0.7433 (t) REVERT: C 486 TYR cc_start: 0.8621 (m-80) cc_final: 0.8337 (m-10) REVERT: D 530 MET cc_start: 0.7200 (mtt) cc_final: 0.6527 (mtt) REVERT: D 588 ARG cc_start: 0.8538 (ttt-90) cc_final: 0.8183 (ttm-80) REVERT: F 107 ASP cc_start: 0.8700 (m-30) cc_final: 0.8283 (m-30) REVERT: F 231 LYS cc_start: 0.8087 (mttt) cc_final: 0.7651 (mttm) outliers start: 63 outliers final: 52 residues processed: 401 average time/residue: 0.0984 time to fit residues: 59.9237 Evaluate side-chains 395 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 341 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 120 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 243 SER 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 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 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 364 SER Chi-restraints excluded: chain C residue 425 ASN Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 573 ILE 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 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 293 GLN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 128 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN F 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.163854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138398 restraints weight = 23709.541| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 3.53 r_work: 0.3562 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.4847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15480 Z= 0.129 Angle : 0.629 15.543 21166 Z= 0.307 Chirality : 0.044 0.220 2584 Planarity : 0.003 0.027 2613 Dihedral : 4.376 28.270 1994 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.06 % Allowed : 18.14 % Favored : 77.79 % 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 are not related in a simple way. whole: 0.03 (0.21), residues: 1622 helix: 1.97 (0.29), residues: 360 sheet: 0.26 (0.24), residues: 420 loop : -0.99 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 469 TYR 0.025 0.001 TYR E 643 PHE 0.013 0.001 PHE A 376 TRP 0.011 0.001 TRP E 631 HIS 0.008 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15389) covalent geometry : angle 0.59903 / 0.30 (20926) SS BOND : bond 0.00447 / 0.24 ( 33) SS BOND : angle 1.73041 / 1.44 ( 66) hydrogen bonds : bond 0.04226 / 2.98 ( 555) hydrogen bonds : angle 5.19258 / 3.67 ( 1596) link_BETA1-4 : bond 0.00604 / 0.33 ( 6) link_BETA1-4 : angle 1.50452 / 0.95 ( 18) link_NAG-ASN : bond 0.00260 / 0.16 ( 52) link_NAG-ASN : angle 1.98896 / 1.43 ( 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 409 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 349 time to evaluate : 0.568 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: 0.9117 (m100) cc_final: 0.8252 (m100) REVERT: A 102 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8131 (mm-30) REVERT: A 269 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7887 (mm-30) REVERT: B 540 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: C 104 MET cc_start: 0.9366 (ttt) cc_final: 0.9118 (ttt) REVERT: C 178 ARG cc_start: 0.8232 (ptm-80) cc_final: 0.7993 (ptm-80) REVERT: C 192 ARG cc_start: 0.7797 (ttm170) cc_final: 0.7468 (tpt170) REVERT: C 394 THR cc_start: 0.7751 (m) cc_final: 0.7440 (t) REVERT: D 530 MET cc_start: 0.7231 (mtt) cc_final: 0.6585 (mtt) REVERT: D 588 ARG cc_start: 0.8564 (ttt-90) cc_final: 0.8201 (ttm-80) REVERT: F 35 TRP cc_start: 0.8073 (m100) cc_final: 0.7871 (m100) REVERT: F 107 ASP cc_start: 0.8707 (m-30) cc_final: 0.8279 (m-30) REVERT: F 231 LYS cc_start: 0.8051 (mttt) cc_final: 0.7632 (mttm) outliers start: 60 outliers final: 49 residues processed: 385 average time/residue: 0.0980 time to fit residues: 57.6940 Evaluate side-chains 390 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 340 time to evaluate : 0.319 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 115 SER 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 243 SER 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 426 MET 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 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 181 VAL Chi-restraints excluded: chain C residue 195 ASN 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 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 573 ILE 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 209 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 105 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN D 651 ASN D 658 GLN E 630 GLN E 653 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.162832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137319 restraints weight = 23758.165| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.52 r_work: 0.3547 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 15480 Z= 0.155 Angle : 0.649 15.407 21166 Z= 0.319 Chirality : 0.044 0.199 2584 Planarity : 0.003 0.030 2613 Dihedral : 4.457 27.398 1994 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.13 % Allowed : 18.48 % Favored : 77.39 % 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 are not related in a simple way. whole: -0.08 (0.21), residues: 1622 helix: 1.78 (0.28), residues: 373 sheet: 0.15 (0.24), residues: 438 loop : -1.06 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 178 TYR 0.024 0.001 TYR E 643 PHE 0.014 0.002 PHE A 376 TRP 0.020 0.001 TRP E 614 HIS 0.009 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (15389) covalent geometry : angle 0.62094 / 0.31 (20926) SS BOND : bond 0.00451 / 0.25 ( 33) SS BOND : angle 1.83220 / 1.52 ( 66) hydrogen bonds : bond 0.04317 / 3.05 ( 555) hydrogen bonds : angle 5.18613 / 3.67 ( 1596) link_BETA1-4 : bond 0.00624 / 0.35 ( 6) link_BETA1-4 : angle 1.50501 / 0.95 ( 18) link_NAG-ASN : bond 0.00279 / 0.16 ( 52) link_NAG-ASN : angle 1.92914 / 1.38 ( 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 414 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 353 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9137 (m100) cc_final: 0.8272 (m100) REVERT: A 51 THR cc_start: 0.9269 (m) cc_final: 0.8956 (p) REVERT: A 102 GLU cc_start: 0.8489 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 190 GLU cc_start: 0.7985 (mp0) cc_final: 0.7759 (mp0) REVERT: A 269 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7903 (mm-30) REVERT: B 540 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.7595 (mp10) REVERT: C 104 MET cc_start: 0.9367 (ttt) cc_final: 0.9125 (ttt) REVERT: C 178 ARG cc_start: 0.8242 (ptm-80) cc_final: 0.8004 (ptm-80) REVERT: C 192 ARG cc_start: 0.7754 (ttm170) cc_final: 0.7377 (tpt170) REVERT: C 248 THR cc_start: 0.8097 (t) cc_final: 0.7872 (p) REVERT: C 394 THR cc_start: 0.7704 (m) cc_final: 0.7391 (t) REVERT: D 530 MET cc_start: 0.7231 (mtt) cc_final: 0.6666 (mtt) REVERT: D 588 ARG cc_start: 0.8569 (ttt-90) cc_final: 0.8209 (ttm-80) REVERT: F 35 TRP cc_start: 0.8122 (m100) cc_final: 0.7917 (m100) REVERT: F 107 ASP cc_start: 0.8712 (m-30) cc_final: 0.8271 (m-30) REVERT: F 231 LYS cc_start: 0.8047 (mttt) cc_final: 0.7629 (mttm) outliers start: 61 outliers final: 55 residues processed: 390 average time/residue: 0.1025 time to fit residues: 61.1056 Evaluate side-chains 403 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 347 time to evaluate : 0.471 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 115 SER 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 243 SER 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 333 VAL Chi-restraints excluded: chain A residue 426 MET 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 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 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 612 SER 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 571 TRP Chi-restraints excluded: chain E residue 573 ILE 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 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 124 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 165 optimal weight: 9.9990 chunk 51 optimal weight: 0.7980 chunk 126 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 195 ASN ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.161438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136004 restraints weight = 23823.383| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.52 r_work: 0.3533 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 15480 Z= 0.178 Angle : 0.666 15.395 21166 Z= 0.331 Chirality : 0.045 0.199 2584 Planarity : 0.003 0.032 2613 Dihedral : 4.570 26.976 1994 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.13 % Allowed : 18.55 % Favored : 77.32 % 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 are not related in a simple way. whole: -0.15 (0.21), residues: 1622 helix: 1.80 (0.28), residues: 371 sheet: 0.01 (0.24), residues: 440 loop : -1.08 (0.21), residues: 811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.024 0.002 TYR E 643 PHE 0.015 0.002 PHE A 376 TRP 0.021 0.001 TRP E 631 HIS 0.009 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.18 (15389) covalent geometry : angle 0.63858 / 0.32 (20926) SS BOND : bond 0.00468 / 0.25 ( 33) SS BOND : angle 1.78083 / 1.45 ( 66) hydrogen bonds : bond 0.04481 / 3.15 ( 555) hydrogen bonds : angle 5.22325 / 3.70 ( 1596) link_BETA1-4 : bond 0.00600 / 0.32 ( 6) link_BETA1-4 : angle 1.51600 / 0.95 ( 18) link_NAG-ASN : bond 0.00281 / 0.17 ( 52) link_NAG-ASN : angle 1.98090 / 1.42 ( 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 412 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 351 time to evaluate : 0.559 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: 0.9163 (m100) cc_final: 0.8293 (m100) REVERT: A 51 THR cc_start: 0.9277 (m) cc_final: 0.8953 (p) REVERT: A 102 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8214 (mm-30) REVERT: B 540 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7599 (mp10) REVERT: C 104 MET cc_start: 0.9352 (ttt) cc_final: 0.9106 (ttt) REVERT: C 178 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.8012 (ptm-80) REVERT: C 192 ARG cc_start: 0.7905 (ttm170) cc_final: 0.7414 (tpt170) REVERT: C 248 THR cc_start: 0.8271 (t) cc_final: 0.8014 (p) REVERT: C 394 THR cc_start: 0.7698 (m) cc_final: 0.7375 (t) REVERT: D 530 MET cc_start: 0.7108 (mtt) cc_final: 0.6573 (mtt) REVERT: D 588 ARG cc_start: 0.8563 (ttt-90) cc_final: 0.8209 (ttm-80) REVERT: F 87 GLU cc_start: 0.7655 (mp0) cc_final: 0.7295 (mp0) REVERT: F 107 ASP cc_start: 0.8709 (m-30) cc_final: 0.8260 (m-30) REVERT: F 231 LYS cc_start: 0.8105 (mttt) cc_final: 0.7646 (mttm) REVERT: F 256 SER cc_start: 0.8913 (t) cc_final: 0.8571 (p) outliers start: 61 outliers final: 58 residues processed: 388 average time/residue: 0.1147 time to fit residues: 67.5245 Evaluate side-chains 405 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 346 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 75 VAL Chi-restraints excluded: chain A residue 115 SER 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 201 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 243 SER 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 333 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 426 MET 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 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 195 ASN 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 612 SER 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 571 TRP Chi-restraints excluded: chain E residue 573 ILE 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 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 288 LEU Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 146 optimal weight: 3.9990 chunk 116 optimal weight: 0.0670 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 143 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 178 optimal weight: 9.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 352 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 616 ASN E 543 ASN E 630 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.162691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137125 restraints weight = 23610.340| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 3.52 r_work: 0.3546 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 15480 Z= 0.140 Angle : 0.643 15.353 21166 Z= 0.317 Chirality : 0.044 0.193 2584 Planarity : 0.003 0.032 2613 Dihedral : 4.495 26.408 1994 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.93 % Allowed : 19.23 % Favored : 76.84 % 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 are not related in a simple way. whole: -0.10 (0.21), residues: 1622 helix: 1.87 (0.28), residues: 372 sheet: 0.07 (0.24), residues: 452 loop : -1.10 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 178 TYR 0.023 0.001 TYR E 643 PHE 0.020 0.001 PHE A 361 TRP 0.025 0.001 TRP F 35 HIS 0.007 0.001 HIS C 352 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15389) covalent geometry : angle 0.61854 / 0.31 (20926) SS BOND : bond 0.00458 / 0.25 ( 33) SS BOND : angle 1.49037 / 1.22 ( 66) hydrogen bonds : bond 0.04298 / 3.03 ( 555) hydrogen bonds : angle 5.17088 / 3.66 ( 1596) link_BETA1-4 : bond 0.00634 / 0.35 ( 6) link_BETA1-4 : angle 1.48698 / 0.93 ( 18) link_NAG-ASN : bond 0.00258 / 0.16 ( 52) link_NAG-ASN : angle 1.91109 / 1.37 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3237.57 seconds wall clock time: 56 minutes 26.51 seconds (3386.51 seconds total)