Starting phenix.real_space_refine on Sat May 17 05:17:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.map" model { file = "/net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sw7_40810/05_2025/8sw7_40810.cif" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15133 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 20, 'TRANS': 419} Chain breaks: 3 Chain: "B" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 998 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 124} Chain breaks: 1 Chain: "C" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3424 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 20, 'TRANS': 412} Chain breaks: 4 Chain: "D" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "E" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 959 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain breaks: 1 Chain: "F" Number of atoms: 3365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 425, 3365 Classifications: {'peptide': 425} Link IDs: {'PTRANS': 18, 'TRANS': 406} Chain breaks: 5 Chain: "H" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 625 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'TRANS': 124} Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 375 Unresolved non-hydrogen dihedrals: 125 Planarities with less than four sites: {'UNK:plan-1': 125} Unresolved non-hydrogen planarities: 125 Chain: "L" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 530 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 106} Link IDs: {'TRANS': 105} Unresolved non-hydrogen bonds: 212 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'UNK:plan-1': 106} Unresolved non-hydrogen planarities: 106 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 9.26, per 1000 atoms: 0.61 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: 4.20 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.84 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: 4.87 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.33: 3792 1.33 - 1.48: 5118 1.48 - 1.63: 6341 1.63 - 1.78: 52 1.78 - 1.94: 86 Bond restraints: 15389 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.406 -0.080 1.10e-02 8.26e+03 5.24e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.399 -0.073 1.10e-02 8.26e+03 4.42e+01 bond pdb=" CD2 TRP E 571 " pdb=" CE3 TRP E 571 " ideal model delta sigma weight residual 1.398 1.504 -0.106 1.60e-02 3.91e+03 4.36e+01 bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.500 -0.102 1.60e-02 3.91e+03 4.07e+01 bond pdb=" CZ2 TRP E 571 " pdb=" CH2 TRP E 571 " ideal model delta sigma weight residual 1.368 1.489 -0.121 1.90e-02 2.77e+03 4.03e+01 ... (remaining 15384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17546 2.22 - 4.43: 2810 4.43 - 6.65: 475 6.65 - 8.87: 86 8.87 - 11.08: 9 Bond angle restraints: 20926 Sorted by residual: angle pdb=" N PRO A 437 " pdb=" CA PRO A 437 " pdb=" C PRO A 437 " ideal model delta sigma weight residual 110.58 100.83 9.75 1.07e+00 8.73e-01 8.30e+01 angle pdb=" N ARG F 476 " pdb=" CA ARG F 476 " pdb=" C ARG F 476 " ideal model delta sigma weight residual 114.04 102.96 11.08 1.24e+00 6.50e-01 7.99e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.25 -7.69 1.01e+00 9.80e-01 5.79e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.19 -7.63 1.01e+00 9.80e-01 5.71e+01 angle pdb=" N PRO F 437 " pdb=" CA PRO F 437 " pdb=" C PRO F 437 " ideal model delta sigma weight residual 110.58 102.50 8.08 1.07e+00 8.73e-01 5.71e+01 ... (remaining 20921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.13: 9708 21.13 - 42.27: 204 42.27 - 63.40: 70 63.40 - 84.54: 32 84.54 - 105.67: 15 Dihedral angle restraints: 10029 sinusoidal: 4537 harmonic: 5492 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 174.83 -81.83 1 1.00e+01 1.00e-02 8.24e+01 dihedral pdb=" CB CYS F 126 " pdb=" SG CYS F 126 " pdb=" SG CYS F 196 " pdb=" CB CYS F 196 " ideal model delta sinusoidal sigma weight residual 93.00 140.08 -47.08 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -129.29 43.29 1 1.00e+01 1.00e-02 2.61e+01 ... (remaining 10026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 1757 0.102 - 0.203: 526 0.203 - 0.304: 170 0.304 - 0.406: 97 0.406 - 0.507: 34 Chirality restraints: 2584 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.52e+02 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 1.04e+02 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.60 0.20 2.00e-02 2.50e+03 9.84e+01 ... (remaining 2581 not shown) Planarity restraints: 2665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 611 " -0.099 2.00e-02 2.50e+03 1.04e-01 1.35e+02 pdb=" CG ASN D 611 " 0.041 2.00e-02 2.50e+03 pdb=" OD1 ASN D 611 " 0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN D 611 " 0.161 2.00e-02 2.50e+03 pdb=" C1 NAG D 701 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.095 2.00e-02 2.50e+03 9.81e-02 1.20e+02 pdb=" CG ASN A 234 " 0.045 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " 0.076 2.00e-02 2.50e+03 7.89e-02 7.77e+01 pdb=" CG ASN C 133 " -0.036 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " -0.121 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " 0.096 2.00e-02 2.50e+03 ... (remaining 2662 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1886 2.73 - 3.27: 14014 3.27 - 3.82: 23448 3.82 - 4.36: 29523 4.36 - 4.90: 47925 Nonbonded interactions: 116796 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" OG1 THR F 499 " model vdw 2.188 3.040 nonbonded pdb=" N UNK H 51 " pdb=" N UNK H 52 " model vdw 2.394 2.560 nonbonded pdb=" NZ LYS C 231 " pdb=" OE1 GLU C 267 " model vdw 2.418 3.120 nonbonded pdb=" N LEU F 125 " pdb=" O LEU F 125 " model vdw 2.419 2.496 nonbonded pdb=" N VAL F 127 " pdb=" O VAL F 127 " model vdw 2.423 2.496 ... (remaining 116791 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 457 or resid 463 through 503 or resid 603 through 614)) selection = (chain 'C' and (resid 32 through 77 or resid 82 through 392 or resid 412 through \ 503 or resid 601 through 612)) selection = (chain 'F' and (resid 32 through 503 or resid 603 through 614)) } ncs_group { reference = (chain 'B' and (resid 522 through 664 or resid 701 through 702)) selection = chain 'D' selection = (chain 'E' and (resid 522 through 664 or resid 701 through 702)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 34.720 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.145 15480 Z= 1.196 Angle : 1.741 12.204 21166 Z= 1.111 Chirality : 0.133 0.507 2584 Planarity : 0.009 0.052 2613 Dihedral : 11.373 105.669 6352 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 1.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.78 % Rotamer: Outliers : 0.14 % Allowed : 0.61 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.045 0.009 TRP F 35 HIS 0.010 0.002 HIS C 374 PHE 0.029 0.006 PHE A 353 TYR 0.038 0.007 TYR B 643 ARG 0.009 0.001 ARG D 617 Details of bonding type rmsd link_NAG-ASN : bond 0.08112 ( 52) link_NAG-ASN : angle 2.67185 ( 156) link_BETA1-4 : bond 0.07521 ( 6) link_BETA1-4 : angle 4.80451 ( 18) hydrogen bonds : bond 0.15922 ( 555) hydrogen bonds : angle 7.89529 ( 1596) SS BOND : bond 0.01589 ( 33) SS BOND : angle 3.60500 ( 66) covalent geometry : bond 0.02220 (15389) covalent geometry : angle 1.71843 (20926) *********************** 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 : 1.615 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: 0.8456 (t) REVERT: F 474 ASP cc_start: 0.7602 (t70) cc_final: 0.7087 (t70) outliers start: 2 outliers final: 0 residues processed: 601 average time/residue: 0.2919 time to fit residues: 252.6448 Evaluate side-chains 368 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 157 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 103 GLN A 195 ASN A 203 GLN A 422 GLN A 425 ASN C 130 GLN C 287 GLN D 607 ASN E 575 GLN E 591 GLN F 203 GLN F 283 ASN F 428 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.165106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.139335 restraints weight = 22756.146| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 3.51 r_work: 0.3553 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15480 Z= 0.182 Angle : 0.823 22.077 21166 Z= 0.400 Chirality : 0.048 0.343 2584 Planarity : 0.004 0.081 2613 Dihedral : 7.978 68.723 3206 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.05 % Allowed : 12.53 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1622 helix: 1.80 (0.28), residues: 360 sheet: 0.65 (0.24), residues: 426 loop : -0.20 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 479 HIS 0.004 0.001 HIS A 249 PHE 0.031 0.002 PHE F 53 TYR 0.038 0.002 TYR E 643 ARG 0.009 0.001 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00549 ( 52) link_NAG-ASN : angle 3.80738 ( 156) link_BETA1-4 : bond 0.00767 ( 6) link_BETA1-4 : angle 3.79252 ( 18) hydrogen bonds : bond 0.06309 ( 555) hydrogen bonds : angle 6.00463 ( 1596) SS BOND : bond 0.00387 ( 33) SS BOND : angle 1.43399 ( 66) covalent geometry : bond 0.00399 (15389) covalent geometry : angle 0.74729 (20926) *********************** 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 472 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 427 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.8929 (m100) cc_final: 0.7961 (m100) REVERT: A 150 MET cc_start: 0.8246 (mmp) cc_final: 0.7636 (mmt) REVERT: A 258 GLN cc_start: 0.9045 (mt0) cc_final: 0.8736 (mt0) REVERT: A 269 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8349 (mm-30) REVERT: A 452 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8164 (pp) REVERT: B 627 THR cc_start: 0.8821 (p) cc_final: 0.8617 (t) REVERT: C 178 ARG cc_start: 0.8276 (ptm-80) cc_final: 0.8058 (ptm-80) REVERT: C 192 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7780 (tpp-160) REVERT: C 230 ASP cc_start: 0.7735 (t0) cc_final: 0.7532 (t0) REVERT: C 492 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 638 TYR cc_start: 0.8331 (m-80) cc_final: 0.8095 (m-80) REVERT: D 651 ASN cc_start: 0.8745 (t0) cc_final: 0.8540 (t0) REVERT: E 542 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8391 (ttm170) REVERT: E 630 GLN cc_start: 0.8357 (mt0) cc_final: 0.7802 (mt0) REVERT: F 46 LYS cc_start: 0.9005 (mttm) cc_final: 0.8800 (mttp) REVERT: F 153 GLU cc_start: 0.8308 (tp30) cc_final: 0.8049 (tp30) REVERT: F 192 ARG cc_start: 0.7374 (ptt180) cc_final: 0.6831 (ptt180) REVERT: F 368 ASP cc_start: 0.7901 (m-30) cc_final: 0.7642 (p0) outliers start: 45 outliers final: 26 residues processed: 446 average time/residue: 0.2640 time to fit residues: 174.0978 Evaluate side-chains 393 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 366 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 587 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 381 GLU Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 140 ASP Chi-restraints excluded: chain F residue 173 TYR Chi-restraints excluded: chain F residue 292 VAL Chi-restraints excluded: chain F residue 377 ASN 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 83 optimal weight: 3.9990 chunk 126 optimal weight: 0.0870 chunk 131 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 51 optimal weight: 0.3980 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN A 302 ASN C 170 GLN E 543 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.158901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.133396 restraints weight = 23334.774| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 3.48 r_work: 0.3482 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 15480 Z= 0.237 Angle : 0.782 17.454 21166 Z= 0.379 Chirality : 0.048 0.260 2584 Planarity : 0.004 0.049 2613 Dihedral : 6.879 48.854 3206 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.06 % Allowed : 13.88 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.21), residues: 1622 helix: 1.66 (0.28), residues: 363 sheet: 0.29 (0.23), residues: 460 loop : -0.60 (0.22), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP F 35 HIS 0.006 0.001 HIS A 72 PHE 0.021 0.002 PHE A 376 TYR 0.018 0.002 TYR A 173 ARG 0.010 0.001 ARG F 166 Details of bonding type rmsd link_NAG-ASN : bond 0.00708 ( 52) link_NAG-ASN : angle 3.07784 ( 156) link_BETA1-4 : bond 0.00801 ( 6) link_BETA1-4 : angle 2.90346 ( 18) hydrogen bonds : bond 0.05553 ( 555) hydrogen bonds : angle 5.68454 ( 1596) SS BOND : bond 0.00600 ( 33) SS BOND : angle 1.82626 ( 66) covalent geometry : bond 0.00545 (15389) covalent geometry : angle 0.72808 (20926) *********************** 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 450 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 390 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9072 (m100) cc_final: 0.8107 (m100) REVERT: A 269 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8383 (mm-30) REVERT: A 275 GLU cc_start: 0.8727 (tt0) cc_final: 0.8463 (tt0) REVERT: B 624 ASP cc_start: 0.8901 (m-30) cc_final: 0.8621 (t0) REVERT: C 90 THR cc_start: 0.8694 (OUTLIER) cc_final: 0.8434 (t) REVERT: C 104 MET cc_start: 0.9371 (ttt) cc_final: 0.9087 (ttt) REVERT: C 150 MET cc_start: 0.7952 (mtp) cc_final: 0.7697 (mtm) REVERT: C 178 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7909 (ptm-80) REVERT: C 191 TYR cc_start: 0.8001 (m-80) cc_final: 0.7714 (m-10) REVERT: C 192 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7425 (tpt170) REVERT: C 394 THR cc_start: 0.7837 (m) cc_final: 0.7525 (t) REVERT: D 530 MET cc_start: 0.6821 (mtt) cc_final: 0.6029 (mtt) REVERT: E 542 ARG cc_start: 0.8800 (ttm170) cc_final: 0.8296 (ttm170) REVERT: E 630 GLN cc_start: 0.8460 (mt0) cc_final: 0.8249 (mt0) REVERT: E 634 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8175 (tm-30) REVERT: E 645 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8661 (mt) REVERT: E 655 LYS cc_start: 0.8448 (mmtp) cc_final: 0.7811 (mtpp) REVERT: F 153 GLU cc_start: 0.8479 (tp30) cc_final: 0.8198 (tp30) REVERT: F 231 LYS cc_start: 0.8157 (mttt) cc_final: 0.7929 (mmtp) REVERT: F 368 ASP cc_start: 0.8026 (m-30) cc_final: 0.7756 (p0) REVERT: F 377 ASN cc_start: 0.8141 (p0) cc_final: 0.7804 (t0) REVERT: F 475 MET cc_start: 0.8987 (mmm) cc_final: 0.8768 (tpp) outliers start: 60 outliers final: 46 residues processed: 422 average time/residue: 0.2534 time to fit residues: 158.6316 Evaluate side-chains 410 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 362 time to evaluate : 1.282 ------------------------------------------------------------------------------- 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 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 264 SER Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 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 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 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 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 645 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER 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 138 ILE Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 209 SER 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 39 optimal weight: 9.9990 chunk 36 optimal weight: 0.0870 chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 141 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 151 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 164 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 425 ASN F 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.162526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.137120 restraints weight = 22906.482| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 3.49 r_work: 0.3527 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 15480 Z= 0.126 Angle : 0.656 16.128 21166 Z= 0.317 Chirality : 0.044 0.234 2584 Planarity : 0.003 0.031 2613 Dihedral : 5.645 38.170 3206 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.32 % Allowed : 15.91 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.21), residues: 1622 helix: 1.90 (0.28), residues: 365 sheet: 0.28 (0.24), residues: 452 loop : -0.65 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 614 HIS 0.003 0.001 HIS C 249 PHE 0.014 0.002 PHE A 53 TYR 0.015 0.002 TYR A 173 ARG 0.004 0.000 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00358 ( 52) link_NAG-ASN : angle 2.70901 ( 156) link_BETA1-4 : bond 0.00617 ( 6) link_BETA1-4 : angle 2.50795 ( 18) hydrogen bonds : bond 0.04602 ( 555) hydrogen bonds : angle 5.38346 ( 1596) SS BOND : bond 0.00396 ( 33) SS BOND : angle 1.51859 ( 66) covalent geometry : bond 0.00277 (15389) covalent geometry : angle 0.60641 (20926) *********************** 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 440 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 391 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9039 (m100) cc_final: 0.8069 (m100) REVERT: A 275 GLU cc_start: 0.8670 (tt0) cc_final: 0.8314 (tt0) REVERT: A 428 GLN cc_start: 0.8642 (mt0) cc_final: 0.8299 (mm110) REVERT: A 440 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: B 540 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6217 (mp10) REVERT: B 624 ASP cc_start: 0.8960 (m-30) cc_final: 0.8698 (t0) REVERT: B 647 GLU cc_start: 0.8114 (tt0) cc_final: 0.7635 (tt0) REVERT: C 104 MET cc_start: 0.9318 (ttt) cc_final: 0.9008 (ttt) REVERT: C 178 ARG cc_start: 0.8228 (ptm-80) cc_final: 0.7957 (ptm-80) REVERT: C 190 GLU cc_start: 0.5286 (pm20) cc_final: 0.5000 (pm20) REVERT: C 191 TYR cc_start: 0.7975 (m-80) cc_final: 0.7582 (m-10) REVERT: C 192 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7625 (tpt170) REVERT: C 195 ASN cc_start: 0.8111 (t0) cc_final: 0.7893 (t0) REVERT: C 394 THR cc_start: 0.7933 (m) cc_final: 0.7530 (t) REVERT: D 530 MET cc_start: 0.6755 (mtt) cc_final: 0.5985 (mtt) REVERT: E 542 ARG cc_start: 0.8761 (ttm170) cc_final: 0.8186 (ttm170) REVERT: E 634 GLU cc_start: 0.8523 (mt-10) cc_final: 0.8165 (tm-30) REVERT: F 107 ASP cc_start: 0.8673 (m-30) cc_final: 0.8221 (m-30) REVERT: F 112 TRP cc_start: 0.8240 (t-100) cc_final: 0.8009 (t-100) REVERT: F 153 GLU cc_start: 0.8394 (tp30) cc_final: 0.8139 (tp30) REVERT: F 274 SER cc_start: 0.8695 (t) cc_final: 0.8423 (p) REVERT: F 368 ASP cc_start: 0.8052 (m-30) cc_final: 0.7768 (p0) outliers start: 49 outliers final: 34 residues processed: 421 average time/residue: 0.2547 time to fit residues: 160.7003 Evaluate side-chains 391 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 355 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 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 440 GLN Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 540 GLN Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 619 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 181 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 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 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 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 102 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 132 optimal weight: 8.9990 chunk 134 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 141 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 425 ASN ** C 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 293 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.156573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130833 restraints weight = 23673.969| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.52 r_work: 0.3451 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 15480 Z= 0.247 Angle : 0.756 15.415 21166 Z= 0.367 Chirality : 0.048 0.244 2584 Planarity : 0.004 0.034 2613 Dihedral : 6.038 43.114 3206 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 5.01 % Allowed : 15.84 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.20), residues: 1622 helix: 1.56 (0.28), residues: 371 sheet: 0.02 (0.24), residues: 436 loop : -0.90 (0.21), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 45 HIS 0.007 0.001 HIS F 330 PHE 0.023 0.002 PHE A 376 TYR 0.020 0.002 TYR C 318 ARG 0.006 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00623 ( 52) link_NAG-ASN : angle 2.85531 ( 156) link_BETA1-4 : bond 0.00646 ( 6) link_BETA1-4 : angle 2.31292 ( 18) hydrogen bonds : bond 0.05195 ( 555) hydrogen bonds : angle 5.52525 ( 1596) SS BOND : bond 0.00536 ( 33) SS BOND : angle 1.88950 ( 66) covalent geometry : bond 0.00576 (15389) covalent geometry : angle 0.70860 (20926) *********************** 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 442 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 368 time to evaluate : 1.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9107 (m100) cc_final: 0.8203 (m100) REVERT: A 51 THR cc_start: 0.9270 (m) cc_final: 0.8918 (p) REVERT: A 428 GLN cc_start: 0.8690 (mt0) cc_final: 0.8328 (mm110) REVERT: A 440 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: B 540 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.6428 (mp10) REVERT: C 104 MET cc_start: 0.9368 (ttt) cc_final: 0.9090 (ttt) REVERT: C 178 ARG cc_start: 0.8322 (ptm-80) cc_final: 0.8121 (ptm-80) REVERT: C 190 GLU cc_start: 0.5488 (pm20) cc_final: 0.5185 (pm20) REVERT: C 192 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7511 (tpt170) REVERT: C 196 CYS cc_start: 0.7274 (t) cc_final: 0.7052 (t) REVERT: C 283 ASN cc_start: 0.8857 (m-40) cc_final: 0.8613 (m-40) REVERT: C 394 THR cc_start: 0.7794 (m) cc_final: 0.7426 (t) REVERT: D 530 MET cc_start: 0.6929 (mtt) cc_final: 0.6270 (mtt) REVERT: E 530 MET cc_start: 0.8891 (mtm) cc_final: 0.8580 (mtm) REVERT: E 542 ARG cc_start: 0.8782 (ttm170) cc_final: 0.8477 (ttm170) REVERT: E 634 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8170 (tm-30) REVERT: F 35 TRP cc_start: 0.8183 (m100) cc_final: 0.7975 (m100) REVERT: F 107 ASP cc_start: 0.8718 (m-30) cc_final: 0.8313 (m-30) REVERT: F 153 GLU cc_start: 0.8480 (tp30) cc_final: 0.8221 (tp30) REVERT: F 241 ASN cc_start: 0.7101 (m-40) cc_final: 0.6754 (t0) REVERT: F 274 SER cc_start: 0.9027 (t) cc_final: 0.8782 (p) outliers start: 74 outliers final: 59 residues processed: 405 average time/residue: 0.2410 time to fit residues: 146.4996 Evaluate side-chains 410 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 349 time to evaluate : 1.454 ------------------------------------------------------------------------------- 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 128 THR 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 373 THR Chi-restraints excluded: chain A residue 424 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 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 44 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU 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 E residue 529 THR Chi-restraints excluded: chain E residue 534 SER 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 122 LEU Chi-restraints excluded: chain F residue 125 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 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 93 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 152 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 46 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN E 543 ASN E 653 GLN F 203 GLN F 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.163901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138142 restraints weight = 23635.854| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 3.56 r_work: 0.3564 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 15480 Z= 0.124 Angle : 0.633 15.523 21166 Z= 0.307 Chirality : 0.044 0.236 2584 Planarity : 0.003 0.034 2613 Dihedral : 5.328 37.992 3206 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.59 % Allowed : 17.60 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1622 helix: 1.97 (0.28), residues: 365 sheet: -0.02 (0.24), residues: 444 loop : -0.87 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 35 HIS 0.004 0.001 HIS A 374 PHE 0.012 0.001 PHE A 53 TYR 0.015 0.001 TYR A 173 ARG 0.008 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 52) link_NAG-ASN : angle 2.47466 ( 156) link_BETA1-4 : bond 0.00596 ( 6) link_BETA1-4 : angle 1.81273 ( 18) hydrogen bonds : bond 0.04282 ( 555) hydrogen bonds : angle 5.26061 ( 1596) SS BOND : bond 0.00412 ( 33) SS BOND : angle 1.68119 ( 66) covalent geometry : bond 0.00277 (15389) covalent geometry : angle 0.59024 (20926) *********************** 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 420 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 367 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9060 (m100) cc_final: 0.8183 (m100) REVERT: A 102 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8142 (mm-30) REVERT: A 269 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7897 (mm-30) REVERT: A 428 GLN cc_start: 0.8596 (mt0) cc_final: 0.8367 (mm110) REVERT: A 440 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: B 540 GLN cc_start: 0.8007 (OUTLIER) cc_final: 0.6392 (mp10) REVERT: C 104 MET cc_start: 0.9360 (ttt) cc_final: 0.9098 (ttt) REVERT: C 178 ARG cc_start: 0.8275 (ptm-80) cc_final: 0.8026 (ptm-80) REVERT: C 192 ARG cc_start: 0.8117 (ttm170) cc_final: 0.7647 (tpt170) REVERT: C 196 CYS cc_start: 0.7191 (t) cc_final: 0.6959 (t) REVERT: C 394 THR cc_start: 0.7816 (m) cc_final: 0.7426 (t) REVERT: D 530 MET cc_start: 0.7080 (mtt) cc_final: 0.6343 (mtt) REVERT: E 634 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8204 (tm-30) REVERT: E 643 TYR cc_start: 0.9127 (m-10) cc_final: 0.8888 (m-80) REVERT: F 35 TRP cc_start: 0.8124 (m100) cc_final: 0.7885 (m100) REVERT: F 107 ASP cc_start: 0.8646 (m-30) cc_final: 0.8219 (m-30) REVERT: F 112 TRP cc_start: 0.8414 (t-100) cc_final: 0.8062 (t-100) REVERT: F 192 ARG cc_start: 0.7495 (ptt180) cc_final: 0.7052 (ptt180) REVERT: F 231 LYS cc_start: 0.7997 (mttt) cc_final: 0.7569 (mttm) REVERT: F 274 SER cc_start: 0.8739 (t) cc_final: 0.8377 (p) REVERT: F 484 TYR cc_start: 0.8802 (p90) cc_final: 0.8460 (p90) outliers start: 53 outliers final: 44 residues processed: 396 average time/residue: 0.2455 time to fit residues: 145.1115 Evaluate side-chains 393 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 347 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 120 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 170 GLN 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 440 GLN Chi-restraints excluded: chain A residue 442 VAL 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 595 ILE Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU 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 545 LEU Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 659 ASP Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 529 THR Chi-restraints excluded: chain E residue 534 SER 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 331 CYS Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 104 optimal weight: 0.0170 chunk 27 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 20 optimal weight: 0.0870 chunk 102 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.164778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.139044 restraints weight = 23677.676| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.58 r_work: 0.3577 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 15480 Z= 0.117 Angle : 0.603 15.435 21166 Z= 0.292 Chirality : 0.043 0.203 2584 Planarity : 0.003 0.026 2613 Dihedral : 5.060 38.053 3206 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.86 % Allowed : 18.14 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1622 helix: 2.07 (0.28), residues: 365 sheet: 0.08 (0.24), residues: 443 loop : -0.86 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 96 HIS 0.005 0.001 HIS A 72 PHE 0.013 0.001 PHE A 376 TYR 0.017 0.002 TYR C 318 ARG 0.007 0.000 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 52) link_NAG-ASN : angle 2.30381 ( 156) link_BETA1-4 : bond 0.00626 ( 6) link_BETA1-4 : angle 1.69805 ( 18) hydrogen bonds : bond 0.04040 ( 555) hydrogen bonds : angle 5.12563 ( 1596) SS BOND : bond 0.00460 ( 33) SS BOND : angle 1.62384 ( 66) covalent geometry : bond 0.00264 (15389) covalent geometry : angle 0.56329 (20926) *********************** 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 419 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 362 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9093 (m100) cc_final: 0.8221 (m100) REVERT: A 190 GLU cc_start: 0.7845 (mp0) cc_final: 0.6997 (mp0) REVERT: A 269 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7880 (mm-30) REVERT: C 104 MET cc_start: 0.9347 (ttt) cc_final: 0.9105 (ttt) REVERT: C 178 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.7996 (ptm-80) REVERT: C 192 ARG cc_start: 0.8031 (ttm170) cc_final: 0.7501 (tpt170) REVERT: C 394 THR cc_start: 0.7837 (m) cc_final: 0.7456 (t) REVERT: C 486 TYR cc_start: 0.8549 (m-10) cc_final: 0.8195 (m-10) REVERT: D 530 MET cc_start: 0.7096 (mtt) cc_final: 0.6411 (mtt) REVERT: F 35 TRP cc_start: 0.8118 (m100) cc_final: 0.7883 (m100) REVERT: F 107 ASP cc_start: 0.8666 (m-30) cc_final: 0.8226 (m-30) REVERT: F 112 TRP cc_start: 0.8464 (t-100) cc_final: 0.8064 (t-100) REVERT: F 192 ARG cc_start: 0.7425 (ptt180) cc_final: 0.6836 (ptt180) REVERT: F 231 LYS cc_start: 0.7934 (mttt) cc_final: 0.7493 (mttm) REVERT: F 484 TYR cc_start: 0.8832 (p90) cc_final: 0.8468 (p90) outliers start: 57 outliers final: 50 residues processed: 392 average time/residue: 0.2565 time to fit residues: 149.9047 Evaluate side-chains 387 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 337 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 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 333 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 478 ASN 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 616 ASN Chi-restraints excluded: chain B residue 619 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 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 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 SER 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 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 92 GLU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 331 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 22 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 174 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 159 optimal weight: 0.0970 chunk 122 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN E 630 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.165231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139497 restraints weight = 23584.358| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.56 r_work: 0.3582 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15480 Z= 0.120 Angle : 0.622 15.322 21166 Z= 0.303 Chirality : 0.043 0.205 2584 Planarity : 0.003 0.029 2613 Dihedral : 4.951 38.294 3206 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.59 % Allowed : 19.16 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.21), residues: 1622 helix: 2.09 (0.29), residues: 365 sheet: 0.23 (0.24), residues: 451 loop : -0.90 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 614 HIS 0.004 0.000 HIS A 374 PHE 0.013 0.001 PHE A 376 TYR 0.014 0.001 TYR C 191 ARG 0.011 0.000 ARG A 480 Details of bonding type rmsd link_NAG-ASN : bond 0.00318 ( 52) link_NAG-ASN : angle 2.22680 ( 156) link_BETA1-4 : bond 0.00601 ( 6) link_BETA1-4 : angle 1.61096 ( 18) hydrogen bonds : bond 0.03947 ( 555) hydrogen bonds : angle 5.06841 ( 1596) SS BOND : bond 0.00420 ( 33) SS BOND : angle 2.26908 ( 66) covalent geometry : bond 0.00272 (15389) covalent geometry : angle 0.57948 (20926) *********************** 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 413 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 360 time to evaluate : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9096 (m100) cc_final: 0.8228 (m100) REVERT: A 102 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8112 (mm-30) REVERT: A 109 ILE cc_start: 0.8739 (mm) cc_final: 0.8500 (mm) REVERT: A 269 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 320 THR cc_start: 0.8913 (m) cc_final: 0.8439 (p) REVERT: C 104 MET cc_start: 0.9332 (ttt) cc_final: 0.9089 (ttt) REVERT: C 178 ARG cc_start: 0.8245 (ptm-80) cc_final: 0.7986 (ptm-80) REVERT: C 192 ARG cc_start: 0.7919 (ttm170) cc_final: 0.7558 (tpt170) REVERT: C 394 THR cc_start: 0.7868 (m) cc_final: 0.7500 (t) REVERT: D 530 MET cc_start: 0.7076 (mtt) cc_final: 0.6391 (mtt) REVERT: F 35 TRP cc_start: 0.8149 (m100) cc_final: 0.7881 (m100) REVERT: F 107 ASP cc_start: 0.8676 (m-30) cc_final: 0.8218 (m-30) REVERT: F 112 TRP cc_start: 0.8461 (t-100) cc_final: 0.8104 (t-100) REVERT: F 192 ARG cc_start: 0.7303 (ptt180) cc_final: 0.6669 (ptt180) REVERT: F 231 LYS cc_start: 0.7885 (mttt) cc_final: 0.7465 (mttm) REVERT: F 248 THR cc_start: 0.8622 (m) cc_final: 0.8357 (p) REVERT: F 484 TYR cc_start: 0.8789 (p90) cc_final: 0.8411 (p90) outliers start: 53 outliers final: 48 residues processed: 391 average time/residue: 0.2430 time to fit residues: 143.7530 Evaluate side-chains 389 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 341 time to evaluate : 1.466 ------------------------------------------------------------------------------- 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 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 333 VAL Chi-restraints excluded: chain A residue 426 MET 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 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 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 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 SER 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 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 148 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 124 optimal weight: 0.0030 overall best weight: 0.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** B 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 ASN D 658 GLN E 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.138318 restraints weight = 23544.528| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.56 r_work: 0.3568 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 15480 Z= 0.138 Angle : 0.614 15.241 21166 Z= 0.301 Chirality : 0.044 0.207 2584 Planarity : 0.003 0.031 2613 Dihedral : 5.026 38.787 3206 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.13 % Allowed : 18.75 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.21), residues: 1622 helix: 2.02 (0.28), residues: 371 sheet: 0.22 (0.24), residues: 453 loop : -0.96 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 614 HIS 0.006 0.001 HIS A 72 PHE 0.033 0.002 PHE A 361 TYR 0.017 0.001 TYR A 173 ARG 0.007 0.000 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 52) link_NAG-ASN : angle 2.21567 ( 156) link_BETA1-4 : bond 0.00623 ( 6) link_BETA1-4 : angle 1.62035 ( 18) hydrogen bonds : bond 0.04049 ( 555) hydrogen bonds : angle 5.01890 ( 1596) SS BOND : bond 0.00471 ( 33) SS BOND : angle 1.71082 ( 66) covalent geometry : bond 0.00319 (15389) covalent geometry : angle 0.57739 (20926) *********************** 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 408 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 347 time to evaluate : 1.582 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: 0.9125 (m100) cc_final: 0.8238 (m100) REVERT: A 51 THR cc_start: 0.9247 (m) cc_final: 0.8952 (p) REVERT: A 102 GLU cc_start: 0.8476 (mm-30) cc_final: 0.8165 (mm-30) REVERT: A 109 ILE cc_start: 0.8770 (mm) cc_final: 0.8544 (mm) REVERT: A 269 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7904 (mm-30) REVERT: C 104 MET cc_start: 0.9330 (ttt) cc_final: 0.9092 (ttt) REVERT: C 178 ARG cc_start: 0.8216 (ptm-80) cc_final: 0.7965 (ptm-80) REVERT: C 394 THR cc_start: 0.7744 (m) cc_final: 0.7391 (t) REVERT: D 530 MET cc_start: 0.7067 (mtt) cc_final: 0.6400 (mtt) REVERT: F 35 TRP cc_start: 0.8193 (m100) cc_final: 0.7935 (m100) REVERT: F 107 ASP cc_start: 0.8679 (m-30) cc_final: 0.8218 (m-30) REVERT: F 112 TRP cc_start: 0.8491 (t-100) cc_final: 0.8096 (t-100) REVERT: F 192 ARG cc_start: 0.7343 (ptt180) cc_final: 0.6767 (ptt180) REVERT: F 231 LYS cc_start: 0.7920 (mttt) cc_final: 0.7491 (mttm) REVERT: F 248 THR cc_start: 0.8645 (m) cc_final: 0.8391 (p) REVERT: F 484 TYR cc_start: 0.8813 (p90) cc_final: 0.8450 (p90) outliers start: 61 outliers final: 56 residues processed: 380 average time/residue: 0.2500 time to fit residues: 141.3399 Evaluate side-chains 407 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 351 time to evaluate : 1.420 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain A residue 478 ASN 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 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 123 THR 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 545 LEU Chi-restraints excluded: chain D residue 612 SER 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 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain E residue 619 LEU Chi-restraints excluded: chain E residue 630 GLN Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 12 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 85 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** E 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.161446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.135529 restraints weight = 23951.071| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 3.58 r_work: 0.3527 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 15480 Z= 0.212 Angle : 0.687 14.892 21166 Z= 0.337 Chirality : 0.046 0.214 2584 Planarity : 0.004 0.039 2613 Dihedral : 5.410 41.023 3206 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 4.13 % Allowed : 19.03 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.21), residues: 1622 helix: 1.99 (0.28), residues: 365 sheet: 0.13 (0.24), residues: 452 loop : -1.06 (0.21), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 96 HIS 0.007 0.001 HIS C 352 PHE 0.022 0.002 PHE A 361 TYR 0.020 0.002 TYR C 191 ARG 0.007 0.001 ARG C 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00334 ( 52) link_NAG-ASN : angle 2.34748 ( 156) link_BETA1-4 : bond 0.00618 ( 6) link_BETA1-4 : angle 1.70737 ( 18) hydrogen bonds : bond 0.04471 ( 555) hydrogen bonds : angle 5.14591 ( 1596) SS BOND : bond 0.00543 ( 33) SS BOND : angle 1.87363 ( 66) covalent geometry : bond 0.00498 (15389) covalent geometry : angle 0.65016 (20926) ********************** 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 : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.9192 (m100) cc_final: 0.8307 (m100) REVERT: A 51 THR cc_start: 0.9279 (m) cc_final: 0.8961 (p) REVERT: A 102 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8238 (mm-30) REVERT: C 104 MET cc_start: 0.9346 (ttt) cc_final: 0.9104 (ttt) REVERT: C 178 ARG cc_start: 0.8251 (ptm-80) cc_final: 0.8009 (ptm-80) REVERT: C 394 THR cc_start: 0.7680 (m) cc_final: 0.7325 (t) REVERT: C 499 THR cc_start: 0.8414 (t) cc_final: 0.7952 (m) REVERT: D 530 MET cc_start: 0.7078 (mtt) cc_final: 0.6431 (mtt) REVERT: E 626 MET cc_start: 0.7398 (ttt) cc_final: 0.7123 (ttt) REVERT: F 35 TRP cc_start: 0.8273 (m100) cc_final: 0.8031 (m100) REVERT: F 107 ASP cc_start: 0.8721 (m-30) cc_final: 0.8304 (m-30) REVERT: F 112 TRP cc_start: 0.8537 (t-100) cc_final: 0.8116 (t-100) REVERT: F 192 ARG cc_start: 0.7494 (ptt180) cc_final: 0.6965 (ptt180) REVERT: F 231 LYS cc_start: 0.7973 (mttt) cc_final: 0.7527 (mttm) REVERT: F 248 THR cc_start: 0.8659 (m) cc_final: 0.8416 (p) REVERT: F 256 SER cc_start: 0.8907 (t) cc_final: 0.8618 (p) REVERT: F 484 TYR cc_start: 0.8896 (p90) cc_final: 0.8523 (p90) outliers start: 61 outliers final: 57 residues processed: 385 average time/residue: 0.2442 time to fit residues: 140.9402 Evaluate side-chains 394 residues out of total 1477 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 337 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 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 443 ILE Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain B residue 538 THR 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 52 LEU Chi-restraints excluded: chain C residue 110 SER Chi-restraints excluded: chain C residue 111 LEU 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 194 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 264 SER Chi-restraints excluded: chain C residue 294 ILE Chi-restraints excluded: chain C residue 303 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 635 ILE 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 540 GLN Chi-restraints excluded: chain E residue 571 TRP Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 138 ILE Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 300 ASN Chi-restraints excluded: chain F residue 331 CYS Chi-restraints excluded: chain F residue 390 LEU Chi-restraints excluded: chain F residue 446 VAL Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 499 THR Chi-restraints excluded: chain F residue 504 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 150 optimal weight: 0.8980 chunk 77 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 171 optimal weight: 7.9990 chunk 121 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN C 279 ASN E 543 ASN E 630 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.163291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137598 restraints weight = 23777.028| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 3.55 r_work: 0.3555 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 15480 Z= 0.145 Angle : 0.665 15.114 21166 Z= 0.325 Chirality : 0.044 0.205 2584 Planarity : 0.003 0.043 2613 Dihedral : 5.297 39.409 3206 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.72 % Allowed : 19.91 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.21), residues: 1622 helix: 2.05 (0.29), residues: 371 sheet: 0.12 (0.24), residues: 448 loop : -1.10 (0.21), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 623 HIS 0.007 0.001 HIS C 352 PHE 0.023 0.001 PHE A 361 TYR 0.032 0.002 TYR F 191 ARG 0.006 0.001 ARG F 178 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 52) link_NAG-ASN : angle 2.45491 ( 156) link_BETA1-4 : bond 0.00585 ( 6) link_BETA1-4 : angle 1.60935 ( 18) hydrogen bonds : bond 0.04234 ( 555) hydrogen bonds : angle 5.09222 ( 1596) SS BOND : bond 0.00532 ( 33) SS BOND : angle 1.84973 ( 66) covalent geometry : bond 0.00341 (15389) covalent geometry : angle 0.62416 (20926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6960.00 seconds wall clock time: 122 minutes 11.21 seconds (7331.21 seconds total)