Starting phenix.real_space_refine on Mon May 26 01:09:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2f_40982/05_2025/8t2f_40982_trim.cif" } resolution = 3.8 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: 5 Type Number sf(0) Gaussians S 98 5.16 5 C 8826 2.51 5 N 2412 2.21 5 O 2761 1.98 5 H 12013 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 26110 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 6678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 6678 Classifications: {'peptide': 426} Link IDs: {'PTRANS': 18, 'TRANS': 407} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1751 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 1, 'TRANS': 109} Chain breaks: 1 Chain: "C" Number of atoms: 1620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1620 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 1 Chain: "E" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 5807 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 20, 'TRANS': 347} Chain breaks: 10 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 1828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1828 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 1 Chain: "F" Number of atoms: 6546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 6546 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 18, 'TRANS': 398} Chain breaks: 7 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 525 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 105} Link IDs: {'TRANS': 104} Unresolved non-hydrogen bonds: 210 Unresolved non-hydrogen angles: 315 Unresolved non-hydrogen dihedrals: 105 Planarities with less than four sites: {'UNK:plan-1': 105} Unresolved non-hydrogen planarities: 105 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: "M" 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: 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: "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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "F" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 224 Unusual residues: {'NAG': 16} Classifications: {'undetermined': 16} Link IDs: {None: 15} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 16 Time building chain proxies: 11.98, per 1000 atoms: 0.46 Number of scatterers: 26110 At special positions: 0 Unit cell: (149.495, 122.689, 116.503, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 O 2761 8.00 N 2412 7.00 C 8826 6.00 H 12013 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=31, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.05 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.10 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 149 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.09 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 598 " - pdb=" SG CYS C 604 " distance=2.02 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.13 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.02 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.04 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.11 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=2.05 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.14 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 149 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " NAG-ASN " NAG A 601 " - " ASN A 88 " " NAG A 602 " - " ASN A 152 " " NAG A 603 " - " ASN A 197 " " NAG A 604 " - " ASN A 234 " " NAG A 605 " - " ASN A 241 " " NAG A 606 " - " ASN A 276 " " NAG A 607 " - " ASN A 363 " " NAG A 608 " - " ASN A 386 " " NAG A 609 " - " ASN A 448 " " NAG A 610 " - " ASN A 295 " " NAG A 611 " - " ASN A 355 " " NAG A 612 " - " ASN A 392 " " NAG A 613 " - " ASN A 339 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 637 " " NAG C 701 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 637 " " NAG E 601 " - " ASN E 152 " " NAG E 602 " - " ASN E 234 " " NAG E 603 " - " ASN E 276 " " NAG E 604 " - " ASN E 301 " " NAG E 605 " - " ASN E 332 " " NAG E 606 " - " ASN E 339 " " NAG E 607 " - " ASN E 448 " " NAG E 608 " - " ASN E 295 " " NAG E 609 " - " ASN E 386 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 152 " " NAG F 603 " - " ASN F 148 " " NAG F 604 " - " ASN F 197 " " 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 332 " " NAG F 611 " - " ASN F 355 " " NAG F 612 " - " ASN F 363 " " NAG F 613 " - " ASN F 386 " " NAG F 614 " - " ASN F 448 " " NAG F 615 " - " ASN F 133 " " NAG F 616 " - " ASN F 301 " " NAG G 1 " - " ASN A 148 " " NAG I 1 " - " ASN A 262 " " NAG J 1 " - " ASN A 332 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN F 262 " Time building additional restraints: 6.30 Conformation dependent library (CDL) restraints added in 1.6 seconds 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3334 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 30 sheets defined 24.2% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.088A 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 335 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 3.796A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 537 removed outlier: 3.881A pdb=" N LEU B 537 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 594 removed outlier: 3.760A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 652 Processing helix chain 'C' and resid 532 through 535 removed outlier: 4.234A pdb=" N MET C 535 " --> pdb=" O ALA C 532 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 532 through 535' Processing helix chain 'C' and resid 536 through 542 Processing helix chain 'C' and resid 573 through 596 Processing helix chain 'C' and resid 611 through 615 Processing helix chain 'C' and resid 618 through 624 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 639 through 649 Processing helix chain 'E' and resid 98 through 115 Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.528A pdb=" N CYS E 126 " --> pdb=" O THR E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 336 through 346 Processing helix chain 'E' and resid 348 through 352 Processing helix chain 'E' and resid 474 through 481 Processing helix chain 'D' and resid 531 through 536 removed outlier: 4.075A pdb=" N MET D 535 " --> pdb=" O ALA D 532 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 Processing helix chain 'D' and resid 611 through 615 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 660 Processing helix chain 'F' and resid 67 through 72 Processing helix chain 'F' and resid 98 through 117 removed outlier: 3.514A pdb=" N GLU F 102 " --> pdb=" O ASN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 169 through 171 No H-bonds generated for 'chain 'F' and resid 169 through 171' Processing helix chain 'F' and resid 334 through 350 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 475 through 480 Processing helix chain 'F' and resid 481 through 484 removed outlier: 4.288A pdb=" N TYR F 484 " --> pdb=" O SER F 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 484' Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.596A pdb=" N VAL A 36 " --> pdb=" O THR B 606 " (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 53 through 55 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 162 through 169 Processing sheet with id=AA6, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.556A 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 312 removed outlier: 6.613A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 467 through 470 Processing sheet with id=AA8, first strand: chain 'C' and resid 603 through 604 Processing sheet with id=AA9, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB1, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB2, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB3, first strand: chain 'E' and resid 130 through 132 Processing sheet with id=AB4, first strand: chain 'E' and resid 173 through 174 Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.263A pdb=" N ALA E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N TYR E 435 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 297 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 333 current: chain 'E' and resid 469 through 470 Processing sheet with id=AB7, first strand: chain 'E' and resid 305 through 312 removed outlier: 6.643A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 603 through 609 removed outlier: 4.820A pdb=" N VAL F 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'F' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'F' and resid 163 through 168 Processing sheet with id=AC4, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.733A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 259 through 261 current: chain 'F' and resid 284 through 302 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 330 through 333 current: chain 'F' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 381 through 385 current: chain 'F' and resid 466 through 470 Processing sheet with id=AC6, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.432A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 3 through 7 removed outlier: 5.923A pdb=" N UNK H 16 " --> pdb=" O UNK H 85 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AC9, first strand: chain 'H' and resid 58 through 60 removed outlier: 7.059A pdb=" N UNK H 36 " --> pdb=" O UNK H 48 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N UNK H 50 " --> pdb=" O UNK H 34 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N UNK H 34 " --> pdb=" O UNK H 50 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD2, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AD3, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.586A pdb=" N UNK L 53 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1152 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: 8.81 Time building geometry restraints manager: 7.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 12009 1.05 - 1.27: 2274 1.27 - 1.48: 6032 1.48 - 1.70: 5904 1.70 - 1.91: 130 Bond restraints: 26349 Sorted by residual: bond pdb=" NE ARG F 504 " pdb=" CZ ARG F 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.71e+01 bond pdb=" CD2 TRP B 571 " pdb=" CE3 TRP B 571 " ideal model delta sigma weight residual 1.398 1.507 -0.109 1.60e-02 3.91e+03 4.65e+01 bond pdb=" NE ARG A 503 " pdb=" CZ ARG A 503 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.57e+01 bond pdb=" CZ2 TRP B 571 " pdb=" CH2 TRP B 571 " ideal model delta sigma weight residual 1.368 1.492 -0.124 1.90e-02 2.77e+03 4.25e+01 bond pdb=" CB ILE F 176 " pdb=" CG1 ILE F 176 " ideal model delta sigma weight residual 1.530 1.660 -0.130 2.00e-02 2.50e+03 4.20e+01 ... (remaining 26344 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.50: 40709 2.50 - 5.01: 5518 5.01 - 7.51: 467 7.51 - 10.01: 50 10.01 - 12.51: 4 Bond angle restraints: 46748 Sorted by residual: angle pdb=" N CYS A 196 " pdb=" CA CYS A 196 " pdb=" C CYS A 196 " ideal model delta sigma weight residual 114.12 101.61 12.51 1.39e+00 5.18e-01 8.11e+01 angle pdb=" N ILE E 424 " pdb=" CA ILE E 424 " pdb=" C ILE E 424 " ideal model delta sigma weight residual 107.80 119.93 -12.13 1.45e+00 4.76e-01 6.99e+01 angle pdb=" N SER A 115 " pdb=" CA SER A 115 " pdb=" C SER A 115 " ideal model delta sigma weight residual 110.53 99.88 10.65 1.29e+00 6.01e-01 6.82e+01 angle pdb=" C CYS E 205 " pdb=" N PRO E 206 " pdb=" CA PRO E 206 " ideal model delta sigma weight residual 119.56 127.93 -8.37 1.02e+00 9.61e-01 6.73e+01 angle pdb=" N PHE E 383 " pdb=" CA PHE E 383 " pdb=" C PHE E 383 " ideal model delta sigma weight residual 112.23 121.44 -9.21 1.26e+00 6.30e-01 5.34e+01 ... (remaining 46743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 12788 21.07 - 42.13: 350 42.13 - 63.20: 155 63.20 - 84.26: 32 84.26 - 105.33: 19 Dihedral angle restraints: 13344 sinusoidal: 7464 harmonic: 5880 Sorted by residual: 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 -177.73 -89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS D 605 " pdb=" SG CYS D 605 " pdb=" SG CYS F 501 " pdb=" CB CYS F 501 " ideal model delta sinusoidal sigma weight residual -86.00 -44.26 -41.74 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS F 119 " pdb=" SG CYS F 119 " pdb=" SG CYS F 205 " pdb=" CB CYS F 205 " ideal model delta sinusoidal sigma weight residual -86.00 -125.46 39.46 1 1.00e+01 1.00e-02 2.19e+01 ... (remaining 13341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1681 0.104 - 0.208: 451 0.208 - 0.311: 164 0.311 - 0.415: 83 0.415 - 0.519: 43 Chirality restraints: 2422 Sorted by residual: chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.31e+01 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.59 0.19 2.00e-02 2.50e+03 9.06e+01 ... (remaining 2419 not shown) Planarity restraints: 3903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 295 " 0.116 2.00e-02 2.50e+03 9.03e-02 1.22e+02 pdb=" CG ASN E 295 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN E 295 " -0.051 2.00e-02 2.50e+03 pdb=" ND2 ASN E 295 " -0.094 2.00e-02 2.50e+03 pdb="HD21 ASN E 295 " -0.075 2.00e-02 2.50e+03 pdb=" C1 NAG E 608 " 0.133 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 301 " -0.105 2.00e-02 2.50e+03 8.30e-02 1.03e+02 pdb=" CG ASN F 301 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN F 301 " 0.056 2.00e-02 2.50e+03 pdb=" ND2 ASN F 301 " 0.085 2.00e-02 2.50e+03 pdb="HD21 ASN F 301 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG F 616 " -0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 339 " -0.105 2.00e-02 2.50e+03 8.07e-02 9.77e+01 pdb=" CG ASN A 339 " 0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN A 339 " 0.054 2.00e-02 2.50e+03 pdb=" ND2 ASN A 339 " 0.082 2.00e-02 2.50e+03 pdb="HD21 ASN A 339 " 0.060 2.00e-02 2.50e+03 pdb=" C1 NAG A 613 " -0.119 2.00e-02 2.50e+03 ... (remaining 3900 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.04: 388 2.04 - 2.68: 36431 2.68 - 3.32: 70557 3.32 - 3.96: 92504 3.96 - 4.60: 143432 Nonbonded interactions: 343312 Sorted by model distance: nonbonded pdb=" OG1 THR F 37 " pdb=" HG1 THR F 499 " model vdw 1.401 2.450 nonbonded pdb=" H CYS A 196 " pdb=" H ASN A 197 " model vdw 1.456 2.100 nonbonded pdb=" OG1 THR A 37 " pdb=" HG1 THR A 499 " model vdw 1.471 2.450 nonbonded pdb=" OE2 GLU F 290 " pdb=" HZ1 LYS F 344 " model vdw 1.666 2.450 nonbonded pdb=" HG1 THR A 37 " pdb=" HG1 THR A 499 " model vdw 1.751 2.100 ... (remaining 343307 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 34 through 132 or (resid 133 and (name N or name CA or nam \ e C or name O or name CB or name CG or name OD1 or name ND2 or name H or name HA \ or name HB2 or name HB3 or name HD21)) or resid 134 through 153 or (resid 161 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD or na \ me CE or name NZ or name HA or name HB2 or name HB3 or name HG2 or name HG3 or n \ ame HD2 or name HD3 or name HE2 or name HE3 or name HZ1 or name HZ2 or name HZ3) \ ) or resid 162 through 288 or (resid 289 and (name N or name CA or name C or nam \ e O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name H \ B2 or name HB3 or name HD21)) or resid 290 through 300 or (resid 301 and (name N \ or name CA or name C or name O or name CB or name CG or name OD1 or name ND2 or \ name H or name HA or name HB2 or name HB3 or name HD21)) or resid 302 through 3 \ 21 or (resid 323 and (name N or name CA or name C or name O or name CB or name C \ G1 or name CG2 or name CD1 or name HA or name HB or name HG12 or name HG13 or na \ me HG21 or name HG22 or name HG23 or name HD11 or name HD12 or name HD13)) or re \ sid 323A through 397 or resid 412 through 455 or (resid 464 and (name N or name \ CA or name C or name O or name CB or name OG1 or name CG2 or name HA or name HB \ or name HG1 or name HG21 or name HG22 or name HG23)) or resid 465 through 503 or \ resid 601 through 613)) selection = (chain 'F' and (resid 34 through 57 or (resid 67 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name ND2 or name HA or name HB2 \ or name HB3 or name HD21 or name HD22)) or resid 68 through 338 or (resid 339 a \ nd (name N or name CA or name C or name O or name CB or name CG or name OD1 or n \ ame ND2 or name H or name HA or name HB2 or name HB3 or name HD21)) or resid 340 \ through 391 or (resid 392 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name ND2 or name H or name HA or name HB2 or name HB3 \ or name HD21)) or resid 393 through 503 or resid 604 through 616)) } ncs_group { reference = (chain 'B' and ((resid 522 and (name N or name CA or name C or name O or name CB \ or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name H \ A or name HB2 or name HB3 or name HD1 or name HD2 or name HE1 or name HE2 or nam \ e HZ )) or resid 523 through 546 or (resid 572 and (name N or name CA or name C \ or name O or name HA2 or name HA3)) or resid 573 through 649 or resid 702)) selection = (chain 'C' and (resid 522 through 604 or (resid 605 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 606 through 610 or (resid 611 and (name N or name CA or name C or n \ ame O or name CB or name CG or name OD1 or name ND2 or name H or name HA or name \ HB2 or name HB3 or name HD21)) or resid 612 through 649 or resid 701)) selection = (chain 'D' and (resid 522 through 546 or (resid 572 and (name N or name CA or na \ me C or name O or name HA2 or name HA3)) or resid 573 through 649 or resid 702)) \ } ncs_group { reference = chain 'G' selection = chain 'J' } ncs_group { reference = (chain 'H' and resid 12 through 116) selection = chain 'L' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.130 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: 0.440 Extract box with map and model: 0.860 Check model and map are aligned: 0.190 Set scattering table: 0.220 Process input model: 49.490 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 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 : 0.022 0.134 14423 Z= 1.159 Angle : 1.714 12.514 19714 Z= 1.100 Chirality : 0.137 0.519 2422 Planarity : 0.009 0.058 2403 Dihedral : 11.356 105.329 5914 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.22 % Allowed : 0.44 % Favored : 99.34 % 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: 0.47 (0.21), residues: 1479 helix: -0.16 (0.27), residues: 336 sheet: 1.14 (0.27), residues: 319 loop : 0.32 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.009 TRP A 35 HIS 0.009 0.002 HIS E 249 PHE 0.030 0.006 PHE A 383 TYR 0.039 0.007 TYR E 486 ARG 0.007 0.001 ARG A 456 Details of bonding type rmsd link_NAG-ASN : bond 0.08200 ( 48) link_NAG-ASN : angle 2.78601 ( 144) link_BETA1-4 : bond 0.07208 ( 8) link_BETA1-4 : angle 4.54864 ( 24) hydrogen bonds : bond 0.15388 ( 438) hydrogen bonds : angle 7.54045 ( 1152) SS BOND : bond 0.03487 ( 31) SS BOND : angle 3.10399 ( 62) covalent geometry : bond 0.02171 (14336) covalent geometry : angle 1.69096 (19484) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 577 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 574 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LEU cc_start: 0.9033 (mt) cc_final: 0.8791 (mt) REVERT: A 352 HIS cc_start: 0.8055 (m-70) cc_final: 0.7837 (m170) REVERT: A 377 ASN cc_start: 0.8457 (t0) cc_final: 0.8257 (t0) REVERT: A 426 MET cc_start: 0.8169 (ttm) cc_final: 0.7561 (ttt) REVERT: A 481 SER cc_start: 0.8593 (p) cc_final: 0.8263 (t) REVERT: B 530 MET cc_start: 0.7844 (mtp) cc_final: 0.7502 (mtp) REVERT: B 588 ARG cc_start: 0.7454 (mtt180) cc_final: 0.7153 (tmm-80) REVERT: B 603 ILE cc_start: 0.8448 (pt) cc_final: 0.8117 (pt) REVERT: B 622 ILE cc_start: 0.8777 (mm) cc_final: 0.8304 (mm) REVERT: C 629 LEU cc_start: 0.9254 (mt) cc_final: 0.9025 (mp) REVERT: E 103 GLN cc_start: 0.8608 (tp40) cc_final: 0.8099 (tm-30) REVERT: E 165 TYR cc_start: 0.6089 (t80) cc_final: 0.5349 (t80) REVERT: E 173 VAL cc_start: 0.7409 (t) cc_final: 0.7069 (t) REVERT: E 376 PHE cc_start: 0.8614 (m-80) cc_final: 0.8385 (m-10) REVERT: D 545 LEU cc_start: 0.8832 (mt) cc_final: 0.8588 (mt) REVERT: D 660 LEU cc_start: 0.7899 (tp) cc_final: 0.7497 (tt) REVERT: F 129 LEU cc_start: 0.8917 (tp) cc_final: 0.8661 (tt) REVERT: F 172 ASP cc_start: 0.7428 (m-30) cc_final: 0.7216 (m-30) REVERT: F 232 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7859 (tptp) REVERT: F 315 GLN cc_start: 0.8227 (mp10) cc_final: 0.7384 (mm-40) REVERT: F 348 GLN cc_start: 0.8168 (mm110) cc_final: 0.7806 (mm-40) outliers start: 3 outliers final: 3 residues processed: 577 average time/residue: 0.5691 time to fit residues: 464.2685 Evaluate side-chains 412 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 409 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain C residue 637 ASN Chi-restraints excluded: chain E residue 339 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.3980 chunk 130 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN B 616 ASN B 618 ASN B 625 ASN E 330 HIS F 85 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.174267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151247 restraints weight = 60971.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156868 restraints weight = 24745.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160292 restraints weight = 13439.428| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 14423 Z= 0.160 Angle : 0.739 8.221 19714 Z= 0.375 Chirality : 0.048 0.427 2422 Planarity : 0.004 0.045 2403 Dihedral : 7.841 67.984 3015 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.91 % Favored : 97.03 % Rotamer: Outliers : 2.92 % Allowed : 11.37 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.52 (0.21), residues: 1479 helix: 0.94 (0.28), residues: 334 sheet: 0.71 (0.26), residues: 344 loop : 0.01 (0.22), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 623 HIS 0.008 0.001 HIS A 249 PHE 0.027 0.002 PHE B 522 TYR 0.018 0.002 TYR D 643 ARG 0.007 0.001 ARG D 585 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 48) link_NAG-ASN : angle 2.67524 ( 144) link_BETA1-4 : bond 0.00826 ( 8) link_BETA1-4 : angle 3.32058 ( 24) hydrogen bonds : bond 0.06520 ( 438) hydrogen bonds : angle 5.78481 ( 1152) SS BOND : bond 0.00470 ( 31) SS BOND : angle 1.38098 ( 62) covalent geometry : bond 0.00352 (14336) covalent geometry : angle 0.69240 (19484) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 483 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 443 time to evaluate : 2.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 426 MET cc_start: 0.8083 (ttm) cc_final: 0.7428 (ttt) REVERT: A 481 SER cc_start: 0.8206 (p) cc_final: 0.7946 (t) REVERT: B 588 ARG cc_start: 0.6881 (mtt180) cc_final: 0.6455 (tmm-80) REVERT: B 603 ILE cc_start: 0.8394 (pt) cc_final: 0.8006 (pt) REVERT: B 622 ILE cc_start: 0.8700 (mm) cc_final: 0.8473 (mm) REVERT: B 650 GLN cc_start: 0.9180 (tp40) cc_final: 0.8894 (tp40) REVERT: C 632 ASP cc_start: 0.8998 (t0) cc_final: 0.8680 (t0) REVERT: E 45 TRP cc_start: 0.8675 (p90) cc_final: 0.8454 (p90) REVERT: E 160 LYS cc_start: 0.7366 (ttpt) cc_final: 0.7034 (tmmt) REVERT: E 173 VAL cc_start: 0.7695 (t) cc_final: 0.7408 (t) REVERT: D 660 LEU cc_start: 0.7502 (tp) cc_final: 0.7288 (tt) REVERT: F 129 LEU cc_start: 0.8403 (tp) cc_final: 0.8043 (tt) REVERT: F 172 ASP cc_start: 0.7981 (m-30) cc_final: 0.7679 (m-30) REVERT: F 232 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7492 (tptp) REVERT: F 318 TYR cc_start: 0.8744 (m-80) cc_final: 0.8247 (m-80) outliers start: 40 outliers final: 29 residues processed: 457 average time/residue: 0.5212 time to fit residues: 349.8521 Evaluate side-chains 438 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 409 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 264 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 636 SER Chi-restraints excluded: chain E residue 36 VAL Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 602 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 209 SER Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 81 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 171 optimal weight: 7.9990 chunk 11 optimal weight: 0.4980 chunk 127 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 GLN A 175 GLN B 640 GLN E 330 HIS F 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.170350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147019 restraints weight = 61901.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.152527 restraints weight = 25500.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.155919 restraints weight = 13988.873| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14423 Z= 0.164 Angle : 0.633 7.609 19714 Z= 0.322 Chirality : 0.045 0.373 2422 Planarity : 0.004 0.061 2403 Dihedral : 6.319 58.675 3013 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.77 % Allowed : 13.63 % Favored : 83.60 % 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: 0.46 (0.22), residues: 1479 helix: 1.32 (0.29), residues: 328 sheet: 0.46 (0.27), residues: 328 loop : -0.10 (0.22), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 623 HIS 0.005 0.001 HIS A 374 PHE 0.020 0.002 PHE B 522 TYR 0.018 0.001 TYR D 643 ARG 0.008 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00369 ( 48) link_NAG-ASN : angle 2.08508 ( 144) link_BETA1-4 : bond 0.00706 ( 8) link_BETA1-4 : angle 2.26011 ( 24) hydrogen bonds : bond 0.05499 ( 438) hydrogen bonds : angle 5.30330 ( 1152) SS BOND : bond 0.00335 ( 31) SS BOND : angle 1.27417 ( 62) covalent geometry : bond 0.00358 (14336) covalent geometry : angle 0.60189 (19484) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 450 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 412 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 143 ARG cc_start: 0.7108 (mmm160) cc_final: 0.5362 (tpt170) REVERT: A 335 LYS cc_start: 0.8192 (tttt) cc_final: 0.7684 (tptm) REVERT: A 481 SER cc_start: 0.8421 (p) cc_final: 0.8057 (t) REVERT: B 530 MET cc_start: 0.7162 (mtp) cc_final: 0.6916 (mtp) REVERT: B 542 ARG cc_start: 0.8378 (ptt180) cc_final: 0.7959 (ttp80) REVERT: B 588 ARG cc_start: 0.7055 (mtt180) cc_final: 0.6495 (tmm-80) REVERT: B 603 ILE cc_start: 0.8344 (pt) cc_final: 0.7964 (pt) REVERT: B 622 ILE cc_start: 0.8642 (mm) cc_final: 0.8337 (mm) REVERT: C 542 ARG cc_start: 0.8037 (ttp80) cc_final: 0.7691 (ptt90) REVERT: C 632 ASP cc_start: 0.9030 (t0) cc_final: 0.8763 (t0) REVERT: E 45 TRP cc_start: 0.8664 (p90) cc_final: 0.8379 (p90) REVERT: E 147 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6108 (mmmt) REVERT: E 160 LYS cc_start: 0.7508 (ttpt) cc_final: 0.7073 (tmmt) REVERT: E 173 VAL cc_start: 0.7755 (t) cc_final: 0.7443 (t) REVERT: D 660 LEU cc_start: 0.7473 (tp) cc_final: 0.7196 (tt) REVERT: F 129 LEU cc_start: 0.8299 (tp) cc_final: 0.7831 (tt) REVERT: F 172 ASP cc_start: 0.7988 (m-30) cc_final: 0.7732 (m-30) REVERT: F 327 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7624 (mtp85) outliers start: 38 outliers final: 35 residues processed: 426 average time/residue: 0.5086 time to fit residues: 316.4607 Evaluate side-chains 427 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 392 time to evaluate : 1.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 175 GLN Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 434 MET Chi-restraints excluded: chain F residue 447 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 31 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 640 GLN ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 330 HIS F 85 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.166889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143318 restraints weight = 62345.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.148699 restraints weight = 26093.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.151980 restraints weight = 14493.073| |-----------------------------------------------------------------------------| r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.4702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14423 Z= 0.194 Angle : 0.625 6.900 19714 Z= 0.315 Chirality : 0.045 0.359 2422 Planarity : 0.004 0.045 2403 Dihedral : 5.948 59.330 3013 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.84 % Allowed : 14.43 % Favored : 82.73 % 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: 0.26 (0.22), residues: 1479 helix: 1.31 (0.29), residues: 328 sheet: 0.24 (0.27), residues: 357 loop : -0.28 (0.22), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 623 HIS 0.006 0.001 HIS F 352 PHE 0.020 0.002 PHE B 522 TYR 0.012 0.001 TYR C 638 ARG 0.004 0.000 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00330 ( 48) link_NAG-ASN : angle 2.09346 ( 144) link_BETA1-4 : bond 0.00358 ( 8) link_BETA1-4 : angle 1.81925 ( 24) hydrogen bonds : bond 0.05024 ( 438) hydrogen bonds : angle 5.23238 ( 1152) SS BOND : bond 0.00435 ( 31) SS BOND : angle 1.24647 ( 62) covalent geometry : bond 0.00428 (14336) covalent geometry : angle 0.59500 (19484) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 395 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LYS cc_start: 0.8217 (tttt) cc_final: 0.7720 (tptm) REVERT: A 481 SER cc_start: 0.8422 (p) cc_final: 0.7963 (t) REVERT: B 530 MET cc_start: 0.7375 (mtp) cc_final: 0.6871 (mtp) REVERT: B 542 ARG cc_start: 0.8274 (ptt180) cc_final: 0.7966 (ttp80) REVERT: B 588 ARG cc_start: 0.7167 (mtt180) cc_final: 0.6623 (tmm-80) REVERT: B 603 ILE cc_start: 0.8345 (pt) cc_final: 0.7969 (pt) REVERT: B 622 ILE cc_start: 0.8712 (mm) cc_final: 0.8243 (mm) REVERT: C 632 ASP cc_start: 0.8944 (t0) cc_final: 0.8652 (t0) REVERT: E 103 GLN cc_start: 0.8490 (tp40) cc_final: 0.8104 (tp40) REVERT: E 147 LYS cc_start: 0.6446 (mmtt) cc_final: 0.6205 (mmmt) REVERT: E 160 LYS cc_start: 0.7626 (ttpt) cc_final: 0.7249 (tmmt) REVERT: E 165 TYR cc_start: 0.5496 (t80) cc_final: 0.4947 (t80) REVERT: E 173 VAL cc_start: 0.7823 (t) cc_final: 0.7490 (t) REVERT: D 591 GLN cc_start: 0.8588 (tt0) cc_final: 0.8373 (tt0) REVERT: D 660 LEU cc_start: 0.7591 (tp) cc_final: 0.7245 (tt) REVERT: F 114 GLN cc_start: 0.8479 (tp40) cc_final: 0.8210 (tp40) outliers start: 39 outliers final: 36 residues processed: 411 average time/residue: 0.5012 time to fit residues: 300.1764 Evaluate side-chains 410 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 374 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 439 ILE Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 447 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 139 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN F 85 HIS F 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.162159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.138624 restraints weight = 62952.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.143797 restraints weight = 26692.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.146979 restraints weight = 14992.016| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 14423 Z= 0.232 Angle : 0.668 7.968 19714 Z= 0.333 Chirality : 0.046 0.361 2422 Planarity : 0.004 0.040 2403 Dihedral : 6.371 58.401 3011 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.57 % Allowed : 15.01 % Favored : 81.41 % 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: -0.37 (0.21), residues: 1479 helix: 1.03 (0.28), residues: 331 sheet: -0.04 (0.27), residues: 334 loop : -0.87 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 338 HIS 0.007 0.002 HIS A 374 PHE 0.019 0.002 PHE A 376 TYR 0.014 0.002 TYR C 638 ARG 0.007 0.001 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00371 ( 48) link_NAG-ASN : angle 2.17828 ( 144) link_BETA1-4 : bond 0.00352 ( 8) link_BETA1-4 : angle 1.36972 ( 24) hydrogen bonds : bond 0.04826 ( 438) hydrogen bonds : angle 5.27353 ( 1152) SS BOND : bond 0.00536 ( 31) SS BOND : angle 1.38565 ( 62) covalent geometry : bond 0.00522 (14336) covalent geometry : angle 0.63847 (19484) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 445 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 396 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.8694 (ppp) cc_final: 0.8383 (ppp) REVERT: A 335 LYS cc_start: 0.8293 (tttt) cc_final: 0.7764 (tptm) REVERT: A 481 SER cc_start: 0.8590 (p) cc_final: 0.8118 (t) REVERT: B 530 MET cc_start: 0.7882 (mtp) cc_final: 0.7417 (mtp) REVERT: B 542 ARG cc_start: 0.8442 (ptt180) cc_final: 0.8036 (ttp80) REVERT: B 588 ARG cc_start: 0.7193 (mtt180) cc_final: 0.6559 (tmm-80) REVERT: B 603 ILE cc_start: 0.8352 (pt) cc_final: 0.8046 (pt) REVERT: B 622 ILE cc_start: 0.8884 (mm) cc_final: 0.8473 (mm) REVERT: E 103 GLN cc_start: 0.8309 (tp40) cc_final: 0.7847 (tp40) REVERT: E 160 LYS cc_start: 0.7739 (ttpt) cc_final: 0.7391 (tmmt) REVERT: E 162 GLN cc_start: 0.7696 (pt0) cc_final: 0.7246 (pm20) REVERT: E 165 TYR cc_start: 0.5299 (t80) cc_final: 0.4941 (t80) REVERT: D 591 GLN cc_start: 0.8652 (tt0) cc_final: 0.8375 (tt0) REVERT: D 631 TRP cc_start: 0.8360 (t-100) cc_final: 0.8155 (t-100) REVERT: D 660 LEU cc_start: 0.7507 (tp) cc_final: 0.7187 (tt) outliers start: 49 outliers final: 46 residues processed: 418 average time/residue: 0.5081 time to fit residues: 311.3182 Evaluate side-chains 419 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 373 time to evaluate : 1.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 613 THR Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 278 THR Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 450 THR Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 101 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.164618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.141172 restraints weight = 62261.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.146411 restraints weight = 26228.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149607 restraints weight = 14678.774| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14423 Z= 0.128 Angle : 0.570 6.126 19714 Z= 0.287 Chirality : 0.043 0.345 2422 Planarity : 0.003 0.041 2403 Dihedral : 5.848 57.163 3011 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.99 % Allowed : 16.62 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.24 (0.21), residues: 1479 helix: 1.31 (0.29), residues: 331 sheet: -0.16 (0.26), residues: 364 loop : -0.77 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 631 HIS 0.005 0.001 HIS A 374 PHE 0.016 0.001 PHE F 151 TYR 0.009 0.001 TYR C 638 ARG 0.004 0.000 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 48) link_NAG-ASN : angle 1.93144 ( 144) link_BETA1-4 : bond 0.00320 ( 8) link_BETA1-4 : angle 1.15810 ( 24) hydrogen bonds : bond 0.04363 ( 438) hydrogen bonds : angle 4.98573 ( 1152) SS BOND : bond 0.00313 ( 31) SS BOND : angle 1.28963 ( 62) covalent geometry : bond 0.00286 (14336) covalent geometry : angle 0.54261 (19484) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 420 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 379 time to evaluate : 2.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7683 (m-10) cc_final: 0.7253 (m-10) REVERT: A 435 TYR cc_start: 0.9010 (t80) cc_final: 0.8771 (t80) REVERT: A 481 SER cc_start: 0.8485 (p) cc_final: 0.7964 (t) REVERT: B 530 MET cc_start: 0.7624 (mtp) cc_final: 0.7220 (mtp) REVERT: B 542 ARG cc_start: 0.8435 (ptt180) cc_final: 0.8053 (ttp80) REVERT: B 587 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9007 (mm) REVERT: B 588 ARG cc_start: 0.7229 (mtt180) cc_final: 0.6591 (tmm-80) REVERT: B 603 ILE cc_start: 0.8507 (pt) cc_final: 0.7934 (pt) REVERT: B 622 ILE cc_start: 0.8863 (mm) cc_final: 0.8442 (mm) REVERT: C 596 TRP cc_start: 0.7765 (m-10) cc_final: 0.7512 (m-10) REVERT: C 632 ASP cc_start: 0.9077 (t0) cc_final: 0.8708 (t0) REVERT: E 92 GLU cc_start: 0.6418 (tm-30) cc_final: 0.6214 (tm-30) REVERT: E 103 GLN cc_start: 0.8211 (tp40) cc_final: 0.7769 (tp40) REVERT: E 160 LYS cc_start: 0.7757 (ttpt) cc_final: 0.7421 (tmmt) REVERT: E 162 GLN cc_start: 0.7758 (pt0) cc_final: 0.7290 (pm20) REVERT: E 165 TYR cc_start: 0.5342 (t80) cc_final: 0.5005 (t80) REVERT: D 643 TYR cc_start: 0.8776 (m-10) cc_final: 0.8538 (m-10) REVERT: D 660 LEU cc_start: 0.7421 (tp) cc_final: 0.7119 (tt) REVERT: F 87 GLU cc_start: 0.8365 (mp0) cc_final: 0.8015 (mp0) outliers start: 41 outliers final: 37 residues processed: 396 average time/residue: 0.5054 time to fit residues: 293.7280 Evaluate side-chains 404 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 366 time to evaluate : 1.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 322 ASP Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 107 ASP Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 271 ILE Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 484 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 23 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.165365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.142011 restraints weight = 62064.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.147270 restraints weight = 26107.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.150492 restraints weight = 14558.547| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14423 Z= 0.114 Angle : 0.542 5.605 19714 Z= 0.272 Chirality : 0.043 0.328 2422 Planarity : 0.003 0.041 2403 Dihedral : 5.474 54.459 3011 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.55 % Allowed : 17.57 % Favored : 79.88 % 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: -0.12 (0.21), residues: 1479 helix: 1.56 (0.29), residues: 326 sheet: -0.13 (0.26), residues: 362 loop : -0.73 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 631 HIS 0.004 0.001 HIS A 374 PHE 0.013 0.001 PHE E 53 TYR 0.027 0.001 TYR F 486 ARG 0.004 0.000 ARG A 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00251 ( 48) link_NAG-ASN : angle 1.80393 ( 144) link_BETA1-4 : bond 0.00315 ( 8) link_BETA1-4 : angle 1.10860 ( 24) hydrogen bonds : bond 0.04107 ( 438) hydrogen bonds : angle 4.81627 ( 1152) SS BOND : bond 0.00276 ( 31) SS BOND : angle 1.24890 ( 62) covalent geometry : bond 0.00258 (14336) covalent geometry : angle 0.51626 (19484) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 409 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 374 time to evaluate : 2.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7652 (m-10) cc_final: 0.7218 (m-10) REVERT: A 153 MET cc_start: 0.8563 (ppp) cc_final: 0.8282 (ppp) REVERT: A 435 TYR cc_start: 0.8990 (t80) cc_final: 0.8761 (t80) REVERT: A 481 SER cc_start: 0.8474 (p) cc_final: 0.7911 (t) REVERT: B 530 MET cc_start: 0.7460 (mtp) cc_final: 0.7053 (mtp) REVERT: B 542 ARG cc_start: 0.8416 (ptt180) cc_final: 0.8059 (ttp80) REVERT: B 587 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8939 (mm) REVERT: B 588 ARG cc_start: 0.7248 (mtt180) cc_final: 0.6599 (tmm-80) REVERT: B 603 ILE cc_start: 0.8316 (pt) cc_final: 0.7950 (pt) REVERT: B 622 ILE cc_start: 0.8895 (mm) cc_final: 0.8473 (mm) REVERT: C 596 TRP cc_start: 0.7721 (m-10) cc_final: 0.7501 (m-10) REVERT: C 632 ASP cc_start: 0.9065 (t0) cc_final: 0.8722 (t0) REVERT: E 92 GLU cc_start: 0.6530 (tm-30) cc_final: 0.6311 (tm-30) REVERT: E 103 GLN cc_start: 0.8214 (tp40) cc_final: 0.7745 (tp40) REVERT: E 160 LYS cc_start: 0.7768 (ttpt) cc_final: 0.7417 (tmmt) REVERT: E 162 GLN cc_start: 0.7797 (pt0) cc_final: 0.7334 (pm20) REVERT: E 165 TYR cc_start: 0.5354 (t80) cc_final: 0.4993 (t80) REVERT: D 660 LEU cc_start: 0.7388 (tp) cc_final: 0.7102 (tt) outliers start: 35 outliers final: 31 residues processed: 387 average time/residue: 0.4994 time to fit residues: 286.1493 Evaluate side-chains 396 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 364 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 90 THR Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 129 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 48 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.7980 chunk 95 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 113 optimal weight: 0.0870 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN E 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.165792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.142436 restraints weight = 62115.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.147733 restraints weight = 25913.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.150962 restraints weight = 14396.576| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14423 Z= 0.102 Angle : 0.526 6.178 19714 Z= 0.265 Chirality : 0.042 0.313 2422 Planarity : 0.003 0.044 2403 Dihedral : 5.142 53.041 3011 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.33 % Allowed : 18.51 % Favored : 79.15 % 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: -0.01 (0.22), residues: 1479 helix: 1.66 (0.29), residues: 327 sheet: -0.11 (0.26), residues: 365 loop : -0.64 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 631 HIS 0.004 0.001 HIS A 249 PHE 0.014 0.001 PHE F 151 TYR 0.046 0.001 TYR D 643 ARG 0.004 0.000 ARG F 469 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 48) link_NAG-ASN : angle 1.70266 ( 144) link_BETA1-4 : bond 0.00322 ( 8) link_BETA1-4 : angle 1.07061 ( 24) hydrogen bonds : bond 0.03940 ( 438) hydrogen bonds : angle 4.65544 ( 1152) SS BOND : bond 0.00284 ( 31) SS BOND : angle 1.23650 ( 62) covalent geometry : bond 0.00231 (14336) covalent geometry : angle 0.50247 (19484) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 376 time to evaluate : 1.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7534 (m-10) cc_final: 0.7131 (m-10) REVERT: A 435 TYR cc_start: 0.8968 (t80) cc_final: 0.8739 (t80) REVERT: B 530 MET cc_start: 0.7371 (mtp) cc_final: 0.6961 (mtp) REVERT: B 542 ARG cc_start: 0.8431 (ptt180) cc_final: 0.8060 (ttp80) REVERT: B 587 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8895 (mm) REVERT: B 588 ARG cc_start: 0.7288 (mtt180) cc_final: 0.6659 (tmm-80) REVERT: B 603 ILE cc_start: 0.8334 (pt) cc_final: 0.7959 (pt) REVERT: B 622 ILE cc_start: 0.8814 (mm) cc_final: 0.8402 (mm) REVERT: C 596 TRP cc_start: 0.7681 (m-10) cc_final: 0.7458 (m-10) REVERT: C 632 ASP cc_start: 0.9022 (t0) cc_final: 0.8698 (t0) REVERT: C 634 GLU cc_start: 0.8654 (tt0) cc_final: 0.8374 (tt0) REVERT: E 103 GLN cc_start: 0.8194 (tp40) cc_final: 0.7752 (tp40) REVERT: E 160 LYS cc_start: 0.7744 (ttpt) cc_final: 0.7393 (tmmt) REVERT: E 162 GLN cc_start: 0.7811 (pt0) cc_final: 0.7370 (pm20) REVERT: D 660 LEU cc_start: 0.7300 (tp) cc_final: 0.7027 (tt) REVERT: F 87 GLU cc_start: 0.8358 (mp0) cc_final: 0.8014 (mp0) REVERT: F 469 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7919 (mmm-85) outliers start: 32 outliers final: 28 residues processed: 389 average time/residue: 0.4776 time to fit residues: 277.0325 Evaluate side-chains 395 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 366 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain E residue 481 SER Chi-restraints excluded: chain D residue 648 GLU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 16 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 160 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 112 optimal weight: 0.9980 chunk 159 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.163107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139817 restraints weight = 62649.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144997 restraints weight = 26610.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.148184 restraints weight = 14931.594| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14423 Z= 0.175 Angle : 0.582 5.528 19714 Z= 0.290 Chirality : 0.043 0.335 2422 Planarity : 0.003 0.040 2403 Dihedral : 5.530 53.051 3011 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.48 % Allowed : 18.73 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.32 (0.21), residues: 1479 helix: 1.44 (0.29), residues: 333 sheet: -0.33 (0.27), residues: 345 loop : -0.86 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 338 HIS 0.005 0.001 HIS A 374 PHE 0.013 0.001 PHE F 151 TYR 0.028 0.002 TYR D 643 ARG 0.004 0.000 ARG F 298 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 48) link_NAG-ASN : angle 1.87369 ( 144) link_BETA1-4 : bond 0.00308 ( 8) link_BETA1-4 : angle 1.12471 ( 24) hydrogen bonds : bond 0.04114 ( 438) hydrogen bonds : angle 4.81255 ( 1152) SS BOND : bond 0.00345 ( 31) SS BOND : angle 1.47783 ( 62) covalent geometry : bond 0.00396 (14336) covalent geometry : angle 0.55490 (19484) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 394 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 360 time to evaluate : 2.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7643 (mtp) cc_final: 0.7240 (mtp) REVERT: B 542 ARG cc_start: 0.8488 (ptt180) cc_final: 0.8089 (ttp80) REVERT: B 587 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8905 (mm) REVERT: B 588 ARG cc_start: 0.7268 (mtt180) cc_final: 0.6661 (tmm-80) REVERT: B 603 ILE cc_start: 0.8297 (pt) cc_final: 0.7933 (pt) REVERT: B 622 ILE cc_start: 0.8903 (mm) cc_final: 0.8495 (mm) REVERT: B 632 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8414 (t0) REVERT: C 590 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8578 (mm110) REVERT: C 601 LYS cc_start: 0.7895 (mtpp) cc_final: 0.7529 (mtmt) REVERT: C 632 ASP cc_start: 0.9120 (t0) cc_final: 0.8755 (t0) REVERT: C 634 GLU cc_start: 0.8699 (tt0) cc_final: 0.8405 (tt0) REVERT: E 103 GLN cc_start: 0.8267 (tp40) cc_final: 0.7807 (tp40) REVERT: E 160 LYS cc_start: 0.7777 (ttpt) cc_final: 0.7416 (tmmt) REVERT: E 162 GLN cc_start: 0.7848 (pt0) cc_final: 0.7378 (pm20) REVERT: E 165 TYR cc_start: 0.5524 (t80) cc_final: 0.5237 (t80) REVERT: D 653 GLN cc_start: 0.7954 (tt0) cc_final: 0.7754 (tt0) REVERT: D 660 LEU cc_start: 0.7293 (tp) cc_final: 0.7029 (tt) outliers start: 34 outliers final: 30 residues processed: 376 average time/residue: 0.5221 time to fit residues: 291.6668 Evaluate side-chains 387 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 355 time to evaluate : 1.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 583 VAL Chi-restraints excluded: chain F residue 77 THR Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 128 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 198 THR Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 268 GLU Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 132 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 144 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.165157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.141849 restraints weight = 62078.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.147116 restraints weight = 26183.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.150346 restraints weight = 14630.493| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14423 Z= 0.114 Angle : 0.539 5.438 19714 Z= 0.270 Chirality : 0.043 0.317 2422 Planarity : 0.003 0.039 2403 Dihedral : 5.262 53.841 3011 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.41 % Allowed : 19.24 % Favored : 78.35 % 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: -0.24 (0.22), residues: 1479 helix: 1.49 (0.29), residues: 333 sheet: -0.30 (0.27), residues: 345 loop : -0.79 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 631 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE F 151 TYR 0.037 0.001 TYR D 643 ARG 0.004 0.000 ARG A 170 Details of bonding type rmsd link_NAG-ASN : bond 0.00236 ( 48) link_NAG-ASN : angle 1.74318 ( 144) link_BETA1-4 : bond 0.00283 ( 8) link_BETA1-4 : angle 1.05078 ( 24) hydrogen bonds : bond 0.03894 ( 438) hydrogen bonds : angle 4.70897 ( 1152) SS BOND : bond 0.00292 ( 31) SS BOND : angle 1.44015 ( 62) covalent geometry : bond 0.00264 (14336) covalent geometry : angle 0.51356 (19484) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2958 Ramachandran restraints generated. 1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Evaluate side-chains 401 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 368 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 530 MET cc_start: 0.7555 (mtp) cc_final: 0.7163 (mtp) REVERT: B 542 ARG cc_start: 0.8456 (ptt180) cc_final: 0.8087 (ttp80) REVERT: B 587 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8867 (mm) REVERT: B 588 ARG cc_start: 0.7464 (mtt180) cc_final: 0.6688 (tmm-80) REVERT: B 603 ILE cc_start: 0.8292 (pt) cc_final: 0.7917 (pt) REVERT: B 622 ILE cc_start: 0.8789 (mm) cc_final: 0.8374 (mm) REVERT: C 601 LYS cc_start: 0.7865 (mtpp) cc_final: 0.7490 (mtmt) REVERT: C 632 ASP cc_start: 0.9073 (t0) cc_final: 0.8702 (t0) REVERT: C 634 GLU cc_start: 0.8617 (tt0) cc_final: 0.8347 (tt0) REVERT: E 103 GLN cc_start: 0.8190 (tp40) cc_final: 0.7746 (tp40) REVERT: E 160 LYS cc_start: 0.7778 (ttpt) cc_final: 0.7493 (tmmt) REVERT: E 162 GLN cc_start: 0.7878 (pt0) cc_final: 0.7423 (pm20) REVERT: E 165 TYR cc_start: 0.5601 (t80) cc_final: 0.5268 (t80) REVERT: D 653 GLN cc_start: 0.7881 (tt0) cc_final: 0.7676 (tt0) REVERT: D 660 LEU cc_start: 0.7246 (tp) cc_final: 0.7001 (tt) outliers start: 33 outliers final: 28 residues processed: 384 average time/residue: 0.5127 time to fit residues: 294.1793 Evaluate side-chains 390 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 361 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 447 SER Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 632 ASP Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain C residue 540 GLN Chi-restraints excluded: chain C residue 593 LEU Chi-restraints excluded: chain C residue 623 TRP Chi-restraints excluded: chain C residue 625 ASN Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 142 MET Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 265 LEU Chi-restraints excluded: chain F residue 447 SER Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.164058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140919 restraints weight = 62396.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.146117 restraints weight = 26378.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149273 restraints weight = 14802.383| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.6063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14423 Z= 0.137 Angle : 0.551 5.990 19714 Z= 0.275 Chirality : 0.043 0.325 2422 Planarity : 0.003 0.056 2403 Dihedral : 5.319 51.993 3011 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.33 % Allowed : 19.24 % Favored : 78.43 % 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: -0.30 (0.22), residues: 1479 helix: 1.50 (0.29), residues: 334 sheet: -0.36 (0.27), residues: 339 loop : -0.85 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 631 HIS 0.006 0.001 HIS A 374 PHE 0.012 0.001 PHE F 151 TYR 0.031 0.001 TYR D 643 ARG 0.012 0.000 ARG F 327 Details of bonding type rmsd link_NAG-ASN : bond 0.00265 ( 48) link_NAG-ASN : angle 1.77595 ( 144) link_BETA1-4 : bond 0.00274 ( 8) link_BETA1-4 : angle 1.07864 ( 24) hydrogen bonds : bond 0.03914 ( 438) hydrogen bonds : angle 4.70031 ( 1152) SS BOND : bond 0.00303 ( 31) SS BOND : angle 1.44169 ( 62) covalent geometry : bond 0.00314 (14336) covalent geometry : angle 0.52526 (19484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8918.66 seconds wall clock time: 154 minutes 27.93 seconds (9267.93 seconds total)