Starting phenix.real_space_refine on Mon Jun 23 20:15:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2f_40982/06_2025/8t2f_40982_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2f_40982/06_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_40982/06_2025/8t2f_40982.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2f_40982/06_2025/8t2f_40982.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2f_40982/06_2025/8t2f_40982_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2f_40982/06_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-5710/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: 13.14, per 1000 atoms: 0.50 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: 7.21 Conformation dependent library (CDL) restraints added in 1.7 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: 2.23 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: 9.61 Time building geometry restraints manager: 8.65 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: 3.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.440 Extract box with map and model: 0.940 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 54.980 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.800 ------------------------------------------------------------------------------- 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 : 2.124 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: 0.5785 time to fit residues: 472.6425 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 : 2.106 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.151263 restraints weight = 60971.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.156888 restraints weight = 24719.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160289 restraints weight = 13411.609| |-----------------------------------------------------------------------------| 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 67.983 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 2.67526 ( 144) link_BETA1-4 : bond 0.00825 ( 8) link_BETA1-4 : angle 3.32056 ( 24) hydrogen bonds : bond 0.06520 ( 438) hydrogen bonds : angle 5.78478 ( 1152) SS BOND : bond 0.00470 ( 31) SS BOND : angle 1.38098 ( 62) covalent geometry : bond 0.00352 (14336) covalent geometry : angle 0.69239 (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 : 1.991 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: 0.7430 (ttt) REVERT: A 481 SER cc_start: 0.8205 (p) cc_final: 0.7946 (t) REVERT: B 588 ARG cc_start: 0.6880 (mtt180) cc_final: 0.6454 (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: 0.9181 (tp40) cc_final: 0.8894 (tp40) REVERT: C 632 ASP cc_start: 0.8999 (t0) cc_final: 0.8681 (t0) REVERT: E 45 TRP cc_start: 0.8676 (p90) cc_final: 0.8454 (p90) REVERT: E 160 LYS cc_start: 0.7365 (ttpt) cc_final: 0.7033 (tmmt) REVERT: E 173 VAL cc_start: 0.7694 (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: 0.7982 (m-30) cc_final: 0.7680 (m-30) REVERT: F 232 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7491 (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: 0.5429 time to fit residues: 366.0733 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 : 1.819 ------------------------------------------------------------------------------- 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: 0.5980 chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 146 optimal weight: 0.5980 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: 0.6980 chunk 127 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.170193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146911 restraints weight = 61896.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.152394 restraints weight = 25580.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.155675 restraints weight = 14065.566| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14423 Z= 0.161 Angle : 0.626 7.371 19714 Z= 0.319 Chirality : 0.045 0.366 2422 Planarity : 0.004 0.061 2403 Dihedral : 6.212 58.889 3013 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.55 % Allowed : 13.56 % Favored : 83.89 % 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: 0.45 (0.22), residues: 1479 helix: 1.31 (0.29), residues: 328 sheet: 0.41 (0.27), residues: 337 loop : -0.09 (0.22), residues: 814 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 0.019 0.002 PHE B 522 TYR 0.019 0.001 TYR D 643 ARG 0.007 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00411 ( 48) link_NAG-ASN : angle 2.03823 ( 144) link_BETA1-4 : bond 0.00628 ( 8) link_BETA1-4 : angle 2.17678 ( 24) hydrogen bonds : bond 0.05435 ( 438) hydrogen bonds : angle 5.25438 ( 1152) SS BOND : bond 0.00384 ( 31) SS BOND : angle 1.27079 ( 62) covalent geometry : bond 0.00349 (14336) covalent geometry : angle 0.59601 (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 446 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 411 time to evaluate : 1.874 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: A 143 ARG cc_start: 0.7105 (mmm160) cc_final: 0.5364 (tpt170) REVERT: A 335 LYS cc_start: 0.8185 (tttt) cc_final: 0.7679 (tptm) REVERT: A 481 SER cc_start: 0.8422 (p) cc_final: 0.8043 (t) REVERT: B 542 ARG cc_start: 0.8350 (ptt180) cc_final: 0.7963 (ttp80) REVERT: B 588 ARG cc_start: 0.7079 (mtt180) cc_final: 0.6527 (tmm-80) REVERT: B 603 ILE cc_start: 0.8332 (pt) cc_final: 0.7953 (pt) REVERT: B 635 ILE cc_start: 0.9045 (pt) cc_final: 0.8647 (mp) REVERT: C 542 ARG cc_start: 0.8017 (ttp80) cc_final: 0.7706 (ptt90) REVERT: C 632 ASP cc_start: 0.9007 (t0) cc_final: 0.8751 (t0) REVERT: C 634 GLU cc_start: 0.8608 (tt0) cc_final: 0.8129 (tt0) REVERT: E 45 TRP cc_start: 0.8678 (p90) cc_final: 0.8409 (p90) REVERT: E 103 GLN cc_start: 0.8502 (tp40) cc_final: 0.8082 (tp40) REVERT: E 147 LYS cc_start: 0.6333 (mmtt) cc_final: 0.6113 (mmmt) REVERT: E 160 LYS cc_start: 0.7528 (ttpt) cc_final: 0.7091 (tmmt) REVERT: E 173 VAL cc_start: 0.7771 (t) cc_final: 0.7467 (t) REVERT: D 660 LEU cc_start: 0.7469 (tp) cc_final: 0.7192 (tt) REVERT: F 129 LEU cc_start: 0.8251 (tp) cc_final: 0.7766 (tt) REVERT: F 172 ASP cc_start: 0.7976 (m-30) cc_final: 0.7724 (m-30) REVERT: F 327 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7635 (mtp85) outliers start: 35 outliers final: 33 residues processed: 424 average time/residue: 0.5220 time to fit residues: 324.0516 Evaluate side-chains 424 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 391 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU 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 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 271 ILE 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 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: 1.9990 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 168 optimal weight: 10.0000 chunk 146 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 159 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 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 = 0.3849 r_free = 0.3849 target = 0.166761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.143221 restraints weight = 62413.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.148559 restraints weight = 26105.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.151829 restraints weight = 14591.032| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.4732 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 : 0.621 6.830 19714 Z= 0.314 Chirality : 0.045 0.360 2422 Planarity : 0.004 0.042 2403 Dihedral : 5.898 59.059 3013 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.99 % Allowed : 14.43 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.29), residues: 333 sheet: 0.23 (0.27), residues: 360 loop : -0.28 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 623 HIS 0.006 0.001 HIS F 352 PHE 0.017 0.001 PHE F 151 TYR 0.012 0.001 TYR C 638 ARG 0.005 0.001 ARG A 308 Details of bonding type rmsd link_NAG-ASN : bond 0.00327 ( 48) link_NAG-ASN : angle 2.07917 ( 144) link_BETA1-4 : bond 0.00423 ( 8) link_BETA1-4 : angle 1.78867 ( 24) hydrogen bonds : bond 0.04973 ( 438) hydrogen bonds : angle 5.19964 ( 1152) SS BOND : bond 0.00409 ( 31) SS BOND : angle 1.24531 ( 62) covalent geometry : bond 0.00429 (14336) covalent geometry : angle 0.59102 (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 435 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 394 time to evaluate : 1.834 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: A 37 THR cc_start: 0.9256 (m) cc_final: 0.9048 (p) REVERT: A 335 LYS cc_start: 0.8214 (tttt) cc_final: 0.7699 (tptm) REVERT: A 481 SER cc_start: 0.8422 (p) cc_final: 0.7957 (t) REVERT: B 530 MET cc_start: 0.7302 (mtp) cc_final: 0.6961 (mtp) REVERT: B 542 ARG cc_start: 0.8253 (ptt180) cc_final: 0.7961 (ttp80) REVERT: B 587 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9156 (mm) REVERT: B 588 ARG cc_start: 0.7153 (mtt180) cc_final: 0.6640 (tmm-80) REVERT: B 603 ILE cc_start: 0.8334 (pt) cc_final: 0.8057 (pt) REVERT: C 632 ASP cc_start: 0.8932 (t0) cc_final: 0.8650 (t0) REVERT: E 103 GLN cc_start: 0.8483 (tp40) cc_final: 0.8098 (tp40) REVERT: E 147 LYS cc_start: 0.6410 (mmtt) cc_final: 0.6181 (mmmt) REVERT: E 148 ASN cc_start: 0.6558 (m110) cc_final: 0.6297 (m-40) REVERT: E 160 LYS cc_start: 0.7638 (ttpt) cc_final: 0.7261 (tmmt) REVERT: E 165 TYR cc_start: 0.5560 (t80) cc_final: 0.4871 (t80) REVERT: E 173 VAL cc_start: 0.7825 (t) cc_final: 0.7488 (t) REVERT: D 591 GLN cc_start: 0.8588 (tt0) cc_final: 0.8345 (tt0) REVERT: D 660 LEU cc_start: 0.7649 (tp) cc_final: 0.7294 (tt) REVERT: F 87 GLU cc_start: 0.8267 (mp0) cc_final: 0.7896 (mp0) REVERT: F 114 GLN cc_start: 0.8473 (tp40) cc_final: 0.8211 (tp40) outliers start: 41 outliers final: 38 residues processed: 411 average time/residue: 0.5080 time to fit residues: 305.1353 Evaluate side-chains 420 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 381 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 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 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 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 284 ILE Chi-restraints excluded: chain E residue 307 ILE Chi-restraints excluded: chain E residue 339 ASN Chi-restraints excluded: chain D residue 581 LEU 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 Chi-restraints excluded: chain F residue 491 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 77 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 chunk 139 optimal weight: 0.0170 chunk 98 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 overall best weight: 1.1422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.143382 restraints weight = 62234.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.148712 restraints weight = 25748.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.151969 restraints weight = 14217.958| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14423 Z= 0.138 Angle : 0.564 6.987 19714 Z= 0.285 Chirality : 0.043 0.334 2422 Planarity : 0.003 0.042 2403 Dihedral : 5.438 51.412 3011 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.48 % Allowed : 15.45 % Favored : 82.07 % 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: 0.19 (0.22), residues: 1479 helix: 1.39 (0.29), residues: 332 sheet: 0.26 (0.27), residues: 350 loop : -0.44 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 623 HIS 0.005 0.001 HIS A 374 PHE 0.019 0.001 PHE A 376 TYR 0.010 0.001 TYR C 638 ARG 0.004 0.000 ARG B 617 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 48) link_NAG-ASN : angle 1.87705 ( 144) link_BETA1-4 : bond 0.00342 ( 8) link_BETA1-4 : angle 1.31101 ( 24) hydrogen bonds : bond 0.04432 ( 438) hydrogen bonds : angle 4.92799 ( 1152) SS BOND : bond 0.00402 ( 31) SS BOND : angle 1.27176 ( 62) covalent geometry : bond 0.00306 (14336) covalent geometry : angle 0.53674 (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 437 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 403 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 TRP cc_start: 0.7623 (m-90) cc_final: 0.7382 (m-10) REVERT: A 153 MET cc_start: 0.8666 (ppp) cc_final: 0.8368 (ppp) REVERT: A 435 TYR cc_start: 0.8991 (t80) cc_final: 0.8768 (t80) REVERT: A 481 SER cc_start: 0.8442 (p) cc_final: 0.7976 (t) REVERT: B 530 MET cc_start: 0.7278 (mtp) cc_final: 0.6638 (mtp) REVERT: B 542 ARG cc_start: 0.8395 (ptt180) cc_final: 0.7995 (ttp80) REVERT: B 588 ARG cc_start: 0.7078 (mtt180) cc_final: 0.6496 (tmm-80) REVERT: B 603 ILE cc_start: 0.8389 (pt) cc_final: 0.7991 (pt) REVERT: C 591 GLN cc_start: 0.8812 (tt0) cc_final: 0.8017 (tt0) REVERT: C 632 ASP cc_start: 0.9081 (t0) cc_final: 0.8765 (t0) REVERT: C 634 GLU cc_start: 0.8676 (tt0) cc_final: 0.8455 (tt0) REVERT: E 103 GLN cc_start: 0.8234 (tp40) cc_final: 0.7802 (tp40) REVERT: E 148 ASN cc_start: 0.6458 (m110) cc_final: 0.6217 (m-40) REVERT: E 160 LYS cc_start: 0.7723 (ttpt) cc_final: 0.7377 (tmmt) REVERT: E 165 TYR cc_start: 0.5513 (t80) cc_final: 0.4946 (t80) REVERT: E 173 VAL cc_start: 0.7794 (t) cc_final: 0.7489 (t) REVERT: D 643 TYR cc_start: 0.8822 (m-10) cc_final: 0.8499 (m-10) REVERT: D 660 LEU cc_start: 0.7368 (tp) cc_final: 0.7053 (tt) REVERT: F 87 GLU cc_start: 0.8228 (mp0) cc_final: 0.7835 (mp0) REVERT: F 95 MET cc_start: 0.8426 (ppp) cc_final: 0.8089 (ptt) REVERT: F 327 ARG cc_start: 0.7901 (mmm-85) cc_final: 0.7581 (mtp85) outliers start: 34 outliers final: 30 residues processed: 418 average time/residue: 0.5078 time to fit residues: 313.9503 Evaluate side-chains 421 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 391 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 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 364 SER 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 116 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 581 LEU 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 125 LEU Chi-restraints excluded: chain F residue 141 ASP Chi-restraints excluded: chain F residue 172 ASP Chi-restraints excluded: chain F residue 264 SER Chi-restraints excluded: chain F residue 265 LEU 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: 0.7980 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 76 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.164932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.141473 restraints weight = 62665.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.146729 restraints weight = 26323.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.149951 restraints weight = 14694.967| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14423 Z= 0.159 Angle : 0.570 5.851 19714 Z= 0.286 Chirality : 0.043 0.336 2422 Planarity : 0.003 0.039 2403 Dihedral : 5.514 53.793 3011 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.77 % Allowed : 16.03 % Favored : 81.20 % 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: 0.00 (0.21), residues: 1479 helix: 1.41 (0.29), residues: 332 sheet: 0.05 (0.26), residues: 354 loop : -0.59 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 623 HIS 0.005 0.001 HIS A 374 PHE 0.015 0.001 PHE F 151 TYR 0.022 0.001 TYR F 486 ARG 0.003 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00292 ( 48) link_NAG-ASN : angle 1.90079 ( 144) link_BETA1-4 : bond 0.00296 ( 8) link_BETA1-4 : angle 1.19382 ( 24) hydrogen bonds : bond 0.04372 ( 438) hydrogen bonds : angle 4.89035 ( 1152) SS BOND : bond 0.00336 ( 31) SS BOND : angle 1.41038 ( 62) covalent geometry : bond 0.00355 (14336) covalent geometry : angle 0.54219 (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 435 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 2.252 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 153 MET cc_start: 0.8670 (ppp) cc_final: 0.8310 (ppp) REVERT: A 435 TYR cc_start: 0.9008 (t80) cc_final: 0.8775 (t80) REVERT: A 481 SER cc_start: 0.8470 (p) cc_final: 0.7954 (t) REVERT: B 530 MET cc_start: 0.7355 (mtp) cc_final: 0.6703 (mtp) REVERT: B 542 ARG cc_start: 0.8406 (ptt180) cc_final: 0.8022 (ttp80) REVERT: B 587 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9045 (mm) REVERT: B 588 ARG cc_start: 0.7180 (mtt180) cc_final: 0.6557 (tmm-80) REVERT: B 603 ILE cc_start: 0.8392 (pt) cc_final: 0.8011 (pt) REVERT: C 596 TRP cc_start: 0.7783 (m-10) cc_final: 0.7546 (m-10) REVERT: C 632 ASP cc_start: 0.9065 (t0) cc_final: 0.8745 (t0) REVERT: E 45 TRP cc_start: 0.8818 (p90) cc_final: 0.8613 (p90) REVERT: E 92 GLU cc_start: 0.6380 (tm-30) cc_final: 0.6168 (tm-30) REVERT: E 103 GLN cc_start: 0.8231 (tp40) cc_final: 0.7803 (tp40) REVERT: E 148 ASN cc_start: 0.6505 (m110) cc_final: 0.6208 (m-40) REVERT: E 160 LYS cc_start: 0.7762 (ttpt) cc_final: 0.7412 (tmmt) REVERT: E 162 GLN cc_start: 0.7742 (pt0) cc_final: 0.7347 (pm20) REVERT: E 165 TYR cc_start: 0.5487 (t80) cc_final: 0.4535 (t80) REVERT: E 486 TYR cc_start: 0.8581 (m-80) cc_final: 0.8330 (m-80) REVERT: D 643 TYR cc_start: 0.8825 (m-10) cc_final: 0.8597 (m-10) REVERT: D 660 LEU cc_start: 0.7441 (tp) cc_final: 0.7138 (tt) REVERT: F 87 GLU cc_start: 0.8242 (mp0) cc_final: 0.7867 (mp0) outliers start: 38 outliers final: 34 residues processed: 410 average time/residue: 0.5078 time to fit residues: 309.4307 Evaluate side-chains 417 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 382 time to evaluate : 2.059 ------------------------------------------------------------------------------- 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 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 364 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 167 LEU Chi-restraints excluded: chain E residue 196 CYS Chi-restraints excluded: chain E residue 254 VAL 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 581 LEU 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 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 447 SER Chi-restraints excluded: chain F residue 484 TYR Chi-restraints excluded: chain F residue 491 ILE 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: 3.9990 chunk 150 optimal weight: 0.4980 chunk 86 optimal weight: 0.1980 chunk 146 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 61 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.167238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.143961 restraints weight = 62010.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.149281 restraints weight = 25903.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.152554 restraints weight = 14387.272| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.5417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14423 Z= 0.101 Angle : 0.527 5.652 19714 Z= 0.265 Chirality : 0.043 0.316 2422 Planarity : 0.003 0.053 2403 Dihedral : 5.122 53.614 3011 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.33 % Allowed : 17.93 % Favored : 79.74 % 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 (0.22), residues: 1479 helix: 1.60 (0.29), residues: 332 sheet: 0.06 (0.26), residues: 355 loop : -0.54 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 623 HIS 0.004 0.001 HIS A 249 PHE 0.016 0.001 PHE F 151 TYR 0.009 0.001 TYR D 643 ARG 0.007 0.000 ARG F 143 Details of bonding type rmsd link_NAG-ASN : bond 0.00261 ( 48) link_NAG-ASN : angle 1.73665 ( 144) link_BETA1-4 : bond 0.00346 ( 8) link_BETA1-4 : angle 1.09711 ( 24) hydrogen bonds : bond 0.03988 ( 438) hydrogen bonds : angle 4.70951 ( 1152) SS BOND : bond 0.00286 ( 31) SS BOND : angle 1.22352 ( 62) covalent geometry : bond 0.00229 (14336) covalent geometry : angle 0.50257 (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 417 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 385 time to evaluate : 1.942 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 435 TYR cc_start: 0.8971 (t80) cc_final: 0.8756 (t80) REVERT: A 481 SER cc_start: 0.8394 (p) cc_final: 0.7852 (t) REVERT: B 530 MET cc_start: 0.6948 (mtp) cc_final: 0.6321 (mtp) REVERT: B 542 ARG cc_start: 0.8412 (ptt180) cc_final: 0.8036 (ttp80) REVERT: B 587 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8977 (mm) REVERT: B 588 ARG cc_start: 0.7175 (mtt180) cc_final: 0.6562 (tmm-80) REVERT: B 603 ILE cc_start: 0.8376 (pt) cc_final: 0.7996 (pt) REVERT: C 596 TRP cc_start: 0.7711 (m-10) cc_final: 0.7489 (m-10) REVERT: C 632 ASP cc_start: 0.9003 (t0) cc_final: 0.8708 (t0) REVERT: E 45 TRP cc_start: 0.8839 (p90) cc_final: 0.8513 (p90) REVERT: E 103 GLN cc_start: 0.8187 (tp40) cc_final: 0.7706 (tp40) REVERT: E 160 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7416 (tmmt) REVERT: E 162 GLN cc_start: 0.7751 (pt0) cc_final: 0.7349 (pm20) REVERT: E 165 TYR cc_start: 0.5303 (t80) cc_final: 0.4826 (t80) REVERT: E 486 TYR cc_start: 0.8668 (m-80) cc_final: 0.8369 (m-80) REVERT: D 660 LEU cc_start: 0.7279 (tp) cc_final: 0.6986 (tt) REVERT: F 469 ARG cc_start: 0.8425 (mtp85) cc_final: 0.7835 (mmm-85) outliers start: 32 outliers final: 28 residues processed: 399 average time/residue: 0.5143 time to fit residues: 305.2545 Evaluate side-chains 404 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 375 time to evaluate : 1.879 ------------------------------------------------------------------------------- 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 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 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 583 VAL 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 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 447 SER 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: 3.9990 chunk 134 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 130 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.164543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.141109 restraints weight = 62792.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.146384 restraints weight = 26490.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.149595 restraints weight = 14802.523| |-----------------------------------------------------------------------------| r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14423 Z= 0.157 Angle : 0.562 5.681 19714 Z= 0.281 Chirality : 0.043 0.329 2422 Planarity : 0.003 0.040 2403 Dihedral : 5.331 52.708 3011 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.55 % Allowed : 17.64 % Favored : 79.81 % 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: -0.06 (0.21), residues: 1479 helix: 1.61 (0.29), residues: 326 sheet: -0.08 (0.26), residues: 355 loop : -0.69 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 628 HIS 0.005 0.001 HIS A 374 PHE 0.014 0.001 PHE F 151 TYR 0.040 0.001 TYR D 643 ARG 0.005 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 48) link_NAG-ASN : angle 1.81780 ( 144) link_BETA1-4 : bond 0.00280 ( 8) link_BETA1-4 : angle 1.12353 ( 24) hydrogen bonds : bond 0.04141 ( 438) hydrogen bonds : angle 4.79142 ( 1152) SS BOND : bond 0.00348 ( 31) SS BOND : angle 1.30166 ( 62) covalent geometry : bond 0.00359 (14336) covalent geometry : angle 0.53680 (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 420 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 385 time to evaluate : 1.978 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 153 MET cc_start: 0.8596 (ppp) cc_final: 0.8321 (ppp) REVERT: A 435 TYR cc_start: 0.8981 (t80) cc_final: 0.8744 (t80) REVERT: A 481 SER cc_start: 0.8496 (p) cc_final: 0.7940 (t) REVERT: B 530 MET cc_start: 0.7218 (mtp) cc_final: 0.6875 (mtp) REVERT: B 542 ARG cc_start: 0.8440 (ptt180) cc_final: 0.8084 (ttp80) REVERT: B 587 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9015 (mm) REVERT: B 588 ARG cc_start: 0.7258 (mtt180) cc_final: 0.6615 (tmm-80) REVERT: B 603 ILE cc_start: 0.8390 (pt) cc_final: 0.8032 (pt) REVERT: B 635 ILE cc_start: 0.9104 (pt) cc_final: 0.8834 (tt) REVERT: C 596 TRP cc_start: 0.7731 (m-10) cc_final: 0.7516 (m-10) REVERT: C 632 ASP cc_start: 0.9065 (t0) cc_final: 0.8729 (t0) REVERT: C 634 GLU cc_start: 0.8674 (tt0) cc_final: 0.8422 (tt0) REVERT: E 103 GLN cc_start: 0.8216 (tp40) cc_final: 0.7746 (tp40) REVERT: E 148 ASN cc_start: 0.6467 (m110) cc_final: 0.6172 (m-40) REVERT: E 160 LYS cc_start: 0.7712 (ttpt) cc_final: 0.7343 (tmmt) REVERT: E 162 GLN cc_start: 0.7776 (pt0) cc_final: 0.7353 (pm20) REVERT: E 165 TYR cc_start: 0.5303 (t80) cc_final: 0.4868 (t80) REVERT: D 660 LEU cc_start: 0.7255 (tp) cc_final: 0.6960 (tt) outliers start: 35 outliers final: 31 residues processed: 402 average time/residue: 0.4996 time to fit residues: 299.1503 Evaluate side-chains 404 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 372 time to evaluate : 1.993 ------------------------------------------------------------------------------- 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 499 THR 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 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 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 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 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: 0.3980 chunk 69 optimal weight: 0.8980 chunk 160 optimal weight: 9.9990 chunk 161 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 112 optimal weight: 0.9980 chunk 159 optimal weight: 9.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.164924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.141675 restraints weight = 62364.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.146948 restraints weight = 26121.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.150117 restraints weight = 14504.263| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14423 Z= 0.125 Angle : 0.542 5.425 19714 Z= 0.271 Chirality : 0.043 0.322 2422 Planarity : 0.003 0.040 2403 Dihedral : 5.238 53.963 3011 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.33 % Allowed : 18.08 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.10 (0.21), residues: 1479 helix: 1.50 (0.29), residues: 334 sheet: -0.13 (0.26), residues: 355 loop : -0.69 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 338 HIS 0.004 0.001 HIS A 374 PHE 0.014 0.001 PHE F 151 TYR 0.032 0.001 TYR D 643 ARG 0.007 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 48) link_NAG-ASN : angle 1.77686 ( 144) link_BETA1-4 : bond 0.00316 ( 8) link_BETA1-4 : angle 1.07512 ( 24) hydrogen bonds : bond 0.03944 ( 438) hydrogen bonds : angle 4.71341 ( 1152) SS BOND : bond 0.00313 ( 31) SS BOND : angle 1.40756 ( 62) covalent geometry : bond 0.00283 (14336) covalent geometry : angle 0.51558 (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 417 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 385 time to evaluate : 2.310 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 153 MET cc_start: 0.8589 (ppp) cc_final: 0.8296 (ppp) REVERT: A 435 TYR cc_start: 0.8968 (t80) cc_final: 0.8746 (t80) REVERT: B 530 MET cc_start: 0.7228 (mtp) cc_final: 0.6903 (mtp) REVERT: B 542 ARG cc_start: 0.8459 (ptt180) cc_final: 0.8092 (ttp80) REVERT: B 587 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8933 (mm) REVERT: B 588 ARG cc_start: 0.7256 (mtt180) cc_final: 0.6616 (tmm-80) REVERT: B 603 ILE cc_start: 0.8275 (pt) cc_final: 0.7915 (pt) REVERT: B 635 ILE cc_start: 0.9080 (pt) cc_final: 0.8860 (tt) REVERT: C 596 TRP cc_start: 0.7684 (m-10) cc_final: 0.7473 (m-10) REVERT: C 601 LYS cc_start: 0.7916 (mtpp) cc_final: 0.7512 (mtmt) REVERT: C 632 ASP cc_start: 0.9055 (t0) cc_final: 0.8740 (t0) REVERT: C 634 GLU cc_start: 0.8629 (tt0) cc_final: 0.8367 (tt0) REVERT: E 92 GLU cc_start: 0.6509 (tm-30) cc_final: 0.6248 (tm-30) REVERT: E 103 GLN cc_start: 0.8224 (tp40) cc_final: 0.7764 (tp40) REVERT: E 148 ASN cc_start: 0.6413 (m110) cc_final: 0.6118 (m-40) REVERT: E 160 LYS cc_start: 0.7751 (ttpt) cc_final: 0.7390 (tmmt) REVERT: E 162 GLN cc_start: 0.7771 (pt0) cc_final: 0.7330 (pm20) REVERT: E 165 TYR cc_start: 0.5192 (t80) cc_final: 0.4828 (t80) REVERT: D 660 LEU cc_start: 0.7261 (tp) cc_final: 0.6991 (tt) REVERT: F 129 LEU cc_start: 0.8339 (tp) cc_final: 0.7926 (tt) outliers start: 32 outliers final: 29 residues processed: 400 average time/residue: 0.6092 time to fit residues: 370.9181 Evaluate side-chains 412 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 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 167 LEU Chi-restraints excluded: chain E residue 196 CYS 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 583 VAL 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 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 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: 0.7980 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.166072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.142883 restraints weight = 62102.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.148193 restraints weight = 25949.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.151403 restraints weight = 14381.767| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.5839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 14423 Z= 0.104 Angle : 0.523 5.430 19714 Z= 0.263 Chirality : 0.042 0.311 2422 Planarity : 0.003 0.040 2403 Dihedral : 4.987 52.192 3011 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.19 % Allowed : 18.22 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1479 helix: 1.64 (0.29), residues: 334 sheet: -0.15 (0.26), residues: 359 loop : -0.66 (0.22), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 69 HIS 0.004 0.001 HIS A 249 PHE 0.015 0.001 PHE F 151 TYR 0.036 0.001 TYR D 643 ARG 0.006 0.000 ARG C 542 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 48) link_NAG-ASN : angle 1.69218 ( 144) link_BETA1-4 : bond 0.00312 ( 8) link_BETA1-4 : angle 1.06329 ( 24) hydrogen bonds : bond 0.03794 ( 438) hydrogen bonds : angle 4.59675 ( 1152) SS BOND : bond 0.00294 ( 31) SS BOND : angle 1.40201 ( 62) covalent geometry : bond 0.00237 (14336) covalent geometry : angle 0.49847 (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 412 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 382 time to evaluate : 4.275 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: A 153 MET cc_start: 0.8576 (ppp) cc_final: 0.8275 (ppp) REVERT: A 435 TYR cc_start: 0.8980 (t80) cc_final: 0.8758 (t80) REVERT: B 530 MET cc_start: 0.7135 (mtp) cc_final: 0.6690 (mtp) REVERT: B 542 ARG cc_start: 0.8452 (ptt180) cc_final: 0.8089 (ttp80) REVERT: B 587 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8866 (mm) REVERT: B 588 ARG cc_start: 0.7335 (mtt180) cc_final: 0.6652 (tmm-80) REVERT: B 603 ILE cc_start: 0.8298 (pt) cc_final: 0.7920 (pt) REVERT: B 635 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8894 (tt) REVERT: C 601 LYS cc_start: 0.7869 (mtpp) cc_final: 0.7493 (mtmt) REVERT: C 632 ASP cc_start: 0.9021 (t0) cc_final: 0.8713 (t0) REVERT: C 634 GLU cc_start: 0.8619 (tt0) cc_final: 0.8360 (tt0) REVERT: E 92 GLU cc_start: 0.6513 (tm-30) cc_final: 0.6256 (tm-30) REVERT: E 103 GLN cc_start: 0.8185 (tp40) cc_final: 0.7738 (tp40) REVERT: E 148 ASN cc_start: 0.6295 (m110) cc_final: 0.6009 (m-40) REVERT: E 160 LYS cc_start: 0.7748 (ttpt) cc_final: 0.7385 (tmmt) REVERT: E 162 GLN cc_start: 0.7770 (pt0) cc_final: 0.7372 (pm20) REVERT: E 165 TYR cc_start: 0.5280 (t80) cc_final: 0.4950 (t80) REVERT: D 660 LEU cc_start: 0.7134 (tp) cc_final: 0.6872 (tt) outliers start: 30 outliers final: 28 residues processed: 394 average time/residue: 0.7592 time to fit residues: 458.9913 Evaluate side-chains 406 residues out of total 1374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 376 time to evaluate : 3.216 ------------------------------------------------------------------------------- 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 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 167 LEU Chi-restraints excluded: chain E residue 191 TYR 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 D residue 646 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 123 THR 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 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: 2.9990 chunk 79 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 145 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3853 r_free = 0.3853 target = 0.166960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.143739 restraints weight = 61982.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.149052 restraints weight = 25885.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152289 restraints weight = 14361.230| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.5919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14423 Z= 0.101 Angle : 0.519 6.077 19714 Z= 0.261 Chirality : 0.042 0.304 2422 Planarity : 0.003 0.040 2403 Dihedral : 4.833 51.061 3011 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.26 % Allowed : 18.37 % Favored : 79.37 % 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: -0.02 (0.22), residues: 1479 helix: 1.63 (0.30), residues: 334 sheet: -0.12 (0.26), residues: 357 loop : -0.65 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 69 HIS 0.004 0.001 HIS A 249 PHE 0.015 0.001 PHE F 151 TYR 0.028 0.001 TYR D 643 ARG 0.010 0.001 ARG C 579 Details of bonding type rmsd link_NAG-ASN : bond 0.00237 ( 48) link_NAG-ASN : angle 1.65183 ( 144) link_BETA1-4 : bond 0.00321 ( 8) link_BETA1-4 : angle 1.06185 ( 24) hydrogen bonds : bond 0.03684 ( 438) hydrogen bonds : angle 4.54586 ( 1152) SS BOND : bond 0.00288 ( 31) SS BOND : angle 1.39791 ( 62) covalent geometry : bond 0.00231 (14336) covalent geometry : angle 0.49423 (19484) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9977.27 seconds wall clock time: 175 minutes 42.81 seconds (10542.81 seconds total)