Starting phenix.real_space_refine on Sat Aug 23 22:08:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.map" model { file = "/net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t2e_40981/08_2025/8t2e_40981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9386 2.51 5 N 2574 2.21 5 O 2959 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15021 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3392 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 20, 'TRANS': 406} Chain breaks: 5 Chain: "B" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1009 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "E" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3333 Classifications: {'peptide': 420} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 401} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 946 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "F" Number of atoms: 3344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3344 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 7 Chain: "H" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 650 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'TRANS': 129} Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 390 Unresolved non-hydrogen dihedrals: 130 Planarities with less than four sites: {'UNK:plan-1': 130} Unresolved non-hydrogen planarities: 130 Chain: "L" Number of atoms: 500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 500 Classifications: {'peptide': 100} Incomplete info: {'truncation_to_alanine': 100} Link IDs: {'TRANS': 99} Unresolved non-hydrogen bonds: 200 Unresolved non-hydrogen angles: 300 Unresolved non-hydrogen dihedrals: 100 Planarities with less than four sites: {'UNK:plan-1': 100} Unresolved non-hydrogen planarities: 100 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: 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" 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: "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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 3.81, per 1000 atoms: 0.25 Number of scatterers: 15021 At special positions: 0 Unit cell: (132.999, 132.999, 117.534, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2959 8.00 N 2574 7.00 C 9386 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.02 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.10 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.09 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.23 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=2.03 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 C 605 " - pdb=" SG CYS E 501 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.09 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.05 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " 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=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 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=2.01 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS F 501 " distance=2.02 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 73 " distance=2.02 Simple disulfide: pdb=" SG CYS F 119 " - pdb=" SG CYS F 205 " distance=2.06 Simple disulfide: pdb=" SG CYS F 126 " - pdb=" SG CYS F 196 " distance=2.10 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 157 " distance=2.02 Simple disulfide: pdb=" SG CYS F 218 " - pdb=" SG CYS F 247 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS F 385 " - pdb=" SG CYS F 418 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A 601 " - " ASN A 133 " " NAG A 602 " - " ASN A 160 " " 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 289 " " NAG A 608 " - " ASN A 301 " " NAG A 609 " - " ASN A 332 " " NAG A 610 " - " ASN A 355 " " NAG A 611 " - " ASN A 363 " " NAG A 612 " - " ASN A 386 " " NAG A 613 " - " ASN A 448 " " NAG A 614 " - " ASN A 392 " " NAG A 615 " - " ASN A 295 " " NAG B 701 " - " ASN B 611 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 637 " " NAG C 701 " - " ASN C 611 " " NAG C 702 " - " ASN C 637 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 637 " " NAG E 601 " - " ASN E 88 " " NAG E 602 " - " ASN E 160 " " NAG E 603 " - " ASN E 197 " " NAG E 604 " - " ASN E 234 " " NAG E 605 " - " ASN E 241 " " NAG E 606 " - " ASN E 276 " " NAG E 607 " - " ASN E 301 " " NAG E 608 " - " ASN E 332 " " NAG E 609 " - " ASN E 339 " " NAG E 610 " - " ASN E 448 " " NAG E 611 " - " ASN E 295 " " NAG E 612 " - " ASN E 386 " " NAG F 601 " - " ASN F 88 " " NAG F 602 " - " ASN F 160 " " NAG F 603 " - " ASN F 156 " " NAG F 604 " - " ASN F 234 " " NAG F 605 " - " ASN F 241 " " NAG F 606 " - " ASN F 276 " " NAG F 607 " - " ASN F 289 " " NAG F 608 " - " ASN F 295 " " NAG F 609 " - " ASN F 301 " " NAG F 610 " - " ASN F 332 " " NAG F 611 " - " ASN F 339 " " NAG F 612 " - " ASN F 355 " " NAG F 613 " - " ASN F 363 " " NAG F 614 " - " ASN F 386 " " NAG F 615 " - " ASN F 448 " " NAG G 1 " - " ASN A 88 " " NAG I 1 " - " ASN A 156 " " NAG J 1 " - " ASN A 262 " " NAG K 1 " - " ASN E 156 " " NAG M 1 " - " ASN E 262 " " NAG N 1 " - " ASN F 262 " Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 432.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3532 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 27 sheets defined 26.7% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 98 through 115 removed outlier: 4.043A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.669A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 541 Processing helix chain 'B' and resid 572 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 662 Processing helix chain 'C' and resid 522 through 528 removed outlier: 4.480A pdb=" N ALA C 525 " --> pdb=" O PHE C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 534 Processing helix chain 'C' and resid 537 through 542 Processing helix chain 'C' and resid 572 through 596 Processing helix chain 'C' and resid 618 through 623 Processing helix chain 'C' and resid 627 through 635 Processing helix chain 'C' and resid 638 through 662 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 116 removed outlier: 3.921A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ILE E 109 " --> pdb=" O HIS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 351 removed outlier: 4.206A pdb=" N LYS E 351 " --> pdb=" O LYS E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 484 removed outlier: 4.604A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.212A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 535 through 537 No H-bonds generated for 'chain 'D' and resid 535 through 537' Processing helix chain 'D' and resid 573 through 596 Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'F' and resid 67 through 73 Processing helix chain 'F' and resid 99 through 117 Processing helix chain 'F' and resid 122 through 126 Processing helix chain 'F' and resid 335 through 354 removed outlier: 4.026A pdb=" N HIS F 352 " --> pdb=" O GLN F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 390 Processing helix chain 'F' and resid 475 through 484 removed outlier: 4.008A pdb=" N SER F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU F 482 " --> pdb=" O ASN F 478 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 5.366A pdb=" N UNK H 66 " --> pdb=" O UNK H 63 " (cutoff:3.500A) 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 91 through 93 No H-bonds generated for 'chain 'L' and resid 91 through 93' Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.351A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.861A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.672A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 93 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.144A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.564A 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 284 through 302 removed outlier: 6.688A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 329 through 334 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 466 through 469 Processing sheet with id=AA8, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.458A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 603 through 609 removed outlier: 8.117A pdb=" N CYS C 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR E 40 " --> pdb=" O CYS C 604 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N THR C 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL E 38 " --> pdb=" O THR C 606 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL C 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB3, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'E' and resid 201 through 203 removed outlier: 6.639A 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 312 removed outlier: 6.933A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 removed outlier: 4.396A pdb=" N PHE E 382 " --> pdb=" O LYS E 421 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 413 through 421 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'D' and resid 603 through 609 removed outlier: 8.262A pdb=" N CYS D 604 " --> pdb=" O TYR F 40 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N TYR F 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N THR D 606 " --> pdb=" O VAL F 38 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL F 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N VAL D 608 " --> pdb=" O VAL F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 45 through 47 Processing sheet with id=AB9, first strand: chain 'F' and resid 75 through 76 removed outlier: 3.558A pdb=" N VAL F 75 " --> pdb=" O CYS F 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 91 through 94 Processing sheet with id=AC2, first strand: chain 'F' and resid 169 through 177 Processing sheet with id=AC3, first strand: chain 'F' and resid 201 through 203 removed outlier: 6.495A pdb=" N THR F 202 " --> pdb=" O TYR F 435 " (cutoff:3.500A) Processing sheet with id=AC4, 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 283 through 302 removed outlier: 6.738A pdb=" N GLN F 293 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER F 334 " --> pdb=" O GLN F 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 329 through 334 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=AC5, first strand: chain 'F' and resid 304 through 312 removed outlier: 6.570A pdb=" N GLN F 315 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'H' and resid 34 through 41 removed outlier: 5.995A pdb=" N UNK H 39 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N UNK H 47 " --> pdb=" O UNK H 39 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N UNK H 41 " --> pdb=" O UNK H 45 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N UNK H 45 " --> pdb=" O UNK H 41 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 58 through 60 current: chain 'H' and resid 117 through 120 Processing sheet with id=AC8, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AC9, first strand: chain 'L' and resid 32 through 36 removed outlier: 6.778A pdb=" N UNK L 33 " --> pdb=" O UNK L 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 51 through 52 current: chain 'L' and resid 94 through 97 476 hydrogen bonds defined for protein. 1308 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.14 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4294 1.33 - 1.48: 4621 1.48 - 1.63: 6211 1.63 - 1.78: 52 1.78 - 1.93: 91 Bond restraints: 15269 Sorted by residual: bond pdb=" CD2 TRP D 571 " pdb=" CE3 TRP D 571 " ideal model delta sigma weight residual 1.398 1.509 -0.111 1.60e-02 3.91e+03 4.84e+01 bond pdb=" NE ARG A 504 " pdb=" CZ ARG A 504 " ideal model delta sigma weight residual 1.326 1.402 -0.076 1.10e-02 8.26e+03 4.79e+01 bond pdb=" NE ARG E 504 " pdb=" CZ ARG E 504 " ideal model delta sigma weight residual 1.326 1.400 -0.074 1.10e-02 8.26e+03 4.49e+01 bond pdb=" CB ILE F 184 " pdb=" CG1 ILE F 184 " ideal model delta sigma weight residual 1.530 1.663 -0.133 2.00e-02 2.50e+03 4.40e+01 bond pdb=" NE ARG F 456 " pdb=" CZ ARG F 456 " ideal model delta sigma weight residual 1.326 1.396 -0.070 1.10e-02 8.26e+03 4.06e+01 ... (remaining 15264 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 18601 2.66 - 5.32: 1946 5.32 - 7.98: 192 7.98 - 10.64: 9 10.64 - 13.30: 2 Bond angle restraints: 20750 Sorted by residual: angle pdb=" N GLU E 87 " pdb=" CA GLU E 87 " pdb=" C GLU E 87 " ideal model delta sigma weight residual 111.28 120.05 -8.77 1.09e+00 8.42e-01 6.47e+01 angle pdb=" C ARG F 298 " pdb=" N PRO F 299 " pdb=" CA PRO F 299 " ideal model delta sigma weight residual 119.56 127.58 -8.02 1.01e+00 9.80e-01 6.30e+01 angle pdb=" C ARG E 298 " pdb=" N PRO E 299 " pdb=" CA PRO E 299 " ideal model delta sigma weight residual 119.56 127.33 -7.77 1.01e+00 9.80e-01 5.92e+01 angle pdb=" C ALA A 219 " pdb=" N PRO A 220 " pdb=" CA PRO A 220 " ideal model delta sigma weight residual 120.31 127.53 -7.22 9.80e-01 1.04e+00 5.43e+01 angle pdb=" N TRP F 395 " pdb=" CA TRP F 395 " pdb=" C TRP F 395 " ideal model delta sigma weight residual 113.17 122.41 -9.24 1.26e+00 6.30e-01 5.37e+01 ... (remaining 20745 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.01: 9725 21.01 - 42.03: 212 42.03 - 63.04: 59 63.04 - 84.06: 29 84.06 - 105.07: 17 Dihedral angle restraints: 10042 sinusoidal: 4637 harmonic: 5405 Sorted by residual: dihedral pdb=" CB CYS A 218 " pdb=" SG CYS A 218 " pdb=" SG CYS A 247 " pdb=" CB CYS A 247 " ideal model delta sinusoidal sigma weight residual 93.00 39.05 53.95 1 1.00e+01 1.00e-02 3.95e+01 dihedral pdb=" CB CYS F 378 " pdb=" SG CYS F 378 " pdb=" SG CYS F 445 " pdb=" CB CYS F 445 " ideal model delta sinusoidal sigma weight residual -86.00 -128.79 42.79 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CB CYS A 119 " pdb=" SG CYS A 119 " pdb=" SG CYS A 205 " pdb=" CB CYS A 205 " ideal model delta sinusoidal sigma weight residual -86.00 -127.32 41.32 1 1.00e+01 1.00e-02 2.39e+01 ... (remaining 10039 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1821 0.111 - 0.222: 467 0.222 - 0.333: 184 0.333 - 0.445: 103 0.445 - 0.556: 20 Chirality restraints: 2595 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-02 2.50e+03 1.20e+02 chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 8.26e+01 chirality pdb=" C1 BMA J 3 " pdb=" O4 NAG J 2 " pdb=" C2 BMA J 3 " pdb=" O5 BMA J 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.58 0.18 2.00e-02 2.50e+03 7.96e+01 ... (remaining 2592 not shown) Planarity restraints: 2615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 339 " 0.083 2.00e-02 2.50e+03 8.66e-02 9.38e+01 pdb=" CG ASN E 339 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN E 339 " -0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN E 339 " -0.135 2.00e-02 2.50e+03 pdb=" C1 NAG E 609 " 0.104 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.071 2.00e-02 2.50e+03 7.44e-02 6.92e+01 pdb=" CG ASN A 392 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.115 2.00e-02 2.50e+03 pdb=" C1 NAG A 614 " -0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 160 " 0.066 2.00e-02 2.50e+03 6.86e-02 5.88e+01 pdb=" CG ASN F 160 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN F 160 " -0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN F 160 " -0.106 2.00e-02 2.50e+03 pdb=" C1 NAG F 602 " 0.084 2.00e-02 2.50e+03 ... (remaining 2612 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 5330 2.88 - 3.38: 13209 3.38 - 3.89: 24306 3.89 - 4.39: 27879 4.39 - 4.90: 45093 Nonbonded interactions: 115817 Sorted by model distance: nonbonded pdb=" OG SER E 334 " pdb=" OG1 THR E 337 " model vdw 2.373 3.040 nonbonded pdb=" O THR F 248 " pdb=" CB THR F 248 " model vdw 2.375 2.776 nonbonded pdb=" N ILE A 213 " pdb=" O ILE A 213 " model vdw 2.416 2.496 nonbonded pdb=" NZ LYS D 574 " pdb=" OD1 ASP F 107 " model vdw 2.430 3.120 nonbonded pdb=" N THR E 240 " pdb=" O THR E 240 " model vdw 2.443 2.496 ... (remaining 115812 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 57 or resid 66 through 77 or resid 83 through 1 \ 40 or resid 150 through 163 or resid 165 through 206 or (resid 207 and (name N o \ r name CA or name C or name O or name CB )) or resid 208 through 355 or resid 35 \ 7 through 364 or resid 370 through 395 or resid 412 through 456 or resid 465 thr \ ough 612)) selection = (chain 'E' and (resid 34 through 77 or resid 83 through 140 or resid 150 through \ 182 or resid 189 through 364 or resid 370 through 456 or resid 465 through 612) \ ) selection = (chain 'F' and (resid 34 through 57 or resid 66 through 163 or resid 165 through \ 182 or resid 189 through 206 or (resid 207 and (name N or name CA or name C or \ name O or name CB )) or resid 208 through 355 or resid 357 through 364 or resid \ 370 through 395 or resid 412 through 456 or resid 465 through 612)) } ncs_group { reference = (chain 'B' and resid 522 through 702) selection = chain 'C' selection = (chain 'D' and resid 522 through 702) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = chain 'M' selection = chain 'N' } 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.202 15367 Z= 1.207 Angle : 1.692 13.300 21011 Z= 1.075 Chirality : 0.140 0.556 2595 Planarity : 0.009 0.048 2559 Dihedral : 11.270 105.070 6411 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 0.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Rotamer: Outliers : 0.14 % Allowed : 0.82 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.20), residues: 1574 helix: -0.28 (0.24), residues: 425 sheet: 1.04 (0.24), residues: 383 loop : 0.77 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 503 TYR 0.034 0.006 TYR E 191 PHE 0.028 0.006 PHE F 383 TRP 0.061 0.010 TRP A 479 HIS 0.006 0.002 HIS A 216 Details of bonding type rmsd covalent geometry : bond 0.02262 (15269) covalent geometry : angle 1.66802 (20750) SS BOND : bond 0.04203 ( 33) SS BOND : angle 3.14221 ( 66) hydrogen bonds : bond 0.15220 ( 476) hydrogen bonds : angle 6.82536 ( 1308) link_BETA1-4 : bond 0.06661 ( 9) link_BETA1-4 : angle 4.58463 ( 27) link_NAG-ASN : bond 0.08023 ( 56) link_NAG-ASN : angle 2.67897 ( 168) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7692 (m-90) cc_final: 0.7300 (m-90) REVERT: A 100 MET cc_start: 0.9169 (mtp) cc_final: 0.8760 (mtp) REVERT: A 150 MET cc_start: 0.8320 (mmm) cc_final: 0.7972 (tpp) REVERT: A 192 ARG cc_start: 0.7471 (mtm180) cc_final: 0.7071 (mtt90) REVERT: A 289 ASN cc_start: 0.8068 (t0) cc_final: 0.7820 (t0) REVERT: B 635 ILE cc_start: 0.8919 (mm) cc_final: 0.8663 (tt) REVERT: C 626 MET cc_start: 0.8128 (ttm) cc_final: 0.7910 (ttm) REVERT: E 39 TYR cc_start: 0.8895 (m-80) cc_final: 0.8676 (m-80) REVERT: E 275 GLU cc_start: 0.7944 (tt0) cc_final: 0.7599 (tt0) REVERT: E 297 THR cc_start: 0.8172 (m) cc_final: 0.7896 (p) REVERT: E 500 ARG cc_start: 0.4442 (mtm180) cc_final: 0.3729 (ptt90) REVERT: F 103 GLN cc_start: 0.8684 (tt0) cc_final: 0.8475 (tt0) REVERT: F 207 LYS cc_start: 0.8636 (pttt) cc_final: 0.8258 (mmtp) REVERT: F 231 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8493 (mmmt) REVERT: F 248 THR cc_start: 0.8649 (p) cc_final: 0.8359 (p) REVERT: F 264 SER cc_start: 0.8368 (m) cc_final: 0.7856 (m) REVERT: F 482 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7603 (mm-30) outliers start: 2 outliers final: 1 residues processed: 480 average time/residue: 0.1313 time to fit residues: 89.1719 Evaluate side-chains 312 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 311 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 197 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 HIS A 105 HIS A 348 GLN A 352 HIS A 356 ASN A 422 GLN B 630 GLN E 72 HIS ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 440 GLN F 105 HIS F 170 GLN F 203 GLN F 283 ASN F 348 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.160761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.138589 restraints weight = 19789.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142621 restraints weight = 10473.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.145231 restraints weight = 6853.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.146941 restraints weight = 5119.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.148040 restraints weight = 4152.820| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15367 Z= 0.157 Angle : 0.689 7.480 21011 Z= 0.336 Chirality : 0.047 0.272 2595 Planarity : 0.004 0.036 2559 Dihedral : 7.580 68.549 3312 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.40 % Allowed : 9.75 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.21), residues: 1574 helix: 1.59 (0.28), residues: 384 sheet: 0.92 (0.24), residues: 421 loop : 0.36 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 166 TYR 0.022 0.002 TYR E 486 PHE 0.021 0.002 PHE E 468 TRP 0.023 0.002 TRP F 479 HIS 0.003 0.001 HIS E 72 Details of bonding type rmsd covalent geometry : bond 0.00348 (15269) covalent geometry : angle 0.63495 (20750) SS BOND : bond 0.00332 ( 33) SS BOND : angle 0.97810 ( 66) hydrogen bonds : bond 0.05458 ( 476) hydrogen bonds : angle 5.02198 ( 1308) link_BETA1-4 : bond 0.00424 ( 9) link_BETA1-4 : angle 3.02011 ( 27) link_NAG-ASN : bond 0.00581 ( 56) link_NAG-ASN : angle 2.78796 ( 168) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 0.525 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: A 82 GLN cc_start: 0.7891 (mt0) cc_final: 0.7604 (mt0) REVERT: A 192 ARG cc_start: 0.6910 (mtm180) cc_final: 0.6297 (mtt90) REVERT: A 469 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.6963 (mmt90) REVERT: A 500 ARG cc_start: 0.7171 (mtt180) cc_final: 0.6491 (mtp-110) REVERT: C 660 LEU cc_start: 0.9071 (tp) cc_final: 0.8855 (tt) REVERT: E 169 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (ttmt) REVERT: E 443 ILE cc_start: 0.8742 (mt) cc_final: 0.8520 (mm) REVERT: F 74 CYS cc_start: 0.7437 (m) cc_final: 0.6717 (t) REVERT: F 150 MET cc_start: 0.7063 (ptp) cc_final: 0.6602 (ptt) REVERT: F 207 LYS cc_start: 0.8477 (pttt) cc_final: 0.8154 (mmtp) REVERT: F 363 ASN cc_start: 0.7325 (t0) cc_final: 0.6811 (p0) outliers start: 35 outliers final: 19 residues processed: 355 average time/residue: 0.1116 time to fit residues: 58.3251 Evaluate side-chains 312 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 292 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 356 ASN Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 169 LYS Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 632 ASP Chi-restraints excluded: chain F residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 62 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 162 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 165 optimal weight: 5.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS A 356 ASN E 195 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 348 GLN F 103 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.151479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128835 restraints weight = 20666.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132666 restraints weight = 11209.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135137 restraints weight = 7484.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.136706 restraints weight = 5695.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.137811 restraints weight = 4722.306| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 15367 Z= 0.281 Angle : 0.744 9.379 21011 Z= 0.362 Chirality : 0.049 0.271 2595 Planarity : 0.004 0.046 2559 Dihedral : 6.807 49.657 3312 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.64 % Allowed : 11.20 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.21), residues: 1574 helix: 1.19 (0.27), residues: 403 sheet: 0.63 (0.24), residues: 425 loop : -0.21 (0.21), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 585 TYR 0.019 0.002 TYR E 486 PHE 0.023 0.003 PHE B 522 TRP 0.019 0.002 TRP F 479 HIS 0.004 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00671 (15269) covalent geometry : angle 0.69990 (20750) SS BOND : bond 0.00435 ( 33) SS BOND : angle 1.08991 ( 66) hydrogen bonds : bond 0.05478 ( 476) hydrogen bonds : angle 4.92974 ( 1308) link_BETA1-4 : bond 0.00601 ( 9) link_BETA1-4 : angle 2.29286 ( 27) link_NAG-ASN : bond 0.00513 ( 56) link_NAG-ASN : angle 2.71591 ( 168) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 309 time to evaluate : 0.328 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: A 153 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6407 (tm-30) REVERT: A 192 ARG cc_start: 0.7291 (mtm180) cc_final: 0.6514 (mtt90) REVERT: A 372 THR cc_start: 0.9156 (OUTLIER) cc_final: 0.8879 (t) REVERT: A 469 ARG cc_start: 0.8142 (mtt-85) cc_final: 0.7138 (mmt90) REVERT: A 500 ARG cc_start: 0.7239 (mtt180) cc_final: 0.6650 (mtp-110) REVERT: B 634 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7444 (tm-30) REVERT: C 660 LEU cc_start: 0.9068 (tp) cc_final: 0.8844 (tt) REVERT: E 371 VAL cc_start: 0.8730 (OUTLIER) cc_final: 0.8359 (t) REVERT: E 482 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7460 (mm-30) REVERT: E 492 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8115 (mt-10) REVERT: F 160 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.7521 (m110) REVERT: F 180 ASP cc_start: 0.7413 (m-30) cc_final: 0.7212 (m-30) REVERT: F 207 LYS cc_start: 0.8500 (pttt) cc_final: 0.7945 (mppt) REVERT: F 264 SER cc_start: 0.8639 (m) cc_final: 0.8415 (m) REVERT: F 475 MET cc_start: 0.8281 (mmt) cc_final: 0.7898 (mmt) outliers start: 53 outliers final: 38 residues processed: 333 average time/residue: 0.1071 time to fit residues: 52.3041 Evaluate side-chains 327 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 285 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 231 LYS Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 295 ASN Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 373 THR Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 50 optimal weight: 0.4980 chunk 86 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 153 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.154232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131911 restraints weight = 20337.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.135715 restraints weight = 10901.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.138246 restraints weight = 7242.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139843 restraints weight = 5457.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.140995 restraints weight = 4493.766| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15367 Z= 0.122 Angle : 0.572 10.397 21011 Z= 0.278 Chirality : 0.044 0.312 2595 Planarity : 0.003 0.036 2559 Dihedral : 5.684 45.084 3312 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.34 % Allowed : 13.80 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1574 helix: 1.57 (0.28), residues: 397 sheet: 0.62 (0.24), residues: 424 loop : -0.20 (0.21), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 360 TYR 0.020 0.001 TYR E 486 PHE 0.015 0.001 PHE E 53 TRP 0.013 0.001 TRP F 479 HIS 0.003 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00275 (15269) covalent geometry : angle 0.52736 (20750) SS BOND : bond 0.00279 ( 33) SS BOND : angle 0.81652 ( 66) hydrogen bonds : bond 0.04384 ( 476) hydrogen bonds : angle 4.52056 ( 1308) link_BETA1-4 : bond 0.00451 ( 9) link_BETA1-4 : angle 1.93356 ( 27) link_NAG-ASN : bond 0.00434 ( 56) link_NAG-ASN : angle 2.38900 ( 168) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 0.323 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: A 96 TRP cc_start: 0.7823 (m-90) cc_final: 0.7372 (m-90) REVERT: A 192 ARG cc_start: 0.7219 (mtm180) cc_final: 0.6496 (mtt90) REVERT: A 363 ASN cc_start: 0.7595 (p0) cc_final: 0.7305 (p0) REVERT: A 372 THR cc_start: 0.9115 (p) cc_final: 0.8874 (t) REVERT: A 469 ARG cc_start: 0.8069 (mtt-85) cc_final: 0.7132 (mmt90) REVERT: A 500 ARG cc_start: 0.7303 (mtt180) cc_final: 0.6764 (mtp-110) REVERT: B 634 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7357 (tm-30) REVERT: C 660 LEU cc_start: 0.9004 (tp) cc_final: 0.8801 (tt) REVERT: E 100 MET cc_start: 0.9128 (mtp) cc_final: 0.8719 (mtm) REVERT: E 347 LYS cc_start: 0.8436 (tttt) cc_final: 0.8196 (tttm) REVERT: E 371 VAL cc_start: 0.8781 (m) cc_final: 0.8433 (t) REVERT: E 482 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7362 (mm-30) REVERT: E 492 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7934 (mt-10) REVERT: F 160 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7470 (m110) REVERT: F 180 ASP cc_start: 0.7414 (m-30) cc_final: 0.7197 (m-30) REVERT: F 207 LYS cc_start: 0.8524 (pttt) cc_final: 0.7929 (mppt) REVERT: F 231 LYS cc_start: 0.8526 (mmtp) cc_final: 0.8299 (mmmt) REVERT: F 264 SER cc_start: 0.8655 (m) cc_final: 0.8412 (m) REVERT: F 363 ASN cc_start: 0.7555 (t0) cc_final: 0.7092 (p0) outliers start: 34 outliers final: 23 residues processed: 325 average time/residue: 0.1088 time to fit residues: 51.7300 Evaluate side-chains 318 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 160 ASN Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 22 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 105 optimal weight: 0.0870 chunk 137 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 3 optimal weight: 0.0040 chunk 97 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 overall best weight: 1.6176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 398 ASN B 616 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 GLN E 425 ASN D 656 ASN F 103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.151495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.128740 restraints weight = 20469.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.132714 restraints weight = 10816.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.135285 restraints weight = 7116.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.136862 restraints weight = 5356.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.138048 restraints weight = 4425.560| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15367 Z= 0.198 Angle : 0.640 10.713 21011 Z= 0.308 Chirality : 0.046 0.289 2595 Planarity : 0.003 0.032 2559 Dihedral : 5.565 39.878 3312 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.50 % Allowed : 14.49 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.20), residues: 1574 helix: 1.62 (0.28), residues: 392 sheet: 0.54 (0.25), residues: 402 loop : -0.43 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 360 TYR 0.016 0.002 TYR E 173 PHE 0.017 0.002 PHE E 53 TRP 0.013 0.001 TRP F 479 HIS 0.003 0.001 HIS F 72 Details of bonding type rmsd covalent geometry : bond 0.00469 (15269) covalent geometry : angle 0.59319 (20750) SS BOND : bond 0.00351 ( 33) SS BOND : angle 1.45536 ( 66) hydrogen bonds : bond 0.04688 ( 476) hydrogen bonds : angle 4.55441 ( 1308) link_BETA1-4 : bond 0.00417 ( 9) link_BETA1-4 : angle 1.76494 ( 27) link_NAG-ASN : bond 0.00390 ( 56) link_NAG-ASN : angle 2.54291 ( 168) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ASP cc_start: 0.7799 (m-30) cc_final: 0.7586 (m-30) REVERT: A 96 TRP cc_start: 0.7741 (m-90) cc_final: 0.7266 (m-90) REVERT: A 153 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: A 192 ARG cc_start: 0.7167 (mtm180) cc_final: 0.6632 (mtm180) REVERT: A 340 GLU cc_start: 0.7938 (tp30) cc_final: 0.7714 (tp30) REVERT: A 372 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 500 ARG cc_start: 0.7401 (mtt180) cc_final: 0.6906 (mtp-110) REVERT: B 595 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8566 (tt) REVERT: B 634 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7368 (tm-30) REVERT: C 660 LEU cc_start: 0.8994 (tp) cc_final: 0.8791 (tt) REVERT: E 100 MET cc_start: 0.9216 (mtp) cc_final: 0.8861 (mtm) REVERT: E 178 ARG cc_start: 0.7164 (ptm-80) cc_final: 0.6791 (ptm-80) REVERT: E 347 LYS cc_start: 0.8489 (tttt) cc_final: 0.8251 (tttm) REVERT: E 371 VAL cc_start: 0.8774 (OUTLIER) cc_final: 0.8386 (t) REVERT: E 492 GLU cc_start: 0.8284 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 647 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: F 161 MET cc_start: 0.7630 (OUTLIER) cc_final: 0.7018 (ttp) REVERT: F 180 ASP cc_start: 0.7562 (m-30) cc_final: 0.7348 (m-30) REVERT: F 207 LYS cc_start: 0.8480 (pttt) cc_final: 0.7899 (mppt) REVERT: F 231 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8284 (mmmt) REVERT: F 264 SER cc_start: 0.8653 (m) cc_final: 0.8416 (m) REVERT: F 316 TRP cc_start: 0.8795 (m100) cc_final: 0.8433 (m-90) REVERT: F 363 ASN cc_start: 0.7654 (t0) cc_final: 0.7165 (p0) outliers start: 51 outliers final: 37 residues processed: 317 average time/residue: 0.1164 time to fit residues: 53.5843 Evaluate side-chains 337 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 294 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 529 THR Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 627 THR Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 346 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 425 ASN Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain D residue 647 GLU Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 370 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 74 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 36 optimal weight: 0.0010 chunk 67 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 160 optimal weight: 8.9990 chunk 12 optimal weight: 0.9990 chunk 112 optimal weight: 0.0060 chunk 155 optimal weight: 4.9990 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN E 425 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.155568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133330 restraints weight = 20088.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.137212 restraints weight = 10703.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.139723 restraints weight = 7094.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.141368 restraints weight = 5354.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.142394 restraints weight = 4393.747| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15367 Z= 0.098 Angle : 0.546 9.706 21011 Z= 0.265 Chirality : 0.042 0.244 2595 Planarity : 0.003 0.036 2559 Dihedral : 5.086 40.134 3312 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.13 % Allowed : 16.00 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.21), residues: 1574 helix: 1.85 (0.28), residues: 393 sheet: 0.66 (0.25), residues: 399 loop : -0.35 (0.21), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 360 TYR 0.016 0.001 TYR E 173 PHE 0.015 0.001 PHE E 53 TRP 0.011 0.001 TRP A 479 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00214 (15269) covalent geometry : angle 0.49896 (20750) SS BOND : bond 0.00248 ( 33) SS BOND : angle 1.13044 ( 66) hydrogen bonds : bond 0.03929 ( 476) hydrogen bonds : angle 4.31680 ( 1308) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.48620 ( 27) link_NAG-ASN : bond 0.00424 ( 56) link_NAG-ASN : angle 2.37359 ( 168) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 308 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7607 (m-90) cc_final: 0.7165 (m-90) REVERT: A 153 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6428 (tm-30) REVERT: A 192 ARG cc_start: 0.7104 (mtm180) cc_final: 0.6644 (mtt90) REVERT: A 340 GLU cc_start: 0.7879 (tp30) cc_final: 0.7677 (tp30) REVERT: A 372 THR cc_start: 0.9086 (p) cc_final: 0.8866 (t) REVERT: A 469 ARG cc_start: 0.8348 (mmt90) cc_final: 0.8131 (mtt-85) REVERT: A 484 TYR cc_start: 0.8939 (p90) cc_final: 0.8257 (p90) REVERT: A 500 ARG cc_start: 0.7331 (mtt180) cc_final: 0.6889 (mtp-110) REVERT: B 634 GLU cc_start: 0.7558 (tm-30) cc_final: 0.7318 (tm-30) REVERT: E 46 LYS cc_start: 0.8024 (mttp) cc_final: 0.7662 (mmtm) REVERT: E 347 LYS cc_start: 0.8485 (tttt) cc_final: 0.8245 (tttm) REVERT: E 457 ASP cc_start: 0.6598 (m-30) cc_final: 0.6347 (m-30) REVERT: D 596 TRP cc_start: 0.8862 (m-10) cc_final: 0.8533 (m-10) REVERT: F 207 LYS cc_start: 0.8443 (pttt) cc_final: 0.7896 (mppt) REVERT: F 264 SER cc_start: 0.8673 (m) cc_final: 0.8448 (m) REVERT: F 363 ASN cc_start: 0.7561 (t0) cc_final: 0.7075 (p0) outliers start: 31 outliers final: 23 residues processed: 325 average time/residue: 0.1198 time to fit residues: 56.8336 Evaluate side-chains 318 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 294 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 126 CYS Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 53 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 106 optimal weight: 5.9990 chunk 133 optimal weight: 0.0570 chunk 91 optimal weight: 0.0770 chunk 121 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 159 optimal weight: 0.0670 chunk 164 optimal weight: 9.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 656 ASN F 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.157097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.134893 restraints weight = 19978.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.138826 restraints weight = 10729.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.141349 restraints weight = 7109.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.142858 restraints weight = 5358.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.144015 restraints weight = 4439.899| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15367 Z= 0.092 Angle : 0.528 9.369 21011 Z= 0.254 Chirality : 0.042 0.231 2595 Planarity : 0.003 0.036 2559 Dihedral : 4.828 38.367 3312 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.34 % Allowed : 16.48 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.21), residues: 1574 helix: 1.99 (0.28), residues: 393 sheet: 0.75 (0.25), residues: 405 loop : -0.27 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 178 TYR 0.020 0.001 TYR A 173 PHE 0.016 0.001 PHE E 53 TRP 0.017 0.001 TRP A 427 HIS 0.003 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00200 (15269) covalent geometry : angle 0.48575 (20750) SS BOND : bond 0.00235 ( 33) SS BOND : angle 0.96011 ( 66) hydrogen bonds : bond 0.03580 ( 476) hydrogen bonds : angle 4.18656 ( 1308) link_BETA1-4 : bond 0.00448 ( 9) link_BETA1-4 : angle 1.35593 ( 27) link_NAG-ASN : bond 0.00407 ( 56) link_NAG-ASN : angle 2.25313 ( 168) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 309 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7502 (m-90) cc_final: 0.7016 (m-90) REVERT: A 153 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6438 (tm-30) REVERT: A 192 ARG cc_start: 0.7080 (mtm180) cc_final: 0.6634 (mtt90) REVERT: A 246 GLN cc_start: 0.8461 (mt0) cc_final: 0.8194 (mt0) REVERT: A 469 ARG cc_start: 0.8372 (mmt90) cc_final: 0.8160 (mtt-85) REVERT: A 484 TYR cc_start: 0.8896 (p90) cc_final: 0.8210 (p90) REVERT: A 500 ARG cc_start: 0.7397 (mtt180) cc_final: 0.6931 (mtp-110) REVERT: B 634 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7336 (tm-30) REVERT: C 623 TRP cc_start: 0.9092 (m100) cc_final: 0.8877 (m100) REVERT: E 347 LYS cc_start: 0.8464 (tttt) cc_final: 0.8210 (tttp) REVERT: D 634 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7480 (mm-30) REVERT: F 161 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.6788 (ttp) REVERT: F 207 LYS cc_start: 0.8415 (pttt) cc_final: 0.7927 (mppt) REVERT: F 264 SER cc_start: 0.8696 (m) cc_final: 0.8457 (m) REVERT: F 363 ASN cc_start: 0.7534 (t0) cc_final: 0.6978 (p0) outliers start: 34 outliers final: 24 residues processed: 326 average time/residue: 0.1033 time to fit residues: 50.1395 Evaluate side-chains 318 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 571 TRP Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 659 ASP Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 167 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.0170 chunk 18 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 540 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133316 restraints weight = 20535.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.137335 restraints weight = 10597.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.139861 restraints weight = 6937.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.141522 restraints weight = 5230.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.142591 restraints weight = 4301.693| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 15367 Z= 0.211 Angle : 0.634 9.345 21011 Z= 0.306 Chirality : 0.046 0.291 2595 Planarity : 0.003 0.030 2559 Dihedral : 5.286 41.025 3310 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.82 % Allowed : 16.41 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1574 helix: 1.71 (0.28), residues: 394 sheet: 0.57 (0.25), residues: 390 loop : -0.50 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 585 TYR 0.017 0.002 TYR A 173 PHE 0.017 0.002 PHE E 53 TRP 0.014 0.001 TRP A 427 HIS 0.002 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00503 (15269) covalent geometry : angle 0.59619 (20750) SS BOND : bond 0.00366 ( 33) SS BOND : angle 1.11065 ( 66) hydrogen bonds : bond 0.04521 ( 476) hydrogen bonds : angle 4.41535 ( 1308) link_BETA1-4 : bond 0.00404 ( 9) link_BETA1-4 : angle 1.52071 ( 27) link_NAG-ASN : bond 0.00480 ( 56) link_NAG-ASN : angle 2.34969 ( 168) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 285 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7696 (m-90) cc_final: 0.7232 (m-90) REVERT: A 153 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6507 (tm-30) REVERT: A 192 ARG cc_start: 0.7178 (mtm180) cc_final: 0.6662 (mtt90) REVERT: A 340 GLU cc_start: 0.7899 (tp30) cc_final: 0.7662 (tp30) REVERT: A 469 ARG cc_start: 0.8559 (mmt90) cc_final: 0.8271 (mtt-85) REVERT: A 500 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6955 (mtp-110) REVERT: B 540 GLN cc_start: 0.8590 (mp-120) cc_final: 0.8370 (mm-40) REVERT: B 595 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8540 (tt) REVERT: B 634 GLU cc_start: 0.7639 (tm-30) cc_final: 0.7362 (tm-30) REVERT: E 46 LYS cc_start: 0.8040 (mttp) cc_final: 0.7777 (mmtt) REVERT: E 100 MET cc_start: 0.9180 (mtp) cc_final: 0.8939 (mtm) REVERT: E 347 LYS cc_start: 0.8443 (tttt) cc_final: 0.8189 (tttm) REVERT: E 358 ILE cc_start: 0.6840 (mt) cc_final: 0.6355 (mm) REVERT: E 482 GLU cc_start: 0.7947 (mm-30) cc_final: 0.7420 (mm-30) REVERT: F 161 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6546 (ttp) REVERT: F 169 LYS cc_start: 0.7906 (mmmt) cc_final: 0.7486 (mmtt) REVERT: F 207 LYS cc_start: 0.8478 (pttt) cc_final: 0.7913 (mppt) REVERT: F 264 SER cc_start: 0.8743 (m) cc_final: 0.8524 (m) REVERT: F 316 TRP cc_start: 0.8810 (m100) cc_final: 0.8412 (m-90) REVERT: F 363 ASN cc_start: 0.7633 (t0) cc_final: 0.7173 (p0) outliers start: 41 outliers final: 32 residues processed: 306 average time/residue: 0.1364 time to fit residues: 61.1616 Evaluate side-chains 317 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 282 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 612 SER Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 416 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 274 SER Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 333 VAL Chi-restraints excluded: chain F residue 370 GLU Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 182 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN D 656 ASN F 103 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136102 restraints weight = 20420.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.140149 restraints weight = 10514.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.142726 restraints weight = 6878.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144271 restraints weight = 5166.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.145422 restraints weight = 4281.847| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15367 Z= 0.124 Angle : 0.560 9.934 21011 Z= 0.271 Chirality : 0.043 0.280 2595 Planarity : 0.003 0.036 2559 Dihedral : 5.056 38.935 3310 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.13 % Allowed : 17.24 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.21), residues: 1574 helix: 1.90 (0.28), residues: 394 sheet: 0.53 (0.25), residues: 397 loop : -0.46 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 178 TYR 0.018 0.001 TYR A 173 PHE 0.016 0.001 PHE E 53 TRP 0.014 0.001 TRP A 427 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00287 (15269) covalent geometry : angle 0.51959 (20750) SS BOND : bond 0.00293 ( 33) SS BOND : angle 0.98638 ( 66) hydrogen bonds : bond 0.04002 ( 476) hydrogen bonds : angle 4.28658 ( 1308) link_BETA1-4 : bond 0.00429 ( 9) link_BETA1-4 : angle 1.36238 ( 27) link_NAG-ASN : bond 0.00490 ( 56) link_NAG-ASN : angle 2.29139 ( 168) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 292 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 TRP cc_start: 0.7629 (m-90) cc_final: 0.7149 (m-90) REVERT: A 153 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6555 (tm-30) REVERT: A 192 ARG cc_start: 0.7165 (mtm180) cc_final: 0.6640 (mtt90) REVERT: A 275 GLU cc_start: 0.8066 (tt0) cc_final: 0.7748 (tt0) REVERT: A 340 GLU cc_start: 0.7848 (tp30) cc_final: 0.7607 (tp30) REVERT: A 432 GLN cc_start: 0.7879 (mp10) cc_final: 0.7406 (mp10) REVERT: A 469 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8257 (mtt-85) REVERT: A 500 ARG cc_start: 0.7348 (mtt180) cc_final: 0.6965 (mtp-110) REVERT: B 540 GLN cc_start: 0.8501 (mp-120) cc_final: 0.8261 (mm-40) REVERT: B 634 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7389 (tm-30) REVERT: C 623 TRP cc_start: 0.9140 (m100) cc_final: 0.8938 (m100) REVERT: E 46 LYS cc_start: 0.8048 (mttp) cc_final: 0.7659 (mmtt) REVERT: E 100 MET cc_start: 0.9175 (mtp) cc_final: 0.8941 (mtm) REVERT: E 347 LYS cc_start: 0.8429 (tttt) cc_final: 0.8167 (tttm) REVERT: E 358 ILE cc_start: 0.6762 (mt) cc_final: 0.6287 (mm) REVERT: E 482 GLU cc_start: 0.7974 (mm-30) cc_final: 0.7336 (mm-30) REVERT: D 596 TRP cc_start: 0.8919 (m-10) cc_final: 0.8586 (m-10) REVERT: F 161 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.6841 (ttp) REVERT: F 207 LYS cc_start: 0.8479 (pttt) cc_final: 0.7927 (mppt) REVERT: F 264 SER cc_start: 0.8755 (m) cc_final: 0.8537 (m) REVERT: F 316 TRP cc_start: 0.8765 (m100) cc_final: 0.8415 (m-90) outliers start: 31 outliers final: 25 residues processed: 307 average time/residue: 0.1341 time to fit residues: 60.7472 Evaluate side-chains 306 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 32 optimal weight: 0.7980 chunk 168 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 103 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.158502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.136029 restraints weight = 20437.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.140049 restraints weight = 10521.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.142600 restraints weight = 6880.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.144247 restraints weight = 5181.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.145321 restraints weight = 4256.968| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15367 Z= 0.129 Angle : 0.560 11.641 21011 Z= 0.269 Chirality : 0.043 0.272 2595 Planarity : 0.003 0.034 2559 Dihedral : 5.034 40.914 3310 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.99 % Allowed : 17.31 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.21), residues: 1574 helix: 1.90 (0.28), residues: 394 sheet: 0.53 (0.26), residues: 385 loop : -0.48 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.017 0.001 TYR A 173 PHE 0.016 0.001 PHE E 53 TRP 0.015 0.001 TRP E 35 HIS 0.002 0.000 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00300 (15269) covalent geometry : angle 0.51941 (20750) SS BOND : bond 0.00310 ( 33) SS BOND : angle 0.95534 ( 66) hydrogen bonds : bond 0.03944 ( 476) hydrogen bonds : angle 4.24890 ( 1308) link_BETA1-4 : bond 0.00416 ( 9) link_BETA1-4 : angle 1.36412 ( 27) link_NAG-ASN : bond 0.00457 ( 56) link_NAG-ASN : angle 2.27734 ( 168) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3148 Ramachandran restraints generated. 1574 Oldfield, 0 Emsley, 1574 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 285 time to evaluate : 0.627 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: A 96 TRP cc_start: 0.7619 (m-90) cc_final: 0.7137 (m-90) REVERT: A 153 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6580 (tm-30) REVERT: A 192 ARG cc_start: 0.7149 (mtm180) cc_final: 0.6645 (mtt90) REVERT: A 275 GLU cc_start: 0.8059 (tt0) cc_final: 0.7795 (tt0) REVERT: A 432 GLN cc_start: 0.7885 (mp10) cc_final: 0.7389 (mp10) REVERT: A 469 ARG cc_start: 0.8452 (mmt90) cc_final: 0.8189 (mtt-85) REVERT: A 500 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6997 (mtp-110) REVERT: B 540 GLN cc_start: 0.8553 (mp-120) cc_final: 0.8334 (mm-40) REVERT: B 634 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7362 (tm-30) REVERT: B 640 GLN cc_start: 0.8034 (mp10) cc_final: 0.7759 (mp10) REVERT: E 100 MET cc_start: 0.9179 (mtp) cc_final: 0.8970 (mtm) REVERT: E 112 TRP cc_start: 0.8363 (t-100) cc_final: 0.8159 (t-100) REVERT: E 347 LYS cc_start: 0.8430 (tttt) cc_final: 0.8175 (tttm) REVERT: E 358 ILE cc_start: 0.6751 (mt) cc_final: 0.6274 (mm) REVERT: E 482 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7410 (mm-30) REVERT: E 492 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7909 (mt-10) REVERT: F 161 MET cc_start: 0.7506 (OUTLIER) cc_final: 0.6834 (ttp) REVERT: F 207 LYS cc_start: 0.8482 (pttt) cc_final: 0.7922 (mppt) REVERT: F 264 SER cc_start: 0.8772 (m) cc_final: 0.8544 (m) REVERT: F 316 TRP cc_start: 0.8775 (m100) cc_final: 0.8409 (m-90) outliers start: 29 outliers final: 25 residues processed: 300 average time/residue: 0.1388 time to fit residues: 60.5174 Evaluate side-chains 306 residues out of total 1457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 279 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 153 GLU Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain C residue 538 THR Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 663 LEU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 128 THR Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 173 TYR Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 364 SER Chi-restraints excluded: chain E residue 372 THR Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 571 TRP Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 161 MET Chi-restraints excluded: chain F residue 325 ASP Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 450 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 183 random chunks: chunk 27 optimal weight: 0.9990 chunk 178 optimal weight: 8.9990 chunk 82 optimal weight: 0.0470 chunk 33 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 chunk 170 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 127 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 656 ASN F 103 GLN ** F 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135074 restraints weight = 20378.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.139080 restraints weight = 10534.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.141622 restraints weight = 6904.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143246 restraints weight = 5202.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.144351 restraints weight = 4291.215| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15367 Z= 0.153 Angle : 0.589 14.209 21011 Z= 0.280 Chirality : 0.044 0.270 2595 Planarity : 0.003 0.037 2559 Dihedral : 5.131 41.794 3310 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.99 % Allowed : 17.79 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.21), residues: 1574 helix: 1.84 (0.28), residues: 394 sheet: 0.48 (0.26), residues: 385 loop : -0.52 (0.21), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 178 TYR 0.016 0.001 TYR A 173 PHE 0.016 0.001 PHE E 53 TRP 0.014 0.001 TRP A 96 HIS 0.002 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00359 (15269) covalent geometry : angle 0.54523 (20750) SS BOND : bond 0.00327 ( 33) SS BOND : angle 0.97012 ( 66) hydrogen bonds : bond 0.04068 ( 476) hydrogen bonds : angle 4.28678 ( 1308) link_BETA1-4 : bond 0.00378 ( 9) link_BETA1-4 : angle 1.36829 ( 27) link_NAG-ASN : bond 0.00578 ( 56) link_NAG-ASN : angle 2.44840 ( 168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.08 seconds wall clock time: 44 minutes 1.91 seconds (2641.91 seconds total)