Starting phenix.real_space_refine on Thu Sep 18 07:58:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.map" model { file = "/net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nhl_49415/09_2025/9nhl_49415.cif" } resolution = 3.7 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= -0.001 sd= 0.038 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 103 5.16 5 C 9350 2.51 5 N 2531 2.21 5 O 3019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15003 Number of models: 1 Model: "" Number of chains: 21 Chain: "H" Number of atoms: 620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 620 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 119} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 527 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'TRANS': 101} Unresolved non-hydrogen bonds: 196 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 98 Planarities with less than four sites: {'UNK:plan-1': 98} Unresolved non-hydrogen planarities: 98 Chain: "A" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3383 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 3 Chain: "Y" Number of atoms: 3383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3383 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 22, 'TRANS': 409} Chain breaks: 3 Chain: "D" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 1, 'TRANS': 117} Chain breaks: 1 Chain: "F" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 1, 'TRANS': 116} Chain breaks: 1 Chain: "C" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3390 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 22, 'TRANS': 410} Chain breaks: 3 Chain: "B" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 931 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 1, 'TRANS': 115} Chain breaks: 1 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "I" Number of atoms: 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: "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: 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: "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: 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: "A" 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: "Y" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.27, per 1000 atoms: 0.28 Number of scatterers: 15003 At special positions: 0 Unit cell: (127.65, 125.35, 133.4, 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 103 16.00 O 3019 8.00 N 2531 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS H 21 " - pdb=" SG CYS H 95 " distance=2.02 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 84 " distance=2.04 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.20 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.05 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.03 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 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 663 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 54 " - pdb=" SG CYS Y 73 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 119 " - pdb=" SG CYS Y 205 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 126 " - pdb=" SG CYS Y 196 " distance=2.04 Simple disulfide: pdb=" SG CYS Y 131 " - pdb=" SG CYS Y 157 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 218 " - pdb=" SG CYS Y 247 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 228 " - pdb=" SG CYS Y 239 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 296 " - pdb=" SG CYS Y 331 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 378 " - pdb=" SG CYS Y 445 " distance=2.03 Simple disulfide: pdb=" SG CYS Y 385 " - pdb=" SG CYS Y 418 " distance=2.02 Simple disulfide: pdb=" SG CYS Y 501 " - pdb=" SG CYS D 663 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS F 663 " - pdb=" SG CYS C 501 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.05 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.02 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.08 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " 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 E 1 " - " NAG E 2 " " NAG E 2 " - " NAG E 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " NAG I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " NAG K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 601 " - " ASN A 130 " " NAG A 602 " - " ASN A 156 " " NAG A 603 " - " ASN A 160 " " NAG A 604 " - " ASN A 197 " " NAG A 605 " - " ASN A 230 " " NAG A 606 " - " ASN A 289 " " NAG A 607 " - " ASN A 301 " " NAG A 608 " - " ASN A 332 " " NAG A 609 " - " ASN A 386 " " NAG A 610 " - " ASN A 442 " " NAG A 611 " - " ASN A 448 " " NAG A 612 " - " ASN A 88 " " NAG B 701 " - " ASN B 625 " " NAG B 702 " - " ASN B 616 " " NAG B 703 " - " ASN B 611 " " NAG B 704 " - " ASN B 637 " " NAG C 601 " - " ASN C 130 " " NAG C 602 " - " ASN C 173 " " NAG C 603 " - " ASN C 160 " " NAG C 604 " - " ASN C 197 " " NAG C 605 " - " ASN C 230 " " NAG C 606 " - " ASN C 289 " " NAG C 607 " - " ASN C 301 " " NAG C 608 " - " ASN C 332 " " NAG C 609 " - " ASN C 386 " " NAG C 610 " - " ASN C 442 " " NAG C 611 " - " ASN C 448 " " NAG D 701 " - " ASN D 611 " " NAG D 702 " - " ASN D 616 " " NAG D 703 " - " ASN D 656 " " NAG E 1 " - " ASN A 241 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN A 262 " " NAG I 1 " - " ASN Y 241 " " NAG J 1 " - " ASN Y 262 " " NAG K 1 " - " ASN C 241 " " NAG M 1 " - " ASN C 262 " " NAG N 1 " - " ASN C 88 " " NAG Y 601 " - " ASN Y 130 " " NAG Y 602 " - " ASN Y 156 " " NAG Y 603 " - " ASN Y 160 " " NAG Y 604 " - " ASN Y 197 " " NAG Y 605 " - " ASN Y 230 " " NAG Y 606 " - " ASN Y 289 " " NAG Y 607 " - " ASN Y 301 " " NAG Y 608 " - " ASN Y 332 " " NAG Y 609 " - " ASN Y 386 " " NAG Y 610 " - " ASN Y 442 " " NAG Y 611 " - " ASN Y 448 " Time building additional restraints: 1.44 Conformation dependent library (CDL) restraints added in 679.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 29 sheets defined 27.1% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 1 through 5 Processing helix chain 'L' and resid 24 through 30 Processing helix chain 'L' and resid 75 through 79 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 117 Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 337 through 350 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 475 through 480 Processing helix chain 'Y' and resid 67 through 73 Processing helix chain 'Y' and resid 98 through 116 removed outlier: 3.896A pdb=" N GLU Y 102 " --> pdb=" O ASN Y 98 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU Y 116 " --> pdb=" O TRP Y 112 " (cutoff:3.500A) Processing helix chain 'Y' and resid 122 through 126 Processing helix chain 'Y' and resid 195 through 198 Processing helix chain 'Y' and resid 335 through 350 Processing helix chain 'Y' and resid 368 through 373 Processing helix chain 'Y' and resid 425 through 429 Processing helix chain 'Y' and resid 476 through 484 removed outlier: 3.932A pdb=" N SER Y 481 " --> pdb=" O ASP Y 477 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLU Y 482 " --> pdb=" O ASN Y 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 537 removed outlier: 3.822A pdb=" N LEU D 537 " --> pdb=" O SER D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 611 through 616 removed outlier: 3.826A pdb=" N ASN D 616 " --> pdb=" O SER D 612 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'F' and resid 537 through 543 Processing helix chain 'F' and resid 569 through 595 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 659 removed outlier: 4.024A pdb=" N GLU F 657 " --> pdb=" O GLN F 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.030A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.716A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.469A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 626 removed outlier: 4.192A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET B 626 " --> pdb=" O ILE B 622 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 658 removed outlier: 3.577A pdb=" N THR B 658 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'H' and resid 32 through 38 removed outlier: 5.926A pdb=" N UNK H 37 " --> pdb=" O UNK H 46 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N UNK H 46 " --> pdb=" O UNK H 37 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 109 through 110 Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 11 removed outlier: 6.674A pdb=" N UNK L 10 " --> pdb=" O UNK L 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 20 through 23 Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 46 Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL A 36 " --> pdb=" O THR D 606 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.626A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 92 Processing sheet with id=AB1, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 202 through 203 removed outlier: 6.788A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, 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 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 323A through 324 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=AB4, first strand: chain 'A' and resid 304 through 312 removed outlier: 6.399A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Y' and resid 494 through 499 removed outlier: 5.400A pdb=" N VAL F 608 " --> pdb=" O VAL Y 36 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N VAL Y 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N THR F 606 " --> pdb=" O VAL Y 38 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N TYR Y 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N CYS F 604 " --> pdb=" O TYR Y 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Y' and resid 45 through 47 Processing sheet with id=AB7, first strand: chain 'Y' and resid 75 through 76 removed outlier: 4.577A pdb=" N VAL Y 75 " --> pdb=" O CYS Y 54 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Y' and resid 91 through 94 Processing sheet with id=AB9, first strand: chain 'Y' and resid 169 through 177 Processing sheet with id=AC1, first strand: chain 'Y' and resid 202 through 203 removed outlier: 6.786A pdb=" N THR Y 202 " --> pdb=" O TYR Y 435 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'Y' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 259 through 261 current: chain 'Y' and resid 284 through 304 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 320 through 324 current: chain 'Y' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'Y' and resid 381 through 385 current: chain 'Y' and resid 466 through 470 Processing sheet with id=AC3, first strand: chain 'Y' and resid 308 through 312 removed outlier: 6.134A pdb=" N GLN Y 315 " --> pdb=" O ILE Y 309 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.265A pdb=" N VAL B 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL C 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N TYR C 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N CYS B 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.759A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.434A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC8, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC9, first strand: chain 'C' and resid 201 through 203 removed outlier: 6.593A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 287 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 284 through 287 current: chain 'C' and resid 393 through 394 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 393 through 394 current: chain 'C' and resid 466 through 469 No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 294 through 311 removed outlier: 5.504A pdb=" N THR C 305 " --> pdb=" O THR C 319 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N THR C 319 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE C 307 " --> pdb=" O TYR C 317 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N TYR C 317 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE C 309 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 314 through 324 current: chain 'C' and resid 381 through 385 removed outlier: 4.375A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) 471 hydrogen bonds defined for protein. 1257 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: 2.79 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4560 1.34 - 1.50: 4912 1.50 - 1.65: 5671 1.65 - 1.81: 76 1.81 - 1.96: 57 Bond restraints: 15276 Sorted by residual: bond pdb=" CZ2 TRP Y 395 " pdb=" CH2 TRP Y 395 " ideal model delta sigma weight residual 1.368 1.474 -0.106 1.90e-02 2.77e+03 3.09e+01 bond pdb=" CD2 TRP Y 395 " pdb=" CE3 TRP Y 395 " ideal model delta sigma weight residual 1.398 1.487 -0.089 1.60e-02 3.91e+03 3.09e+01 bond pdb=" CZ2 TRP C 395 " pdb=" CH2 TRP C 395 " ideal model delta sigma weight residual 1.368 1.472 -0.104 1.90e-02 2.77e+03 2.99e+01 bond pdb=" NE1 TRP D 623 " pdb=" CE2 TRP D 623 " ideal model delta sigma weight residual 1.370 1.310 0.060 1.10e-02 8.26e+03 2.94e+01 bond pdb=" CD2 TRP C 395 " pdb=" CE3 TRP C 395 " ideal model delta sigma weight residual 1.398 1.483 -0.085 1.60e-02 3.91e+03 2.81e+01 ... (remaining 15271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 18904 2.81 - 5.63: 1710 5.63 - 8.44: 174 8.44 - 11.25: 13 11.25 - 14.07: 4 Bond angle restraints: 20805 Sorted by residual: angle pdb=" N SER A 481 " pdb=" CA SER A 481 " pdb=" C SER A 481 " ideal model delta sigma weight residual 114.62 103.95 10.67 1.14e+00 7.69e-01 8.75e+01 angle pdb=" C PHE A 353 " pdb=" N PRO A 354 " pdb=" CA PRO A 354 " ideal model delta sigma weight residual 119.56 128.27 -8.71 1.01e+00 9.80e-01 7.43e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.90 -8.34 1.02e+00 9.61e-01 6.69e+01 angle pdb=" C ILE C 141 " pdb=" N ILE C 142 " pdb=" CA ILE C 142 " ideal model delta sigma weight residual 122.48 112.27 10.21 1.25e+00 6.40e-01 6.68e+01 angle pdb=" N ASN F 656 " pdb=" CA ASN F 656 " pdb=" C ASN F 656 " ideal model delta sigma weight residual 110.19 100.17 10.02 1.24e+00 6.50e-01 6.53e+01 ... (remaining 20800 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.66: 9706 22.66 - 45.31: 179 45.31 - 67.97: 71 67.97 - 90.62: 30 90.62 - 113.28: 15 Dihedral angle restraints: 10001 sinusoidal: 4570 harmonic: 5431 Sorted by residual: dihedral pdb=" CB CYS F 598 " pdb=" SG CYS F 598 " pdb=" SG CYS F 604 " pdb=" CB CYS F 604 " ideal model delta sinusoidal sigma weight residual 93.00 -179.35 -87.65 1 1.00e+01 1.00e-02 9.21e+01 dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 73 " pdb=" CB CYS A 73 " ideal model delta sinusoidal sigma weight residual -86.00 -6.04 -79.96 1 1.00e+01 1.00e-02 7.93e+01 dihedral pdb=" CB CYS C 378 " pdb=" SG CYS C 378 " pdb=" SG CYS C 445 " pdb=" CB CYS C 445 " ideal model delta sinusoidal sigma weight residual -86.00 -132.40 46.40 1 1.00e+01 1.00e-02 2.98e+01 ... (remaining 9998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1793 0.106 - 0.213: 504 0.213 - 0.319: 176 0.319 - 0.425: 87 0.425 - 0.532: 31 Chirality restraints: 2591 Sorted by residual: 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 -2.63 0.23 2.00e-02 2.50e+03 1.29e+02 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 chirality pdb=" C1 NAG I 3 " pdb=" O4 NAG I 2 " pdb=" C2 NAG I 3 " pdb=" O5 NAG I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.27e+02 ... (remaining 2588 not shown) Planarity restraints: 2634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 604 " -0.310 2.00e-02 2.50e+03 2.63e-01 8.64e+02 pdb=" C7 NAG C 604 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG C 604 " -0.179 2.00e-02 2.50e+03 pdb=" N2 NAG C 604 " 0.458 2.00e-02 2.50e+03 pdb=" O7 NAG C 604 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 173 " -0.079 2.00e-02 2.50e+03 8.35e-02 8.71e+01 pdb=" CG ASN C 173 " 0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN C 173 " 0.015 2.00e-02 2.50e+03 pdb=" ND2 ASN C 173 " 0.131 2.00e-02 2.50e+03 pdb=" C1 NAG C 602 " -0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 332 " 0.074 2.00e-02 2.50e+03 7.66e-02 7.33e+01 pdb=" CG ASN A 332 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 332 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 332 " -0.118 2.00e-02 2.50e+03 pdb=" C1 NAG A 608 " 0.092 2.00e-02 2.50e+03 ... (remaining 2631 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 5165 2.86 - 3.37: 13789 3.37 - 3.88: 24844 3.88 - 4.39: 28811 4.39 - 4.90: 45636 Nonbonded interactions: 118245 Sorted by model distance: nonbonded pdb=" N ASN D 637 " pdb=" O ASN D 637 " model vdw 2.354 2.496 nonbonded pdb=" OG SER C 139 " pdb=" N SER C 140 " model vdw 2.355 3.120 nonbonded pdb=" N ASN F 656 " pdb=" O ASN F 656 " model vdw 2.360 2.496 nonbonded pdb=" NZ LYS A 46 " pdb=" OD2 ASP D 632 " model vdw 2.384 3.120 nonbonded pdb=" NZ LYS Y 46 " pdb=" OD2 ASP F 632 " model vdw 2.402 3.120 ... (remaining 118240 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 505 or resid 602 through 611)) selection = (chain 'C' and (resid 32 through 505 or resid 601 through 610)) selection = (chain 'Y' and (resid 32 through 505 or resid 602 through 611)) } ncs_group { reference = (chain 'B' and resid 527 through 702) selection = (chain 'D' and (resid 527 through 539 or resid 568 through 702)) selection = (chain 'F' and (resid 527 through 539 or resid 568 through 702)) } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'M' and resid 1 through 2) } 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: 6.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 16.030 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.022 0.174 15374 Z= 1.146 Angle : 1.728 18.086 21064 Z= 1.097 Chirality : 0.136 0.532 2591 Planarity : 0.011 0.263 2584 Dihedral : 11.797 113.277 6360 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 1.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.20), residues: 1615 helix: -0.23 (0.23), residues: 413 sheet: 0.58 (0.24), residues: 423 loop : 0.41 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 480 TYR 0.065 0.009 TYR D 638 PHE 0.036 0.006 PHE Y 353 TRP 0.058 0.009 TRP A 112 HIS 0.013 0.002 HIS C 374 Details of bonding type rmsd covalent geometry : bond 0.02101 (15276) covalent geometry : angle 1.69874 (20805) SS BOND : bond 0.03134 ( 35) SS BOND : angle 2.76649 ( 70) hydrogen bonds : bond 0.14450 ( 471) hydrogen bonds : angle 7.13245 ( 1257) link_BETA1-4 : bond 0.07137 ( 13) link_BETA1-4 : angle 4.76801 ( 39) link_NAG-ASN : bond 0.08148 ( 50) link_NAG-ASN : angle 3.09340 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 104 MET cc_start: 0.8639 (ttt) cc_final: 0.8399 (ttm) REVERT: A 215 ILE cc_start: 0.8956 (mm) cc_final: 0.8677 (mm) REVERT: A 425 ASN cc_start: 0.8425 (m-40) cc_final: 0.8055 (p0) REVERT: A 475 MET cc_start: 0.8844 (mmm) cc_final: 0.8380 (mmt) REVERT: Y 154 MET cc_start: 0.8038 (mmm) cc_final: 0.7756 (mmt) REVERT: D 590 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8663 (mm-40) REVERT: F 545 LEU cc_start: 0.8348 (mt) cc_final: 0.8062 (mt) REVERT: F 599 SER cc_start: 0.8771 (m) cc_final: 0.8379 (p) REVERT: F 631 TRP cc_start: 0.7213 (t-100) cc_final: 0.6980 (t-100) REVERT: B 601 LYS cc_start: 0.9192 (mmtt) cc_final: 0.8981 (mtpt) REVERT: B 615 SER cc_start: 0.8939 (t) cc_final: 0.8523 (p) REVERT: B 625 ASN cc_start: 0.8286 (t0) cc_final: 0.7905 (t0) REVERT: B 652 GLN cc_start: 0.8145 (tp40) cc_final: 0.7778 (tm-30) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1459 time to fit residues: 72.2800 Evaluate side-chains 158 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.6980 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 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 315 GLN D 570 HIS D 625 ASN C 425 ASN B 640 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.114366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.092578 restraints weight = 30129.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.095378 restraints weight = 18648.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.097262 restraints weight = 13541.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.098558 restraints weight = 10811.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.099409 restraints weight = 9188.997| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15374 Z= 0.174 Angle : 0.741 10.675 21064 Z= 0.364 Chirality : 0.047 0.436 2591 Planarity : 0.004 0.052 2584 Dihedral : 8.850 103.475 3271 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 7.51 % Favored : 90.47 % 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: 0.46 (0.20), residues: 1615 helix: 1.09 (0.27), residues: 405 sheet: 0.23 (0.24), residues: 422 loop : 0.07 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 169 TYR 0.019 0.002 TYR F 638 PHE 0.018 0.002 PHE Y 176 TRP 0.023 0.002 TRP C 479 HIS 0.004 0.001 HIS B 585 Details of bonding type rmsd covalent geometry : bond 0.00378 (15276) covalent geometry : angle 0.68149 (20805) SS BOND : bond 0.00312 ( 35) SS BOND : angle 1.15793 ( 70) hydrogen bonds : bond 0.04890 ( 471) hydrogen bonds : angle 5.40730 ( 1257) link_BETA1-4 : bond 0.00937 ( 13) link_BETA1-4 : angle 2.95642 ( 39) link_NAG-ASN : bond 0.00574 ( 50) link_NAG-ASN : angle 3.12671 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 425 ASN cc_start: 0.7725 (m-40) cc_final: 0.7503 (p0) REVERT: A 475 MET cc_start: 0.8410 (mmm) cc_final: 0.8203 (mmt) REVERT: Y 69 TRP cc_start: 0.8227 (m100) cc_final: 0.7650 (m100) REVERT: Y 318 TYR cc_start: 0.8393 (m-80) cc_final: 0.8192 (m-80) REVERT: D 590 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8608 (mm-40) REVERT: F 599 SER cc_start: 0.8733 (m) cc_final: 0.8247 (p) REVERT: F 632 ASP cc_start: 0.8620 (t70) cc_final: 0.8323 (t0) REVERT: F 634 GLU cc_start: 0.7473 (pt0) cc_final: 0.7230 (pt0) REVERT: C 207 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8048 (mmmm) REVERT: C 257 THR cc_start: 0.9080 (p) cc_final: 0.8866 (t) REVERT: B 591 GLN cc_start: 0.8714 (tt0) cc_final: 0.8477 (tt0) REVERT: B 652 GLN cc_start: 0.7824 (tp40) cc_final: 0.7591 (tm-30) outliers start: 30 outliers final: 16 residues processed: 201 average time/residue: 0.1336 time to fit residues: 40.1851 Evaluate side-chains 158 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 112 TRP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 33 ASN Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 466 GLU Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 150 optimal weight: 0.0980 chunk 123 optimal weight: 0.0010 chunk 161 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 190 GLN A 229 ASN D 625 ASN B 651 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.089007 restraints weight = 31144.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.091549 restraints weight = 19906.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.093297 restraints weight = 14741.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.094508 restraints weight = 11957.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095355 restraints weight = 10271.288| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15374 Z= 0.179 Angle : 0.665 10.786 21064 Z= 0.324 Chirality : 0.046 0.422 2591 Planarity : 0.004 0.045 2584 Dihedral : 7.341 96.860 3271 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.16 % Allowed : 8.25 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.20), residues: 1615 helix: 1.13 (0.27), residues: 404 sheet: 0.04 (0.24), residues: 424 loop : -0.13 (0.21), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 327 TYR 0.021 0.002 TYR D 643 PHE 0.015 0.002 PHE Y 176 TRP 0.014 0.001 TRP C 479 HIS 0.005 0.001 HIS Y 287 Details of bonding type rmsd covalent geometry : bond 0.00407 (15276) covalent geometry : angle 0.61275 (20805) SS BOND : bond 0.00294 ( 35) SS BOND : angle 1.00611 ( 70) hydrogen bonds : bond 0.04285 ( 471) hydrogen bonds : angle 4.94633 ( 1257) link_BETA1-4 : bond 0.00529 ( 13) link_BETA1-4 : angle 2.29371 ( 39) link_NAG-ASN : bond 0.00410 ( 50) link_NAG-ASN : angle 2.86535 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 158 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 475 MET cc_start: 0.8339 (mmm) cc_final: 0.8101 (mmt) REVERT: D 542 ARG cc_start: 0.7960 (ptm160) cc_final: 0.7748 (ptm160) REVERT: D 652 GLN cc_start: 0.8183 (mt0) cc_final: 0.7928 (mt0) REVERT: D 653 GLN cc_start: 0.8259 (tm-30) cc_final: 0.7993 (tm-30) REVERT: F 599 SER cc_start: 0.8776 (m) cc_final: 0.8254 (p) REVERT: F 632 ASP cc_start: 0.8593 (t70) cc_final: 0.8315 (t0) REVERT: F 653 GLN cc_start: 0.8851 (tt0) cc_final: 0.8633 (tt0) REVERT: C 207 LYS cc_start: 0.8461 (mtmm) cc_final: 0.8020 (mmmt) REVERT: C 257 THR cc_start: 0.9046 (p) cc_final: 0.8780 (t) REVERT: B 625 ASN cc_start: 0.7378 (t0) cc_final: 0.6905 (t0) REVERT: B 647 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7269 (mt-10) outliers start: 32 outliers final: 17 residues processed: 179 average time/residue: 0.1288 time to fit residues: 34.5543 Evaluate side-chains 159 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 33 ASN Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 66 HIS Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 294 ILE Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 599 SER Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 48 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 625 ASN C 464 ASN B 591 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.110538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088855 restraints weight = 30874.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091516 restraints weight = 19419.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093326 restraints weight = 14289.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.094583 restraints weight = 11529.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.095481 restraints weight = 9878.228| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15374 Z= 0.168 Angle : 0.625 9.793 21064 Z= 0.306 Chirality : 0.045 0.403 2591 Planarity : 0.004 0.063 2584 Dihedral : 6.542 90.337 3271 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.03 % Allowed : 9.60 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.13 (0.21), residues: 1615 helix: 1.20 (0.27), residues: 404 sheet: 0.03 (0.25), residues: 391 loop : -0.38 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 308 TYR 0.024 0.002 TYR Y 318 PHE 0.028 0.002 PHE Y 53 TRP 0.035 0.002 TRP F 610 HIS 0.007 0.001 HIS Y 287 Details of bonding type rmsd covalent geometry : bond 0.00385 (15276) covalent geometry : angle 0.58383 (20805) SS BOND : bond 0.00288 ( 35) SS BOND : angle 0.94198 ( 70) hydrogen bonds : bond 0.03840 ( 471) hydrogen bonds : angle 4.72738 ( 1257) link_BETA1-4 : bond 0.00475 ( 13) link_BETA1-4 : angle 1.78962 ( 39) link_NAG-ASN : bond 0.00347 ( 50) link_NAG-ASN : angle 2.51020 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8484 (mp) REVERT: A 202 THR cc_start: 0.9159 (m) cc_final: 0.8894 (p) REVERT: A 357 LYS cc_start: 0.4707 (mtmt) cc_final: 0.3924 (tttm) REVERT: A 475 MET cc_start: 0.8355 (mmm) cc_final: 0.8070 (mmt) REVERT: Y 475 MET cc_start: 0.8385 (mmm) cc_final: 0.8164 (tpp) REVERT: D 542 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7732 (ptm160) REVERT: D 653 GLN cc_start: 0.8371 (tm-30) cc_final: 0.7955 (tm-30) REVERT: F 599 SER cc_start: 0.8812 (m) cc_final: 0.8310 (p) REVERT: F 631 TRP cc_start: 0.7644 (t-100) cc_final: 0.6709 (t-100) REVERT: B 625 ASN cc_start: 0.7277 (t0) cc_final: 0.6883 (t0) REVERT: B 647 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7363 (mt-10) REVERT: B 659 ASP cc_start: 0.8210 (t70) cc_final: 0.7970 (p0) outliers start: 30 outliers final: 17 residues processed: 178 average time/residue: 0.1375 time to fit residues: 36.0858 Evaluate side-chains 164 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 294 ILE Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 63 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN C 72 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.110090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088575 restraints weight = 30997.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.091173 restraints weight = 19791.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.092910 restraints weight = 14601.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.094062 restraints weight = 11888.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.094927 restraints weight = 10283.095| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15374 Z= 0.157 Angle : 0.596 9.379 21064 Z= 0.292 Chirality : 0.045 0.389 2591 Planarity : 0.003 0.046 2584 Dihedral : 6.369 87.113 3271 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.96 % Allowed : 10.21 % Favored : 87.83 % 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: 0.14 (0.21), residues: 1615 helix: 1.33 (0.28), residues: 403 sheet: 0.07 (0.25), residues: 396 loop : -0.46 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 327 TYR 0.016 0.001 TYR D 586 PHE 0.022 0.002 PHE Y 53 TRP 0.061 0.002 TRP F 610 HIS 0.004 0.001 HIS B 570 Details of bonding type rmsd covalent geometry : bond 0.00360 (15276) covalent geometry : angle 0.55355 (20805) SS BOND : bond 0.00307 ( 35) SS BOND : angle 0.95868 ( 70) hydrogen bonds : bond 0.03670 ( 471) hydrogen bonds : angle 4.64545 ( 1257) link_BETA1-4 : bond 0.00430 ( 13) link_BETA1-4 : angle 1.51388 ( 39) link_NAG-ASN : bond 0.00333 ( 50) link_NAG-ASN : angle 2.52546 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 151 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 202 THR cc_start: 0.9114 (m) cc_final: 0.8864 (p) REVERT: A 357 LYS cc_start: 0.4872 (mtmt) cc_final: 0.4116 (tttm) REVERT: A 475 MET cc_start: 0.8348 (mmm) cc_final: 0.8085 (mmt) REVERT: Y 69 TRP cc_start: 0.8137 (m100) cc_final: 0.7616 (m100) REVERT: Y 125 LEU cc_start: 0.8512 (mt) cc_final: 0.8215 (mt) REVERT: Y 317 PHE cc_start: 0.8567 (t80) cc_final: 0.8234 (t80) REVERT: D 542 ARG cc_start: 0.8195 (ptm160) cc_final: 0.7751 (ptm160) REVERT: D 653 GLN cc_start: 0.8431 (tm-30) cc_final: 0.7865 (tm-30) REVERT: F 599 SER cc_start: 0.8719 (m) cc_final: 0.8187 (p) REVERT: B 625 ASN cc_start: 0.7231 (t0) cc_final: 0.6852 (t0) REVERT: B 647 GLU cc_start: 0.7984 (mt-10) cc_final: 0.7347 (mt-10) REVERT: B 657 GLU cc_start: 0.7646 (tt0) cc_final: 0.7387 (tt0) REVERT: B 659 ASP cc_start: 0.8247 (t70) cc_final: 0.8014 (p0) outliers start: 29 outliers final: 21 residues processed: 171 average time/residue: 0.1251 time to fit residues: 32.1717 Evaluate side-chains 163 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 294 ILE Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 653 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 60 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 625 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.109825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.088472 restraints weight = 30915.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.091002 restraints weight = 19699.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092749 restraints weight = 14596.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.093955 restraints weight = 11853.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.094696 restraints weight = 10221.914| |-----------------------------------------------------------------------------| r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15374 Z= 0.148 Angle : 0.584 9.031 21064 Z= 0.285 Chirality : 0.044 0.382 2591 Planarity : 0.003 0.047 2584 Dihedral : 6.231 84.273 3271 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.10 % Allowed : 10.21 % Favored : 87.69 % 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: 0.10 (0.21), residues: 1615 helix: 1.35 (0.28), residues: 403 sheet: 0.01 (0.26), residues: 395 loop : -0.50 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 327 TYR 0.012 0.001 TYR D 638 PHE 0.022 0.002 PHE Y 53 TRP 0.030 0.002 TRP F 610 HIS 0.004 0.001 HIS Y 287 Details of bonding type rmsd covalent geometry : bond 0.00341 (15276) covalent geometry : angle 0.54375 (20805) SS BOND : bond 0.00285 ( 35) SS BOND : angle 0.96993 ( 70) hydrogen bonds : bond 0.03559 ( 471) hydrogen bonds : angle 4.55466 ( 1257) link_BETA1-4 : bond 0.00457 ( 13) link_BETA1-4 : angle 1.42159 ( 39) link_NAG-ASN : bond 0.00309 ( 50) link_NAG-ASN : angle 2.43790 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 202 THR cc_start: 0.9057 (m) cc_final: 0.8812 (p) REVERT: A 357 LYS cc_start: 0.4905 (mtmt) cc_final: 0.4269 (tttm) REVERT: A 475 MET cc_start: 0.8342 (mmm) cc_final: 0.7981 (mmt) REVERT: Y 125 LEU cc_start: 0.8549 (mt) cc_final: 0.8186 (mt) REVERT: Y 317 PHE cc_start: 0.8675 (t80) cc_final: 0.8241 (t80) REVERT: D 542 ARG cc_start: 0.8207 (ptm160) cc_final: 0.7721 (ptm160) REVERT: D 653 GLN cc_start: 0.8440 (tm-30) cc_final: 0.7820 (tm-30) REVERT: F 599 SER cc_start: 0.8726 (m) cc_final: 0.8187 (p) REVERT: F 633 LYS cc_start: 0.8815 (mttp) cc_final: 0.8544 (mmtm) REVERT: B 625 ASN cc_start: 0.7195 (t0) cc_final: 0.6863 (t0) REVERT: B 647 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7362 (mt-10) REVERT: B 657 GLU cc_start: 0.7664 (tt0) cc_final: 0.7400 (tt0) REVERT: B 659 ASP cc_start: 0.8281 (t70) cc_final: 0.8057 (p0) outliers start: 31 outliers final: 24 residues processed: 167 average time/residue: 0.1224 time to fit residues: 30.8935 Evaluate side-chains 160 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 294 ILE Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 638 TYR Chi-restraints excluded: chain B residue 648 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 229 ASN D 625 ASN F 640 GLN C 94 ASN C 425 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.104047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.082851 restraints weight = 31588.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.086055 restraints weight = 21623.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087940 restraints weight = 14511.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088050 restraints weight = 11424.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.088388 restraints weight = 11444.127| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.4729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 15374 Z= 0.364 Angle : 0.824 10.747 21064 Z= 0.400 Chirality : 0.052 0.425 2591 Planarity : 0.005 0.047 2584 Dihedral : 7.497 83.961 3271 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.43 % Allowed : 10.55 % Favored : 87.02 % 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: -0.63 (0.21), residues: 1615 helix: 0.83 (0.27), residues: 399 sheet: -0.51 (0.26), residues: 390 loop : -0.96 (0.20), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 480 TYR 0.016 0.002 TYR B 638 PHE 0.021 0.003 PHE A 361 TRP 0.035 0.003 TRP A 427 HIS 0.007 0.002 HIS Y 352 Details of bonding type rmsd covalent geometry : bond 0.00853 (15276) covalent geometry : angle 0.78285 (20805) SS BOND : bond 0.00646 ( 35) SS BOND : angle 1.53016 ( 70) hydrogen bonds : bond 0.04512 ( 471) hydrogen bonds : angle 5.17810 ( 1257) link_BETA1-4 : bond 0.00480 ( 13) link_BETA1-4 : angle 1.71169 ( 39) link_NAG-ASN : bond 0.00504 ( 50) link_NAG-ASN : angle 2.89898 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8383 (p0) cc_final: 0.8171 (p0) REVERT: A 116 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8744 (mp) REVERT: A 202 THR cc_start: 0.9127 (m) cc_final: 0.8827 (p) REVERT: A 475 MET cc_start: 0.8544 (mmm) cc_final: 0.8308 (mmt) REVERT: Y 317 PHE cc_start: 0.8878 (t80) cc_final: 0.8531 (t80) REVERT: Y 371 VAL cc_start: 0.9405 (m) cc_final: 0.9198 (p) REVERT: D 542 ARG cc_start: 0.8297 (ptm160) cc_final: 0.7790 (ptm160) REVERT: D 634 GLU cc_start: 0.8515 (tm-30) cc_final: 0.8060 (tm-30) REVERT: D 653 GLN cc_start: 0.8588 (tm-30) cc_final: 0.7850 (tm-30) REVERT: F 599 SER cc_start: 0.9074 (m) cc_final: 0.8465 (p) REVERT: C 78 ASP cc_start: 0.8079 (t0) cc_final: 0.7811 (m-30) REVERT: C 217 TYR cc_start: 0.8831 (m-80) cc_final: 0.8609 (m-10) REVERT: C 319 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8609 (p) REVERT: B 625 ASN cc_start: 0.7824 (t0) cc_final: 0.7489 (t0) REVERT: B 647 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 657 GLU cc_start: 0.7774 (tt0) cc_final: 0.7538 (tt0) REVERT: B 659 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8003 (p0) outliers start: 36 outliers final: 29 residues processed: 176 average time/residue: 0.1300 time to fit residues: 34.2636 Evaluate side-chains 175 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 143 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain Y residue 33 ASN Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 294 ILE Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain Y residue 373 THR Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 439 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 618 THR Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain F residue 603 ILE Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 319 THR Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 653 GLN Chi-restraints excluded: chain B residue 659 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 97 optimal weight: 7.9990 chunk 161 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN C 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.108349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.087212 restraints weight = 30988.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.089675 restraints weight = 19830.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091369 restraints weight = 14790.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.092532 restraints weight = 12032.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.093361 restraints weight = 10398.138| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15374 Z= 0.129 Angle : 0.603 11.125 21064 Z= 0.295 Chirality : 0.044 0.382 2591 Planarity : 0.004 0.048 2584 Dihedral : 6.700 82.817 3271 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.16 % Allowed : 11.22 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.21), residues: 1615 helix: 1.29 (0.28), residues: 399 sheet: -0.39 (0.25), residues: 425 loop : -0.78 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG Y 166 TYR 0.011 0.001 TYR B 638 PHE 0.021 0.001 PHE Y 53 TRP 0.024 0.002 TRP F 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00289 (15276) covalent geometry : angle 0.56360 (20805) SS BOND : bond 0.00245 ( 35) SS BOND : angle 0.86765 ( 70) hydrogen bonds : bond 0.03584 ( 471) hydrogen bonds : angle 4.70166 ( 1257) link_BETA1-4 : bond 0.00463 ( 13) link_BETA1-4 : angle 1.28787 ( 39) link_NAG-ASN : bond 0.00352 ( 50) link_NAG-ASN : angle 2.48653 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 146 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 202 THR cc_start: 0.9025 (m) cc_final: 0.8741 (p) REVERT: A 330 TYR cc_start: 0.8926 (p90) cc_final: 0.8706 (p90) REVERT: A 357 LYS cc_start: 0.3167 (ttpp) cc_final: 0.2693 (ptpp) REVERT: A 475 MET cc_start: 0.8397 (mmm) cc_final: 0.8086 (mmt) REVERT: Y 69 TRP cc_start: 0.8140 (m100) cc_final: 0.7697 (m100) REVERT: Y 371 VAL cc_start: 0.9347 (m) cc_final: 0.9145 (p) REVERT: D 542 ARG cc_start: 0.8235 (ptm160) cc_final: 0.7827 (ptm160) REVERT: D 590 GLN cc_start: 0.8749 (mm-40) cc_final: 0.7837 (tt0) REVERT: F 599 SER cc_start: 0.8911 (m) cc_final: 0.8247 (p) REVERT: B 647 GLU cc_start: 0.7971 (mt-10) cc_final: 0.7376 (mt-10) REVERT: B 657 GLU cc_start: 0.7659 (tt0) cc_final: 0.7411 (mt-10) REVERT: B 659 ASP cc_start: 0.8257 (t70) cc_final: 0.7927 (p0) outliers start: 32 outliers final: 21 residues processed: 169 average time/residue: 0.1309 time to fit residues: 33.1765 Evaluate side-chains 161 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 49 GLU Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 638 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 30 optimal weight: 0.0000 chunk 136 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 17 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** Y 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN F 640 GLN C 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.105980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085285 restraints weight = 31364.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.088346 restraints weight = 20449.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089444 restraints weight = 14302.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089596 restraints weight = 11783.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.089973 restraints weight = 11410.633| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15374 Z= 0.248 Angle : 0.684 9.520 21064 Z= 0.337 Chirality : 0.048 0.393 2591 Planarity : 0.004 0.036 2584 Dihedral : 6.880 81.545 3271 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.10 % Allowed : 11.90 % Favored : 86.00 % 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: -0.51 (0.21), residues: 1615 helix: 1.17 (0.28), residues: 399 sheet: -0.55 (0.27), residues: 384 loop : -0.95 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 480 TYR 0.013 0.002 TYR B 638 PHE 0.018 0.002 PHE Y 53 TRP 0.064 0.002 TRP F 610 HIS 0.005 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00577 (15276) covalent geometry : angle 0.64591 (20805) SS BOND : bond 0.00442 ( 35) SS BOND : angle 1.15111 ( 70) hydrogen bonds : bond 0.03900 ( 471) hydrogen bonds : angle 4.84135 ( 1257) link_BETA1-4 : bond 0.00415 ( 13) link_BETA1-4 : angle 1.44572 ( 39) link_NAG-ASN : bond 0.00359 ( 50) link_NAG-ASN : angle 2.59845 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8410 (p0) cc_final: 0.8187 (p0) REVERT: A 116 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 202 THR cc_start: 0.9057 (m) cc_final: 0.8811 (p) REVERT: A 330 TYR cc_start: 0.8969 (p90) cc_final: 0.8706 (p90) REVERT: A 357 LYS cc_start: 0.3280 (ttpp) cc_final: 0.2778 (ptpp) REVERT: A 475 MET cc_start: 0.8489 (mmm) cc_final: 0.8213 (mmt) REVERT: Y 154 MET cc_start: 0.8772 (mmm) cc_final: 0.8398 (mtp) REVERT: D 542 ARG cc_start: 0.8312 (ptm160) cc_final: 0.7914 (ptm160) REVERT: D 634 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8248 (tm-30) REVERT: F 599 SER cc_start: 0.9056 (m) cc_final: 0.8419 (p) REVERT: F 633 LYS cc_start: 0.8822 (mttp) cc_final: 0.8539 (mmtm) REVERT: B 647 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7437 (mt-10) REVERT: B 657 GLU cc_start: 0.7744 (tt0) cc_final: 0.7473 (mt-10) REVERT: B 659 ASP cc_start: 0.8260 (t70) cc_final: 0.7849 (p0) outliers start: 31 outliers final: 26 residues processed: 158 average time/residue: 0.1283 time to fit residues: 30.6484 Evaluate side-chains 160 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 133 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 97 LYS Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 346 VAL Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 439 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 655 LYS Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 653 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 154 optimal weight: 0.7980 chunk 160 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 136 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 147 optimal weight: 0.0030 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 7.9990 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN ** Y 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 625 ASN C 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.108537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.087391 restraints weight = 31025.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.089840 restraints weight = 19905.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091523 restraints weight = 14800.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.092702 restraints weight = 12078.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.093536 restraints weight = 10416.552| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15374 Z= 0.123 Angle : 0.588 8.758 21064 Z= 0.292 Chirality : 0.044 0.368 2591 Planarity : 0.003 0.034 2584 Dihedral : 6.496 81.045 3271 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.69 % Allowed : 12.58 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.29 (0.21), residues: 1615 helix: 1.34 (0.28), residues: 398 sheet: -0.36 (0.25), residues: 419 loop : -0.84 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Y 166 TYR 0.009 0.001 TYR D 638 PHE 0.011 0.001 PHE A 53 TRP 0.056 0.002 TRP F 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00273 (15276) covalent geometry : angle 0.55162 (20805) SS BOND : bond 0.00205 ( 35) SS BOND : angle 0.82468 ( 70) hydrogen bonds : bond 0.03436 ( 471) hydrogen bonds : angle 4.64483 ( 1257) link_BETA1-4 : bond 0.00463 ( 13) link_BETA1-4 : angle 1.27057 ( 39) link_NAG-ASN : bond 0.00317 ( 50) link_NAG-ASN : angle 2.36116 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3230 Ramachandran restraints generated. 1615 Oldfield, 0 Emsley, 1615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8657 (mp) REVERT: A 202 THR cc_start: 0.8982 (m) cc_final: 0.8728 (p) REVERT: A 330 TYR cc_start: 0.8930 (p90) cc_final: 0.8723 (p90) REVERT: A 357 LYS cc_start: 0.3361 (ttpp) cc_final: 0.2786 (ptpp) REVERT: A 475 MET cc_start: 0.8423 (mmm) cc_final: 0.8095 (mmt) REVERT: Y 154 MET cc_start: 0.8646 (mmm) cc_final: 0.8340 (mtp) REVERT: D 542 ARG cc_start: 0.8233 (ptm160) cc_final: 0.7811 (ptm160) REVERT: D 586 TYR cc_start: 0.9113 (t80) cc_final: 0.8331 (t80) REVERT: D 590 GLN cc_start: 0.8776 (mm-40) cc_final: 0.7870 (tt0) REVERT: F 599 SER cc_start: 0.8948 (m) cc_final: 0.8263 (p) REVERT: C 97 LYS cc_start: 0.8508 (mptt) cc_final: 0.8168 (mtmm) REVERT: B 530 MET cc_start: 0.9391 (mmm) cc_final: 0.9082 (mmm) REVERT: B 647 GLU cc_start: 0.7927 (mt-10) cc_final: 0.7283 (mt-10) REVERT: B 657 GLU cc_start: 0.7596 (tt0) cc_final: 0.7395 (tt0) REVERT: B 659 ASP cc_start: 0.8277 (t70) cc_final: 0.7971 (p0) outliers start: 25 outliers final: 21 residues processed: 161 average time/residue: 0.1197 time to fit residues: 29.6647 Evaluate side-chains 163 residues out of total 1479 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 94 PHE Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain Y residue 52 LEU Chi-restraints excluded: chain Y residue 75 VAL Chi-restraints excluded: chain Y residue 111 LEU Chi-restraints excluded: chain Y residue 120 VAL Chi-restraints excluded: chain Y residue 123 THR Chi-restraints excluded: chain Y residue 434 MET Chi-restraints excluded: chain Y residue 439 ILE Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain C residue 296 CYS Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain B residue 615 SER Chi-restraints excluded: chain B residue 648 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN D 625 ASN F 640 GLN C 138 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.088014 restraints weight = 30991.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.089809 restraints weight = 24629.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.091258 restraints weight = 17732.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.091524 restraints weight = 14402.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.091703 restraints weight = 13639.351| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15374 Z= 0.157 Angle : 0.618 9.353 21064 Z= 0.307 Chirality : 0.045 0.362 2591 Planarity : 0.004 0.034 2584 Dihedral : 6.418 79.475 3271 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.83 % Allowed : 12.71 % Favored : 85.46 % 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: -0.35 (0.21), residues: 1615 helix: 1.27 (0.28), residues: 399 sheet: -0.35 (0.26), residues: 403 loop : -0.89 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Y 166 TYR 0.010 0.001 TYR D 638 PHE 0.011 0.002 PHE A 361 TRP 0.052 0.002 TRP F 610 HIS 0.004 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00362 (15276) covalent geometry : angle 0.57926 (20805) SS BOND : bond 0.00328 ( 35) SS BOND : angle 1.23230 ( 70) hydrogen bonds : bond 0.03526 ( 471) hydrogen bonds : angle 4.66421 ( 1257) link_BETA1-4 : bond 0.00439 ( 13) link_BETA1-4 : angle 1.32160 ( 39) link_NAG-ASN : bond 0.00296 ( 50) link_NAG-ASN : angle 2.43268 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2476.13 seconds wall clock time: 43 minutes 51.57 seconds (2631.57 seconds total)