Starting phenix.real_space_refine on Sat Jul 4 07:30:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x98_22104/07_2026/6x98_22104.map" } resolution = 3.38 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= 0.005 sd= 0.101 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 135 5.16 5 C 12078 2.51 5 N 3228 2.21 5 O 3828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19269 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "B" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "L" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "H" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "D" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "E" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "F" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "G" Number of atoms: 3435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3435 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 22, 'TRANS': 413} Chain breaks: 4 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 971 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 1, 'TRANS': 120} Chain breaks: 1 Chain: "J" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 823 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 107} Chain: "K" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 892 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "M" 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 chiralities: 2 Chain: "N" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "O" 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 chiralities: 2 Chain: "P" 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 chiralities: 2 Chain: "Q" 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 chiralities: 2 Chain: "R" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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 chiralities: 2 Chain: "X" 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 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 chiralities: 12 Chain: "C" 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 chiralities: 12 Chain: "G" 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 chiralities: 12 Time building chain proxies: 4.28, per 1000 atoms: 0.22 Number of scatterers: 19269 At special positions: 0 Unit cell: (157.59, 143.17, 118.45, 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 135 16.00 O 3828 8.00 N 3228 7.00 C 12078 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.05 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.04 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.04 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.06 Simple disulfide: pdb=" SG CYS H 35A" - pdb=" SG CYS H 50 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.04 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.05 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.04 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.06 Simple disulfide: pdb=" SG CYS F 35A" - pdb=" SG CYS F 50 " distance=2.02 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 74 " distance=2.03 Simple disulfide: pdb=" SG CYS G 119 " - pdb=" SG CYS G 205 " distance=2.05 Simple disulfide: pdb=" SG CYS G 126 " - pdb=" SG CYS G 196 " distance=2.04 Simple disulfide: pdb=" SG CYS G 131 " - pdb=" SG CYS G 157 " distance=2.04 Simple disulfide: pdb=" SG CYS G 218 " - pdb=" SG CYS G 247 " distance=2.04 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS G 239 " distance=2.05 Simple disulfide: pdb=" SG CYS G 296 " - pdb=" SG CYS G 331 " distance=2.03 Simple disulfide: pdb=" SG CYS G 378 " - pdb=" SG CYS G 445 " distance=2.02 Simple disulfide: pdb=" SG CYS G 385 " - pdb=" SG CYS G 418 " distance=2.03 Simple disulfide: pdb=" SG CYS G 501 " - pdb=" SG CYS I 605 " distance=2.04 Simple disulfide: pdb=" SG CYS I 598 " - pdb=" SG CYS I 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.06 Simple disulfide: pdb=" SG CYS K 35A" - pdb=" SG CYS K 50 " 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 ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA R 3 " - " MAN R 4 " " BMA V 3 " - " MAN V 4 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 607 " - " ASN A 448 " " NAG A 608 " - " ASN A 295 " " NAG A 609 " - " ASN A 301 " " NAG A 610 " - " ASN A 156 " " NAG A 611 " - " ASN A 160 " " NAG A 612 " - " ASN A 133 " " NAG A 615 " - " ASN A 276 " " NAG A 616 " - " ASN A 339 " " NAG A 619 " - " ASN A 363 " " NAG A 620 " - " ASN A 332 " " NAG A 621 " - " ASN A 234 " " NAG A 622 " - " ASN A 392 " " NAG C 607 " - " ASN C 448 " " NAG C 608 " - " ASN C 295 " " NAG C 609 " - " ASN C 301 " " NAG C 610 " - " ASN C 156 " " NAG C 611 " - " ASN C 160 " " NAG C 612 " - " ASN C 133 " " NAG C 615 " - " ASN C 276 " " NAG C 616 " - " ASN C 339 " " NAG C 619 " - " ASN C 363 " " NAG C 620 " - " ASN C 332 " " NAG C 621 " - " ASN C 234 " " NAG C 622 " - " ASN C 392 " " NAG G 607 " - " ASN G 448 " " NAG G 608 " - " ASN G 295 " " NAG G 609 " - " ASN G 301 " " NAG G 610 " - " ASN G 156 " " NAG G 611 " - " ASN G 160 " " NAG G 612 " - " ASN G 133 " " NAG G 615 " - " ASN G 276 " " NAG G 616 " - " ASN G 339 " " NAG G 619 " - " ASN G 363 " " NAG G 620 " - " ASN G 332 " " NAG G 621 " - " ASN G 234 " " NAG G 622 " - " ASN G 392 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 262 " " NAG O 1 " - " ASN A 197 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN C 88 " " NAG R 1 " - " ASN C 262 " " NAG S 1 " - " ASN C 197 " " NAG T 1 " - " ASN C 386 " " NAG U 1 " - " ASN G 88 " " NAG V 1 " - " ASN G 262 " " NAG W 1 " - " ASN G 197 " " NAG X 1 " - " ASN G 386 " Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 726.0 milliseconds 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 48 sheets defined 20.8% alpha, 42.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 99 through 117 removed outlier: 3.633A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 117 " --> pdb=" O ASP A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 Processing helix chain 'B' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN B 540 " --> pdb=" O THR B 536 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU B 576 " --> pdb=" O GLY B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 626 removed outlier: 3.763A pdb=" N ASP B 624 " --> pdb=" O SER B 620 " (cutoff:3.500A) removed outlier: 3.812A 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 662 Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU H 64 " --> pdb=" O ARG H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS C 117 " --> pdb=" O ASP C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'D' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 Processing helix chain 'D' and resid 536 through 542 removed outlier: 4.244A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP D 624 " --> pdb=" O SER D 620 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 626 " --> pdb=" O ILE D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 662 Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU F 64 " --> pdb=" O ARG F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 70 through 74 Processing helix chain 'G' and resid 99 through 117 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O TRP G 112 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 126 Processing helix chain 'G' and resid 335 through 350 Processing helix chain 'G' and resid 351 through 353 No H-bonds generated for 'chain 'G' and resid 351 through 353' Processing helix chain 'G' and resid 368 through 373 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 474 through 479 Processing helix chain 'G' and resid 482 through 484 No H-bonds generated for 'chain 'G' and resid 482 through 484' Processing helix chain 'I' and resid 523 through 528 removed outlier: 4.216A pdb=" N GLY I 527 " --> pdb=" O GLY I 524 " (cutoff:3.500A) Processing helix chain 'I' and resid 529 through 534 Processing helix chain 'I' and resid 536 through 542 removed outlier: 4.245A pdb=" N GLN I 540 " --> pdb=" O THR I 536 " (cutoff:3.500A) Processing helix chain 'I' and resid 572 through 596 removed outlier: 3.506A pdb=" N LEU I 576 " --> pdb=" O GLY I 572 " (cutoff:3.500A) Processing helix chain 'I' and resid 618 through 626 removed outlier: 3.762A pdb=" N ASP I 624 " --> pdb=" O SER I 620 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET I 626 " --> pdb=" O ILE I 622 " (cutoff:3.500A) Processing helix chain 'I' and resid 627 through 635 Processing helix chain 'I' and resid 638 through 662 Processing helix chain 'K' and resid 61 through 64 removed outlier: 3.720A pdb=" N GLU K 64 " --> pdb=" O ARG K 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 61 through 64' Processing helix chain 'K' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.166A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 443 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY A 451 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE A 453 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 334 " --> pdb=" O GLN A 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 274 Processing sheet with id=AB1, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE A 309 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN A 301 " --> pdb=" O ILE A 323A" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL L 11 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR H 33 " --> pdb=" O PHE H 52 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N PHE H 52 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET H 35 " --> pdb=" O CYS H 50 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N CYS H 50 " --> pdb=" O MET H 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 11 removed outlier: 3.505A pdb=" N LEU H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP H 96 " --> pdb=" O ALA H 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA H 100E" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE C 443 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY C 451 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE C 453 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 11.988A pdb=" N PHE C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.801A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.652A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 271 through 274 Processing sheet with id=AC8, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE C 309 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN C 301 " --> pdb=" O ILE C 323A" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL E 11 " --> pdb=" O VAL E 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AD4, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.950A pdb=" N TYR F 33 " --> pdb=" O PHE F 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE F 52 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N MET F 35 " --> pdb=" O CYS F 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS F 50 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU F 102 " --> pdb=" O ARG F 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP F 96 " --> pdb=" O ALA F 100E" (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 100E" --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 494 through 498 Processing sheet with id=AD7, first strand: chain 'G' and resid 45 through 47 Processing sheet with id=AD8, first strand: chain 'G' and resid 75 through 76 Processing sheet with id=AD9, first strand: chain 'G' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'G' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'G' and resid 200 through 203 removed outlier: 6.167A pdb=" N ALA G 200 " --> pdb=" O ALA G 433 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR G 435 " --> pdb=" O ALA G 200 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N THR G 202 " --> pdb=" O TYR G 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 393 through 395 removed outlier: 6.288A pdb=" N ILE G 358 " --> pdb=" O GLU G 466 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N PHE G 468 " --> pdb=" O ILE G 358 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG G 360 " --> pdb=" O PHE G 468 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N GLY G 441 " --> pdb=" O ASN G 300 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN G 300 " --> pdb=" O GLY G 441 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE G 443 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLY G 451 " --> pdb=" O THR G 290 " (cutoff:3.500A) removed outlier: 10.655A pdb=" N THR G 290 " --> pdb=" O GLY G 451 " (cutoff:3.500A) removed outlier: 11.905A pdb=" N ILE G 453 " --> pdb=" O PHE G 288 " (cutoff:3.500A) removed outlier: 11.987A pdb=" N PHE G 288 " --> pdb=" O ILE G 453 " (cutoff:3.500A) removed outlier: 10.800A pdb=" N THR G 455 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 10.651A pdb=" N VAL G 286 " --> pdb=" O THR G 455 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLN G 293 " --> pdb=" O SER G 334 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER G 334 " --> pdb=" O GLN G 293 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE G 382 " --> pdb=" O LYS G 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 259 through 260 removed outlier: 6.617A pdb=" N LEU G 260 " --> pdb=" O THR G 450 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 271 through 274 Processing sheet with id=AE6, first strand: chain 'G' and resid 315 through 323A removed outlier: 7.135A pdb=" N ALA G 316 " --> pdb=" O ILE G 309 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ILE G 309 " --> pdb=" O ALA G 316 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N TYR G 318 " --> pdb=" O ILE G 307 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE G 307 " --> pdb=" O TYR G 318 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR G 320 " --> pdb=" O LYS G 305 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS G 305 " --> pdb=" O THR G 320 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ASP G 322 " --> pdb=" O THR G 303 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN G 301 " --> pdb=" O ILE G 323A" (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLN J 37 " --> pdb=" O LEU J 46 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU J 46 " --> pdb=" O GLN J 37 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.752A pdb=" N VAL J 11 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.949A pdb=" N TYR K 33 " --> pdb=" O PHE K 52 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N PHE K 52 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET K 35 " --> pdb=" O CYS K 50 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N CYS K 50 " --> pdb=" O MET K 35 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 10 through 11 removed outlier: 3.504A pdb=" N LEU K 102 " --> pdb=" O ARG K 94 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ASP K 96 " --> pdb=" O ALA K 100E" (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA K 100E" --> pdb=" O ASP K 96 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 1908 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.05 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4334 1.32 - 1.45: 5735 1.45 - 1.58: 9392 1.58 - 1.72: 9 1.72 - 1.85: 180 Bond restraints: 19650 Sorted by residual: bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.426 0.071 1.40e-02 5.10e+03 2.54e+01 bond pdb=" CB HIS G 374 " pdb=" CG HIS G 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.50e+01 bond pdb=" CB HIS A 374 " pdb=" CG HIS A 374 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" N PRO G 470 " pdb=" CA PRO G 470 " ideal model delta sigma weight residual 1.465 1.414 0.052 1.19e-02 7.06e+03 1.88e+01 bond pdb=" N PRO A 470 " pdb=" CA PRO A 470 " ideal model delta sigma weight residual 1.465 1.414 0.051 1.19e-02 7.06e+03 1.87e+01 ... (remaining 19645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 22595 2.26 - 4.52: 3457 4.52 - 6.78: 560 6.78 - 9.04: 70 9.04 - 11.30: 21 Bond angle restraints: 26703 Sorted by residual: angle pdb=" N LEU A 261 " pdb=" CA LEU A 261 " pdb=" C LEU A 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.57e+01 angle pdb=" N LEU C 261 " pdb=" CA LEU C 261 " pdb=" C LEU C 261 " ideal model delta sigma weight residual 113.28 123.89 -10.61 1.22e+00 6.72e-01 7.56e+01 angle pdb=" N LEU G 261 " pdb=" CA LEU G 261 " pdb=" C LEU G 261 " ideal model delta sigma weight residual 113.28 123.87 -10.59 1.22e+00 6.72e-01 7.53e+01 angle pdb=" C CYS G 239 " pdb=" N PRO G 240 " pdb=" CA PRO G 240 " ideal model delta sigma weight residual 119.56 127.82 -8.26 1.02e+00 9.61e-01 6.55e+01 angle pdb=" C CYS C 239 " pdb=" N PRO C 240 " pdb=" CA PRO C 240 " ideal model delta sigma weight residual 119.56 127.79 -8.23 1.02e+00 9.61e-01 6.51e+01 ... (remaining 26698 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 10790 17.69 - 35.38: 277 35.38 - 53.07: 84 53.07 - 70.76: 24 70.76 - 88.45: 18 Dihedral angle restraints: 11193 sinusoidal: 4419 harmonic: 6774 Sorted by residual: dihedral pdb=" CB CYS A 228 " pdb=" SG CYS A 228 " pdb=" SG CYS A 239 " pdb=" CB CYS A 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.45 88.45 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS C 228 " pdb=" SG CYS C 228 " pdb=" SG CYS C 239 " pdb=" CB CYS C 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.44 88.44 1 1.00e+01 1.00e-02 9.34e+01 dihedral pdb=" CB CYS G 228 " pdb=" SG CYS G 228 " pdb=" SG CYS G 239 " pdb=" CB CYS G 239 " ideal model delta sinusoidal sigma weight residual -86.00 -174.43 88.43 1 1.00e+01 1.00e-02 9.34e+01 ... (remaining 11190 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 2400 0.103 - 0.206: 719 0.206 - 0.308: 97 0.308 - 0.411: 0 0.411 - 0.514: 3 Chirality restraints: 3219 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.38e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.37e+01 chirality pdb=" C1 NAG X 2 " pdb=" O4 NAG X 1 " pdb=" C2 NAG X 2 " pdb=" O5 NAG X 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.30e+01 ... (remaining 3216 not shown) Planarity restraints: 3351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 620 " -0.055 2.00e-02 2.50e+03 4.48e-02 2.50e+01 pdb=" C7 NAG A 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG A 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG A 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG A 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 620 " -0.055 2.00e-02 2.50e+03 4.47e-02 2.49e+01 pdb=" C7 NAG G 620 " 0.012 2.00e-02 2.50e+03 pdb=" C8 NAG G 620 " -0.041 2.00e-02 2.50e+03 pdb=" N2 NAG G 620 " 0.071 2.00e-02 2.50e+03 pdb=" O7 NAG G 620 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 620 " 0.054 2.00e-02 2.50e+03 4.44e-02 2.46e+01 pdb=" C7 NAG C 620 " -0.012 2.00e-02 2.50e+03 pdb=" C8 NAG C 620 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG C 620 " -0.071 2.00e-02 2.50e+03 pdb=" O7 NAG C 620 " -0.012 2.00e-02 2.50e+03 ... (remaining 3348 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 7360 2.87 - 3.38: 16296 3.38 - 3.89: 32071 3.89 - 4.39: 36098 4.39 - 4.90: 60324 Nonbonded interactions: 152149 Sorted by model distance: nonbonded pdb=" OG1 THR G 37 " pdb=" OG1 THR G 499 " model vdw 2.363 3.040 nonbonded pdb=" OG1 THR C 37 " pdb=" OG1 THR C 499 " model vdw 2.364 3.040 nonbonded pdb=" OG1 THR A 37 " pdb=" OG1 THR A 499 " model vdw 2.364 3.040 nonbonded pdb=" N ASN G 133 " pdb=" OD1 ASN G 133 " model vdw 2.368 3.120 nonbonded pdb=" N ASN A 133 " pdb=" OD1 ASN A 133 " model vdw 2.368 3.120 ... (remaining 152144 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'N' selection = chain 'R' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.480 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 22.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 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 : 0.020 0.126 19758 Z= 1.043 Angle : 1.726 11.300 26985 Z= 1.116 Chirality : 0.093 0.514 3219 Planarity : 0.009 0.045 3303 Dihedral : 9.820 88.441 6711 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.15 (0.17), residues: 2313 helix: 0.54 (0.26), residues: 354 sheet: 0.85 (0.19), residues: 708 loop : 0.98 (0.18), residues: 1251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 298 TYR 0.050 0.008 TYR A 40 PHE 0.027 0.006 PHE F 67 TRP 0.052 0.009 TRP B 571 HIS 0.008 0.002 HIS C 374 Details of bonding type rmsd/Z covalent geometry : bond 0.01967 / 1.04 (19650) covalent geometry : angle 1.71144 / 1.12 (26703) SS BOND : bond 0.01209 / 0.80 ( 42) SS BOND : angle 2.80689 / 1.84 ( 84) hydrogen bonds : bond 0.17909 / 12.03 ( 732) hydrogen bonds : angle 6.89014 / 4.78 ( 1908) link_ALPHA1-3 : bond 0.03519 / 1.76 ( 3) link_ALPHA1-3 : angle 1.92749 / 1.27 ( 9) link_BETA1-4 : bond 0.02682 / 1.42 ( 15) link_BETA1-4 : angle 3.89926 / 2.89 ( 45) link_NAG-ASN : bond 0.02800 / 1.80 ( 48) link_NAG-ASN : angle 2.34003 / 1.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 529 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6820 (p-80) cc_final: 0.6505 (m170) REVERT: C 72 HIS cc_start: 0.7000 (p-80) cc_final: 0.6443 (m170) REVERT: G 72 HIS cc_start: 0.6797 (p-80) cc_final: 0.6446 (m170) REVERT: G 95 MET cc_start: 0.9027 (ptm) cc_final: 0.8701 (ptm) REVERT: G 424 ILE cc_start: 0.9129 (mm) cc_final: 0.8866 (mm) REVERT: I 632 ASP cc_start: 0.8405 (t70) cc_final: 0.8134 (t0) outliers start: 3 outliers final: 3 residues processed: 532 average time/residue: 0.1442 time to fit residues: 114.9533 Evaluate side-chains 256 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 253 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain G residue 133 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 478 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 640 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN I 640 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.115436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091372 restraints weight = 33316.231| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.46 r_work: 0.3209 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19758 Z= 0.167 Angle : 0.711 9.140 26985 Z= 0.374 Chirality : 0.046 0.164 3219 Planarity : 0.004 0.045 3303 Dihedral : 5.184 29.717 2523 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 8.17 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 1.12 (0.17), residues: 2313 helix: 2.00 (0.28), residues: 336 sheet: 0.64 (0.18), residues: 735 loop : 0.59 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 66 TYR 0.026 0.002 TYR B 638 PHE 0.016 0.002 PHE A 383 TRP 0.018 0.002 TRP G 479 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.17 (19650) covalent geometry : angle 0.68440 / 0.37 (26703) SS BOND : bond 0.00854 / 0.63 ( 42) SS BOND : angle 1.17882 / 0.79 ( 84) hydrogen bonds : bond 0.06130 / 4.09 ( 732) hydrogen bonds : angle 5.46266 / 3.80 ( 1908) link_ALPHA1-3 : bond 0.00657 / 0.33 ( 3) link_ALPHA1-3 : angle 1.39818 / 0.86 ( 9) link_BETA1-4 : bond 0.00609 / 0.33 ( 15) link_BETA1-4 : angle 1.98913 / 1.47 ( 45) link_NAG-ASN : bond 0.00305 / 0.18 ( 48) link_NAG-ASN : angle 2.37970 / 1.83 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 326 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6649 (p-80) cc_final: 0.5953 (m170) REVERT: B 543 ASN cc_start: 0.8543 (m110) cc_final: 0.8217 (m110) REVERT: B 617 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6794 (mtm180) REVERT: B 621 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7595 (mp0) REVERT: B 632 ASP cc_start: 0.8755 (t70) cc_final: 0.8332 (t0) REVERT: B 634 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7242 (mm-30) REVERT: L 4 MET cc_start: 0.8090 (mmm) cc_final: 0.7847 (mmm) REVERT: L 48 ILE cc_start: 0.9077 (mt) cc_final: 0.8732 (mm) REVERT: C 72 HIS cc_start: 0.6752 (p-80) cc_final: 0.5797 (m170) REVERT: C 486 TYR cc_start: 0.8963 (m-80) cc_final: 0.8612 (m-10) REVERT: D 543 ASN cc_start: 0.8754 (m110) cc_final: 0.8266 (m110) REVERT: D 632 ASP cc_start: 0.8776 (t70) cc_final: 0.8344 (t0) REVERT: E 48 ILE cc_start: 0.8871 (mt) cc_final: 0.8647 (mm) REVERT: E 89 GLN cc_start: 0.9029 (tt0) cc_final: 0.8794 (tt0) REVERT: G 72 HIS cc_start: 0.6546 (p-80) cc_final: 0.5798 (m170) REVERT: G 95 MET cc_start: 0.9284 (ptm) cc_final: 0.9040 (ptm) REVERT: I 617 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7488 (mtm180) REVERT: I 621 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7192 (pt0) REVERT: I 632 ASP cc_start: 0.8929 (t70) cc_final: 0.8377 (t0) REVERT: I 634 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7149 (mm-30) outliers start: 62 outliers final: 42 residues processed: 372 average time/residue: 0.1378 time to fit residues: 79.6313 Evaluate side-chains 290 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ASP Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 74 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 68 VAL Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 199 SER Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 100 LEU Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 43 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 36 optimal weight: 0.3980 chunk 227 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 140 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 543 ASN B 658 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 411 ASN C 478 ASN D 575 GLN ** E 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 82 GLN G 411 ASN I 658 GLN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.112756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087233 restraints weight = 35013.219| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 3.50 r_work: 0.3096 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 19758 Z= 0.254 Angle : 0.724 7.662 26985 Z= 0.375 Chirality : 0.047 0.156 3219 Planarity : 0.005 0.050 3303 Dihedral : 4.988 21.303 2517 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.59 % Allowed : 9.55 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.66 (0.17), residues: 2313 helix: 1.93 (0.29), residues: 357 sheet: 0.58 (0.19), residues: 684 loop : -0.00 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 617 TYR 0.022 0.002 TYR K 58 PHE 0.020 0.003 PHE C 383 TRP 0.014 0.002 TRP I 614 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00602 / 0.25 (19650) covalent geometry : angle 0.69591 / 0.37 (26703) SS BOND : bond 0.00667 / 0.41 ( 42) SS BOND : angle 1.35028 / 0.89 ( 84) hydrogen bonds : bond 0.05760 / 3.84 ( 732) hydrogen bonds : angle 5.19272 / 3.63 ( 1908) link_ALPHA1-3 : bond 0.00871 / 0.44 ( 3) link_ALPHA1-3 : angle 1.32572 / 0.80 ( 9) link_BETA1-4 : bond 0.00434 / 0.24 ( 15) link_BETA1-4 : angle 1.72763 / 1.30 ( 45) link_NAG-ASN : bond 0.00469 / 0.31 ( 48) link_NAG-ASN : angle 2.48870 / 1.97 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 269 time to evaluate : 0.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6659 (p-80) cc_final: 0.6056 (m-70) REVERT: B 535 MET cc_start: 0.8574 (mtp) cc_final: 0.8355 (mtt) REVERT: B 543 ASN cc_start: 0.8733 (m-40) cc_final: 0.8475 (m110) REVERT: B 632 ASP cc_start: 0.8783 (t70) cc_final: 0.8448 (t0) REVERT: B 654 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7764 (mt-10) REVERT: L 4 MET cc_start: 0.8283 (mmm) cc_final: 0.7691 (mmt) REVERT: L 58 VAL cc_start: 0.8182 (m) cc_final: 0.7852 (m) REVERT: C 72 HIS cc_start: 0.6690 (p-80) cc_final: 0.5811 (m170) REVERT: D 543 ASN cc_start: 0.8780 (m110) cc_final: 0.8319 (m110) REVERT: D 621 GLU cc_start: 0.8083 (tt0) cc_final: 0.7622 (pt0) REVERT: D 627 THR cc_start: 0.8100 (OUTLIER) cc_final: 0.7895 (t) REVERT: D 632 ASP cc_start: 0.8884 (t70) cc_final: 0.8444 (t0) REVERT: D 634 GLU cc_start: 0.8306 (mm-30) cc_final: 0.7953 (mt-10) REVERT: D 661 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6772 (mm) REVERT: E 33 LEU cc_start: 0.9202 (tt) cc_final: 0.8942 (tt) REVERT: E 48 ILE cc_start: 0.9022 (mt) cc_final: 0.8750 (mm) REVERT: E 63 LYS cc_start: 0.7425 (ttmm) cc_final: 0.6865 (mtmm) REVERT: E 89 GLN cc_start: 0.9262 (tt0) cc_final: 0.8953 (tt0) REVERT: F 6 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7840 (tp30) REVERT: G 72 HIS cc_start: 0.6597 (p-80) cc_final: 0.5942 (m-70) REVERT: G 92 GLU cc_start: 0.8267 (mm-30) cc_final: 0.8038 (mm-30) REVERT: I 535 MET cc_start: 0.8438 (mtp) cc_final: 0.8124 (mtt) REVERT: I 617 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7755 (mtm180) REVERT: I 621 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7423 (mp0) REVERT: I 632 ASP cc_start: 0.8946 (t70) cc_final: 0.8359 (t0) REVERT: J 4 MET cc_start: 0.8589 (mmt) cc_final: 0.8114 (mmm) REVERT: J 63 LYS cc_start: 0.7771 (ttmm) cc_final: 0.7302 (mtpp) outliers start: 73 outliers final: 52 residues processed: 327 average time/residue: 0.1397 time to fit residues: 70.9494 Evaluate side-chains 295 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 241 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 167 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 615 SER Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 627 THR Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 184 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 102 optimal weight: 0.9980 chunk 199 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 146 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 163 optimal weight: 4.9990 chunk 151 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 37 GLN C 411 ASN E 37 GLN G 188 ASN G 411 ASN ** J 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.111154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.086181 restraints weight = 34874.226| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.62 r_work: 0.3117 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19758 Z= 0.163 Angle : 0.611 8.356 26985 Z= 0.313 Chirality : 0.044 0.145 3219 Planarity : 0.004 0.044 3303 Dihedral : 4.761 21.496 2517 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.55 % Allowed : 10.29 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.58 (0.17), residues: 2313 helix: 2.03 (0.29), residues: 357 sheet: 0.59 (0.19), residues: 711 loop : -0.17 (0.17), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 61 TYR 0.030 0.002 TYR I 638 PHE 0.014 0.002 PHE C 383 TRP 0.012 0.001 TRP B 571 HIS 0.005 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.16 (19650) covalent geometry : angle 0.58591 / 0.31 (26703) SS BOND : bond 0.00832 / 0.69 ( 42) SS BOND : angle 1.05354 / 0.68 ( 84) hydrogen bonds : bond 0.04852 / 3.25 ( 732) hydrogen bonds : angle 4.87787 / 3.40 ( 1908) link_ALPHA1-3 : bond 0.00856 / 0.43 ( 3) link_ALPHA1-3 : angle 1.38849 / 0.84 ( 9) link_BETA1-4 : bond 0.00382 / 0.21 ( 15) link_BETA1-4 : angle 1.49442 / 1.10 ( 45) link_NAG-ASN : bond 0.00259 / 0.16 ( 48) link_NAG-ASN : angle 2.20544 / 1.69 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 247 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 HIS cc_start: 0.6713 (p-80) cc_final: 0.6063 (m-70) REVERT: A 97 LYS cc_start: 0.9154 (tptt) cc_final: 0.8666 (tppp) REVERT: A 114 GLN cc_start: 0.8661 (tt0) cc_final: 0.8280 (tt0) REVERT: B 535 MET cc_start: 0.8592 (mtp) cc_final: 0.8262 (mtt) REVERT: B 543 ASN cc_start: 0.8634 (m-40) cc_final: 0.8199 (m110) REVERT: B 621 GLU cc_start: 0.8294 (tt0) cc_final: 0.7977 (tm-30) REVERT: B 632 ASP cc_start: 0.8770 (t70) cc_final: 0.8436 (t0) REVERT: B 654 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7718 (mt-10) REVERT: L 48 ILE cc_start: 0.8978 (mt) cc_final: 0.8704 (mm) REVERT: H 38 ARG cc_start: 0.7546 (ptt180) cc_final: 0.7086 (ptt180) REVERT: C 46 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7845 (mmtt) REVERT: C 72 HIS cc_start: 0.6654 (p-80) cc_final: 0.5819 (m170) REVERT: D 543 ASN cc_start: 0.8758 (m110) cc_final: 0.8402 (m110) REVERT: D 621 GLU cc_start: 0.8288 (tt0) cc_final: 0.8012 (pt0) REVERT: D 632 ASP cc_start: 0.8887 (t70) cc_final: 0.8257 (t0) REVERT: D 661 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6686 (mm) REVERT: E 48 ILE cc_start: 0.8901 (mt) cc_final: 0.8685 (mm) REVERT: E 63 LYS cc_start: 0.7240 (ttmm) cc_final: 0.6690 (mtmm) REVERT: E 89 GLN cc_start: 0.9214 (tt0) cc_final: 0.8897 (tt0) REVERT: F 6 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7786 (mm-30) REVERT: F 31 ASP cc_start: 0.7895 (m-30) cc_final: 0.7443 (m-30) REVERT: F 100 VAL cc_start: 0.8743 (t) cc_final: 0.8508 (p) REVERT: G 72 HIS cc_start: 0.6572 (p-80) cc_final: 0.5910 (m-70) REVERT: G 92 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8097 (mm-30) REVERT: G 475 MET cc_start: 0.8125 (mmm) cc_final: 0.7902 (tpp) REVERT: I 535 MET cc_start: 0.8491 (mtp) cc_final: 0.8195 (mtt) REVERT: I 621 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7164 (tt0) REVERT: I 632 ASP cc_start: 0.8930 (t70) cc_final: 0.8393 (t0) REVERT: J 4 MET cc_start: 0.8556 (mmt) cc_final: 0.8096 (mmm) REVERT: J 63 LYS cc_start: 0.7757 (ttmm) cc_final: 0.7321 (mtpp) outliers start: 72 outliers final: 51 residues processed: 302 average time/residue: 0.1283 time to fit residues: 59.9326 Evaluate side-chains 284 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 232 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 411 ASN Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 568 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 188 ASN Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 615 SER Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 9 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 134 optimal weight: 8.9990 chunk 185 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN G 188 ASN G 411 ASN J 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.108671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.083548 restraints weight = 35239.405| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.68 r_work: 0.3068 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 19758 Z= 0.253 Angle : 0.670 8.560 26985 Z= 0.345 Chirality : 0.046 0.147 3219 Planarity : 0.004 0.049 3303 Dihedral : 4.845 22.270 2517 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.40 % Allowed : 11.82 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.35 (0.17), residues: 2313 helix: 1.67 (0.29), residues: 375 sheet: 0.47 (0.19), residues: 678 loop : -0.29 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 61 TYR 0.025 0.002 TYR B 638 PHE 0.018 0.002 PHE C 383 TRP 0.012 0.002 TRP G 69 HIS 0.008 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00603 / 0.25 (19650) covalent geometry : angle 0.64576 / 0.34 (26703) SS BOND : bond 0.00756 / 0.53 ( 42) SS BOND : angle 1.21622 / 0.83 ( 84) hydrogen bonds : bond 0.05249 / 3.50 ( 732) hydrogen bonds : angle 4.92377 / 3.45 ( 1908) link_ALPHA1-3 : bond 0.00821 / 0.41 ( 3) link_ALPHA1-3 : angle 1.36152 / 0.82 ( 9) link_BETA1-4 : bond 0.00391 / 0.22 ( 15) link_BETA1-4 : angle 1.68219 / 1.25 ( 45) link_NAG-ASN : bond 0.00408 / 0.26 ( 48) link_NAG-ASN : angle 2.23775 / 1.72 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 238 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7494 (mmtt) REVERT: A 72 HIS cc_start: 0.6714 (p-80) cc_final: 0.6084 (m-70) REVERT: A 114 GLN cc_start: 0.8749 (tt0) cc_final: 0.8387 (tt0) REVERT: B 535 MET cc_start: 0.8760 (mtp) cc_final: 0.8466 (mtt) REVERT: B 543 ASN cc_start: 0.8750 (m-40) cc_final: 0.8431 (m110) REVERT: B 632 ASP cc_start: 0.8863 (t70) cc_final: 0.8574 (t0) REVERT: B 654 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7800 (mt-10) REVERT: L 3 VAL cc_start: 0.8543 (t) cc_final: 0.8230 (m) REVERT: L 23 CYS cc_start: 0.6983 (t) cc_final: 0.6640 (t) REVERT: H 38 ARG cc_start: 0.7789 (ptt180) cc_final: 0.7307 (ptt180) REVERT: C 46 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7996 (mmtt) REVERT: C 72 HIS cc_start: 0.6739 (p-80) cc_final: 0.5848 (m170) REVERT: C 323 ILE cc_start: 0.7956 (mm) cc_final: 0.7734 (mm) REVERT: D 543 ASN cc_start: 0.8806 (m110) cc_final: 0.8355 (m110) REVERT: D 621 GLU cc_start: 0.8314 (tt0) cc_final: 0.7953 (pt0) REVERT: D 632 ASP cc_start: 0.9012 (t70) cc_final: 0.8499 (t0) REVERT: D 661 LEU cc_start: 0.7072 (OUTLIER) cc_final: 0.6777 (mm) REVERT: E 3 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8204 (m) REVERT: E 48 ILE cc_start: 0.9010 (mt) cc_final: 0.8779 (mm) REVERT: E 63 LYS cc_start: 0.7326 (ttmm) cc_final: 0.6776 (mtmm) REVERT: E 89 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8905 (tt0) REVERT: F 31 ASP cc_start: 0.8057 (m-30) cc_final: 0.7585 (m-30) REVERT: F 100 VAL cc_start: 0.8850 (t) cc_final: 0.8577 (p) REVERT: G 46 LYS cc_start: 0.8258 (mmmt) cc_final: 0.7723 (mmtt) REVERT: G 72 HIS cc_start: 0.6638 (p-80) cc_final: 0.5946 (m-70) REVERT: I 535 MET cc_start: 0.8667 (mtp) cc_final: 0.8384 (mtt) REVERT: I 621 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7431 (mp0) REVERT: I 632 ASP cc_start: 0.8860 (t70) cc_final: 0.8351 (t0) REVERT: J 4 MET cc_start: 0.8588 (mmt) cc_final: 0.8129 (mmm) REVERT: J 63 LYS cc_start: 0.7880 (ttmm) cc_final: 0.7448 (mtpp) outliers start: 69 outliers final: 54 residues processed: 292 average time/residue: 0.1425 time to fit residues: 64.7992 Evaluate side-chains 285 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 213 ILE Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 3 VAL Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 178 optimal weight: 0.0020 chunk 6 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 398 ASN A 478 ASN G 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.087163 restraints weight = 34719.408| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 3.63 r_work: 0.3101 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19758 Z= 0.113 Angle : 0.566 6.912 26985 Z= 0.290 Chirality : 0.042 0.149 3219 Planarity : 0.004 0.042 3303 Dihedral : 4.587 21.460 2517 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.90 % Allowed : 12.65 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.48 (0.17), residues: 2313 helix: 1.92 (0.29), residues: 375 sheet: 0.50 (0.19), residues: 684 loop : -0.22 (0.17), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 61 TYR 0.019 0.001 TYR B 638 PHE 0.017 0.001 PHE A 53 TRP 0.012 0.001 TRP A 69 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (19650) covalent geometry : angle 0.54413 / 0.29 (26703) SS BOND : bond 0.00269 / 0.19 ( 42) SS BOND : angle 0.89507 / 0.58 ( 84) hydrogen bonds : bond 0.04210 / 2.82 ( 732) hydrogen bonds : angle 4.62580 / 3.24 ( 1908) link_ALPHA1-3 : bond 0.00778 / 0.39 ( 3) link_ALPHA1-3 : angle 1.36723 / 0.83 ( 9) link_BETA1-4 : bond 0.00403 / 0.22 ( 15) link_BETA1-4 : angle 1.41902 / 1.03 ( 45) link_NAG-ASN : bond 0.00207 / 0.13 ( 48) link_NAG-ASN : angle 1.99398 / 1.51 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 249 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8016 (mmmt) cc_final: 0.7518 (mmtt) REVERT: A 72 HIS cc_start: 0.6643 (p-80) cc_final: 0.6006 (m-70) REVERT: A 95 MET cc_start: 0.9033 (ttp) cc_final: 0.8764 (ttp) REVERT: A 114 GLN cc_start: 0.8560 (tt0) cc_final: 0.8196 (tt0) REVERT: B 535 MET cc_start: 0.8623 (mtp) cc_final: 0.8305 (mtt) REVERT: B 543 ASN cc_start: 0.8605 (m-40) cc_final: 0.8260 (m110) REVERT: B 632 ASP cc_start: 0.8722 (t70) cc_final: 0.8497 (t0) REVERT: B 654 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7669 (mt-10) REVERT: L 3 VAL cc_start: 0.8373 (t) cc_final: 0.8016 (m) REVERT: L 23 CYS cc_start: 0.7043 (t) cc_final: 0.6344 (t) REVERT: L 48 ILE cc_start: 0.8910 (mt) cc_final: 0.8697 (mm) REVERT: H 38 ARG cc_start: 0.7470 (ptt180) cc_final: 0.7012 (ptt180) REVERT: C 53 PHE cc_start: 0.7954 (p90) cc_final: 0.7749 (p90) REVERT: C 72 HIS cc_start: 0.6626 (p-80) cc_final: 0.5778 (m170) REVERT: D 543 ASN cc_start: 0.8671 (m110) cc_final: 0.8325 (m110) REVERT: D 621 GLU cc_start: 0.8265 (tt0) cc_final: 0.7977 (pt0) REVERT: D 632 ASP cc_start: 0.8919 (t70) cc_final: 0.8491 (t0) REVERT: D 661 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6520 (mm) REVERT: E 3 VAL cc_start: 0.8353 (t) cc_final: 0.8016 (m) REVERT: E 48 ILE cc_start: 0.8802 (mt) cc_final: 0.8599 (mm) REVERT: E 63 LYS cc_start: 0.7128 (ttmm) cc_final: 0.6784 (mtpp) REVERT: E 89 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8845 (tt0) REVERT: F 31 ASP cc_start: 0.7848 (m-30) cc_final: 0.7385 (m-30) REVERT: F 38 ARG cc_start: 0.7631 (ptt180) cc_final: 0.7272 (ptt180) REVERT: F 100 VAL cc_start: 0.8678 (t) cc_final: 0.8425 (p) REVERT: G 46 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7485 (mmtt) REVERT: G 72 HIS cc_start: 0.6538 (p-80) cc_final: 0.5790 (m-70) REVERT: G 486 TYR cc_start: 0.8991 (m-80) cc_final: 0.8754 (m-10) REVERT: I 535 MET cc_start: 0.8551 (mtp) cc_final: 0.8278 (mtt) REVERT: I 632 ASP cc_start: 0.8740 (t70) cc_final: 0.8280 (t0) REVERT: I 657 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7180 (mt-10) REVERT: J 63 LYS cc_start: 0.7736 (ttmm) cc_final: 0.7295 (mtpp) REVERT: J 88 CYS cc_start: 0.7330 (p) cc_final: 0.7039 (p) REVERT: K 100 VAL cc_start: 0.8766 (t) cc_final: 0.8480 (p) outliers start: 59 outliers final: 40 residues processed: 290 average time/residue: 0.1447 time to fit residues: 65.1730 Evaluate side-chains 272 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 230 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 641 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 411 ASN Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 83 optimal weight: 0.4980 chunk 177 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 215 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 398 ASN A 478 ASN I 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.109617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.084616 restraints weight = 35089.148| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.67 r_work: 0.3086 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19758 Z= 0.205 Angle : 0.624 7.473 26985 Z= 0.321 Chirality : 0.044 0.144 3219 Planarity : 0.004 0.048 3303 Dihedral : 4.630 21.325 2517 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.30 % Allowed : 13.24 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.40 (0.17), residues: 2313 helix: 1.81 (0.29), residues: 375 sheet: 0.51 (0.19), residues: 678 loop : -0.31 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG K 61 TYR 0.023 0.002 TYR E 95D PHE 0.015 0.002 PHE C 383 TRP 0.013 0.002 TRP I 596 HIS 0.006 0.002 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.20 (19650) covalent geometry : angle 0.60202 / 0.32 (26703) SS BOND : bond 0.00504 / 0.31 ( 42) SS BOND : angle 1.12546 / 0.76 ( 84) hydrogen bonds : bond 0.04709 / 3.15 ( 732) hydrogen bonds : angle 4.69399 / 3.29 ( 1908) link_ALPHA1-3 : bond 0.00919 / 0.46 ( 3) link_ALPHA1-3 : angle 1.41015 / 0.85 ( 9) link_BETA1-4 : bond 0.00386 / 0.21 ( 15) link_BETA1-4 : angle 1.57998 / 1.17 ( 45) link_NAG-ASN : bond 0.00340 / 0.22 ( 48) link_NAG-ASN : angle 2.01171 / 1.53 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 238 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8150 (mmmt) cc_final: 0.7622 (mmtt) REVERT: A 66 HIS cc_start: 0.5792 (p-80) cc_final: 0.5562 (p90) REVERT: A 72 HIS cc_start: 0.6689 (p-80) cc_final: 0.6061 (m-70) REVERT: A 114 GLN cc_start: 0.8703 (tt0) cc_final: 0.8345 (tt0) REVERT: B 535 MET cc_start: 0.8716 (mtp) cc_final: 0.8433 (mtt) REVERT: B 543 ASN cc_start: 0.8742 (m-40) cc_final: 0.8401 (m110) REVERT: B 632 ASP cc_start: 0.8866 (t70) cc_final: 0.8588 (t0) REVERT: B 654 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7605 (mt-10) REVERT: L 23 CYS cc_start: 0.6789 (t) cc_final: 0.6333 (t) REVERT: L 48 ILE cc_start: 0.9007 (mt) cc_final: 0.8791 (mm) REVERT: H 38 ARG cc_start: 0.7681 (ptt180) cc_final: 0.7180 (ptt180) REVERT: C 72 HIS cc_start: 0.6795 (p-80) cc_final: 0.5950 (m170) REVERT: D 543 ASN cc_start: 0.8803 (m110) cc_final: 0.8350 (m110) REVERT: D 632 ASP cc_start: 0.9045 (t70) cc_final: 0.8371 (t0) REVERT: D 655 LYS cc_start: 0.7740 (tptp) cc_final: 0.7521 (tptt) REVERT: D 661 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6643 (mm) REVERT: E 48 ILE cc_start: 0.8929 (mt) cc_final: 0.8725 (mm) REVERT: E 63 LYS cc_start: 0.7271 (ttmm) cc_final: 0.6884 (mtpp) REVERT: E 89 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8896 (tt0) REVERT: F 31 ASP cc_start: 0.7996 (m-30) cc_final: 0.7527 (m-30) REVERT: F 100 VAL cc_start: 0.8783 (t) cc_final: 0.8534 (p) REVERT: G 46 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7917 (mmtt) REVERT: G 72 HIS cc_start: 0.6738 (p-80) cc_final: 0.6035 (m-70) REVERT: G 161 MET cc_start: 0.8604 (ttm) cc_final: 0.8319 (ttm) REVERT: G 486 TYR cc_start: 0.9084 (m-80) cc_final: 0.8756 (m-10) REVERT: I 535 MET cc_start: 0.8621 (mtp) cc_final: 0.8342 (mtt) REVERT: I 632 ASP cc_start: 0.8854 (t70) cc_final: 0.8335 (t0) REVERT: I 657 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7318 (mt-10) REVERT: J 3 VAL cc_start: 0.8564 (t) cc_final: 0.8226 (m) REVERT: J 63 LYS cc_start: 0.7885 (ttmm) cc_final: 0.7468 (mtpp) REVERT: K 100 VAL cc_start: 0.8782 (t) cc_final: 0.8465 (p) outliers start: 67 outliers final: 56 residues processed: 293 average time/residue: 0.1445 time to fit residues: 65.9768 Evaluate side-chains 286 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 228 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 398 ASN Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 54 CYS Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 652 GLN Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 54 CYS Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 434 MET Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 620 SER Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 150 optimal weight: 6.9990 chunk 218 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 223 optimal weight: 5.9990 chunk 164 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 123 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 478 ASN C 478 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.107660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.082181 restraints weight = 35140.831| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.61 r_work: 0.2999 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.061 19758 Z= 0.358 Angle : 0.768 7.882 26985 Z= 0.396 Chirality : 0.049 0.203 3219 Planarity : 0.005 0.047 3303 Dihedral : 5.092 23.166 2517 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.45 % Allowed : 13.29 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: -0.01 (0.17), residues: 2313 helix: 1.26 (0.29), residues: 384 sheet: 0.38 (0.18), residues: 741 loop : -0.64 (0.17), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 61 TYR 0.023 0.002 TYR C 486 PHE 0.021 0.003 PHE A 383 TRP 0.019 0.002 TRP G 69 HIS 0.008 0.003 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00854 / 0.36 (19650) covalent geometry : angle 0.74248 / 0.39 (26703) SS BOND : bond 0.00651 / 0.42 ( 42) SS BOND : angle 1.63069 / 1.10 ( 84) hydrogen bonds : bond 0.05781 / 3.85 ( 732) hydrogen bonds : angle 5.06579 / 3.55 ( 1908) link_ALPHA1-3 : bond 0.00899 / 0.45 ( 3) link_ALPHA1-3 : angle 1.46985 / 0.88 ( 9) link_BETA1-4 : bond 0.00409 / 0.22 ( 15) link_BETA1-4 : angle 1.91650 / 1.44 ( 45) link_NAG-ASN : bond 0.00608 / 0.39 ( 48) link_NAG-ASN : angle 2.31426 / 1.75 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 229 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8163 (mmmt) cc_final: 0.7666 (mmtt) REVERT: A 72 HIS cc_start: 0.6889 (p-80) cc_final: 0.6208 (m-70) REVERT: A 114 GLN cc_start: 0.8578 (tt0) cc_final: 0.8236 (tt0) REVERT: A 198 THR cc_start: 0.9429 (OUTLIER) cc_final: 0.9105 (p) REVERT: B 535 MET cc_start: 0.8786 (mtp) cc_final: 0.8486 (mtt) REVERT: B 543 ASN cc_start: 0.8752 (m-40) cc_final: 0.8367 (m110) REVERT: B 632 ASP cc_start: 0.8909 (t70) cc_final: 0.8630 (t0) REVERT: L 3 VAL cc_start: 0.8402 (t) cc_final: 0.8094 (m) REVERT: L 4 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7992 (tpt) REVERT: L 23 CYS cc_start: 0.6956 (t) cc_final: 0.5706 (t) REVERT: H 38 ARG cc_start: 0.7643 (ptt180) cc_final: 0.7160 (ptt180) REVERT: H 46 GLU cc_start: 0.7671 (tp30) cc_final: 0.7311 (tp30) REVERT: H 100 VAL cc_start: 0.8745 (t) cc_final: 0.8458 (p) REVERT: C 72 HIS cc_start: 0.7015 (p-80) cc_final: 0.6249 (m-70) REVERT: D 543 ASN cc_start: 0.8821 (m110) cc_final: 0.8381 (m110) REVERT: D 624 ASP cc_start: 0.8564 (m-30) cc_final: 0.8328 (m-30) REVERT: D 632 ASP cc_start: 0.9028 (t70) cc_final: 0.8365 (t0) REVERT: D 661 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6809 (mm) REVERT: E 4 MET cc_start: 0.8588 (tpt) cc_final: 0.7846 (tpt) REVERT: E 48 ILE cc_start: 0.8940 (mt) cc_final: 0.8668 (mm) REVERT: F 31 ASP cc_start: 0.8030 (m-30) cc_final: 0.7506 (m-30) REVERT: F 100 VAL cc_start: 0.8805 (t) cc_final: 0.8469 (p) REVERT: G 46 LYS cc_start: 0.8189 (mmmt) cc_final: 0.7840 (mmtt) REVERT: G 72 HIS cc_start: 0.6599 (p-80) cc_final: 0.6091 (m-70) REVERT: G 161 MET cc_start: 0.8553 (ttm) cc_final: 0.8319 (ttm) REVERT: G 207 LYS cc_start: 0.9022 (tptt) cc_final: 0.8620 (pttm) REVERT: I 535 MET cc_start: 0.8696 (mtp) cc_final: 0.8417 (mtt) REVERT: I 632 ASP cc_start: 0.8786 (t70) cc_final: 0.8231 (t0) REVERT: I 657 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7308 (mt-10) REVERT: J 3 VAL cc_start: 0.8582 (t) cc_final: 0.8228 (m) REVERT: J 4 MET cc_start: 0.8549 (mmm) cc_final: 0.8264 (tpp) REVERT: K 100 VAL cc_start: 0.8785 (t) cc_final: 0.8501 (p) outliers start: 70 outliers final: 59 residues processed: 285 average time/residue: 0.1382 time to fit residues: 61.7131 Evaluate side-chains 280 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 218 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 491 ILE Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 661 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 30 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain G residue 377 ASN Chi-restraints excluded: chain G residue 443 ILE Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 616 ASN Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 120 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 185 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 195 optimal weight: 0.8980 chunk 225 optimal weight: 2.9990 chunk 172 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 GLN A 478 ASN C 398 ASN C 478 ASN G 398 ASN G 411 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.111007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086215 restraints weight = 34899.154| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.68 r_work: 0.3087 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19758 Z= 0.123 Angle : 0.592 9.355 26985 Z= 0.303 Chirality : 0.042 0.142 3219 Planarity : 0.004 0.042 3303 Dihedral : 4.650 22.704 2517 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.71 % Allowed : 14.08 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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 are not related in a simple way. whole: 0.29 (0.17), residues: 2313 helix: 1.65 (0.29), residues: 384 sheet: 0.51 (0.18), residues: 753 loop : -0.47 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 61 TYR 0.015 0.002 TYR E 95D PHE 0.016 0.001 PHE C 53 TRP 0.018 0.001 TRP A 69 HIS 0.003 0.001 HIS A 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (19650) covalent geometry : angle 0.56910 / 0.30 (26703) SS BOND : bond 0.00324 / 0.21 ( 42) SS BOND : angle 1.07658 / 0.69 ( 84) hydrogen bonds : bond 0.04262 / 2.87 ( 732) hydrogen bonds : angle 4.64039 / 3.26 ( 1908) link_ALPHA1-3 : bond 0.00819 / 0.41 ( 3) link_ALPHA1-3 : angle 1.42663 / 0.86 ( 9) link_BETA1-4 : bond 0.00400 / 0.22 ( 15) link_BETA1-4 : angle 1.47546 / 1.08 ( 45) link_NAG-ASN : bond 0.00208 / 0.13 ( 48) link_NAG-ASN : angle 2.00713 / 1.49 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 243 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7558 (mmtt) REVERT: A 72 HIS cc_start: 0.6804 (p-80) cc_final: 0.6110 (m-70) REVERT: A 114 GLN cc_start: 0.8506 (tt0) cc_final: 0.8177 (tt0) REVERT: A 198 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9110 (p) REVERT: B 530 MET cc_start: 0.8057 (mtm) cc_final: 0.7723 (mtm) REVERT: B 535 MET cc_start: 0.8638 (mtp) cc_final: 0.8307 (mtt) REVERT: B 543 ASN cc_start: 0.8536 (m-40) cc_final: 0.8194 (m110) REVERT: B 632 ASP cc_start: 0.8838 (t70) cc_final: 0.8429 (t0) REVERT: L 3 VAL cc_start: 0.8376 (t) cc_final: 0.8099 (m) REVERT: L 4 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7929 (tpt) REVERT: L 23 CYS cc_start: 0.6710 (t) cc_final: 0.5299 (t) REVERT: L 48 ILE cc_start: 0.8932 (mt) cc_final: 0.8699 (mm) REVERT: H 38 ARG cc_start: 0.7488 (ptt180) cc_final: 0.7059 (ptt180) REVERT: H 46 GLU cc_start: 0.7663 (tp30) cc_final: 0.7288 (tp30) REVERT: H 100 VAL cc_start: 0.8580 (t) cc_final: 0.8215 (p) REVERT: C 72 HIS cc_start: 0.6979 (p-80) cc_final: 0.6202 (m-70) REVERT: D 535 MET cc_start: 0.8693 (mtp) cc_final: 0.8288 (mtt) REVERT: D 543 ASN cc_start: 0.8699 (m110) cc_final: 0.8256 (m110) REVERT: D 632 ASP cc_start: 0.8969 (t70) cc_final: 0.8426 (t0) REVERT: E 3 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8054 (m) REVERT: E 4 MET cc_start: 0.8496 (tpt) cc_final: 0.7811 (tpt) REVERT: E 63 LYS cc_start: 0.7207 (ttmm) cc_final: 0.6846 (mtpp) REVERT: E 89 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8893 (tt0) REVERT: F 31 ASP cc_start: 0.7956 (m-30) cc_final: 0.7422 (m-30) REVERT: F 38 ARG cc_start: 0.7543 (ptt180) cc_final: 0.7177 (ptt180) REVERT: F 100 VAL cc_start: 0.8687 (t) cc_final: 0.8420 (p) REVERT: G 46 LYS cc_start: 0.8072 (mmmt) cc_final: 0.7780 (mmtt) REVERT: G 72 HIS cc_start: 0.6509 (p-80) cc_final: 0.5929 (m-70) REVERT: G 161 MET cc_start: 0.8515 (ttm) cc_final: 0.8189 (ttm) REVERT: G 207 LYS cc_start: 0.9001 (tptt) cc_final: 0.8604 (pttm) REVERT: G 474 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7789 (t0) REVERT: G 486 TYR cc_start: 0.9048 (m-80) cc_final: 0.8737 (m-10) REVERT: I 535 MET cc_start: 0.8610 (mtp) cc_final: 0.8262 (mtt) REVERT: I 632 ASP cc_start: 0.8721 (t70) cc_final: 0.8166 (t0) REVERT: I 633 LYS cc_start: 0.9361 (mttm) cc_final: 0.9097 (mmtm) REVERT: I 634 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7530 (mm-30) REVERT: I 657 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7292 (mt-10) REVERT: J 3 VAL cc_start: 0.8356 (t) cc_final: 0.8024 (m) REVERT: J 63 LYS cc_start: 0.7697 (ttmm) cc_final: 0.7264 (mtpp) REVERT: J 89 GLN cc_start: 0.8623 (tt0) cc_final: 0.8234 (pt0) REVERT: K 82 LEU cc_start: 0.7937 (tp) cc_final: 0.7735 (tp) REVERT: K 100 VAL cc_start: 0.8658 (t) cc_final: 0.8370 (p) outliers start: 55 outliers final: 39 residues processed: 286 average time/residue: 0.1440 time to fit residues: 64.0947 Evaluate side-chains 278 residues out of total 2031 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 234 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 198 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 652 GLN Chi-restraints excluded: chain B residue 661 LEU Chi-restraints excluded: chain L residue 4 MET Chi-restraints excluded: chain L residue 24 GLN Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 30 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 108 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain C residue 499 THR Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 11 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 120 VAL Chi-restraints excluded: chain G residue 474 ASP Chi-restraints excluded: chain G residue 488 VAL Chi-restraints excluded: chain G residue 499 THR Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain I residue 661 LEU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 24 GLN Chi-restraints excluded: chain J residue 26 SER Chi-restraints excluded: chain J residue 47 LEU Chi-restraints excluded: chain J residue 48 ILE Chi-restraints excluded: chain J residue 106 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.8293 > 50: distance: 59 - 149: 22.535 distance: 62 - 146: 7.988 distance: 72 - 126: 32.118 distance: 75 - 123: 16.426 distance: 90 - 106: 25.269 distance: 93 - 103: 9.685 distance: 101 - 103: 11.154 distance: 103 - 104: 5.003 distance: 104 - 105: 11.213 distance: 104 - 107: 17.184 distance: 105 - 106: 9.914 distance: 105 - 112: 18.261 distance: 107 - 108: 9.035 distance: 108 - 109: 15.991 distance: 109 - 110: 7.426 distance: 109 - 111: 17.048 distance: 112 - 113: 4.785 distance: 113 - 114: 10.750 distance: 113 - 116: 3.202 distance: 114 - 115: 11.957 distance: 114 - 123: 5.079 distance: 115 - 235: 23.167 distance: 116 - 117: 16.492 distance: 117 - 118: 7.747 distance: 117 - 119: 26.799 distance: 118 - 120: 11.049 distance: 119 - 121: 13.890 distance: 120 - 122: 18.325 distance: 121 - 122: 13.466 distance: 123 - 124: 17.240 distance: 124 - 125: 23.507 distance: 124 - 127: 13.370 distance: 125 - 126: 19.649 distance: 125 - 134: 19.257 distance: 127 - 128: 8.655 distance: 128 - 129: 4.710 distance: 128 - 130: 24.396 distance: 129 - 131: 18.763 distance: 130 - 132: 12.104 distance: 131 - 133: 14.131 distance: 132 - 133: 12.284 distance: 134 - 135: 27.383 distance: 134 - 224: 25.776 distance: 135 - 136: 17.871 distance: 135 - 138: 9.800 distance: 136 - 137: 15.721 distance: 136 - 146: 14.683 distance: 137 - 221: 15.116 distance: 138 - 139: 9.842 distance: 139 - 140: 6.516 distance: 139 - 141: 14.831 distance: 140 - 142: 8.465 distance: 141 - 143: 24.008 distance: 142 - 144: 8.728 distance: 143 - 144: 12.131 distance: 144 - 145: 5.464 distance: 146 - 147: 13.475 distance: 147 - 148: 16.721 distance: 147 - 150: 29.228 distance: 148 - 149: 13.224 distance: 148 - 152: 12.915 distance: 150 - 151: 11.032 distance: 151 - 220: 30.669 distance: 152 - 153: 10.264 distance: 153 - 154: 29.678 distance: 153 - 156: 9.246 distance: 154 - 155: 18.541 distance: 154 - 160: 35.096 distance: 156 - 157: 14.133 distance: 157 - 158: 18.830 distance: 157 - 159: 10.910 distance: 159 - 264: 15.831 distance: 160 - 161: 5.725 distance: 161 - 162: 38.167 distance: 161 - 164: 16.188 distance: 162 - 163: 9.964 distance: 162 - 167: 16.285 distance: 163 - 177: 28.828 distance: 164 - 165: 14.569 distance: 164 - 166: 33.930 distance: 167 - 168: 14.884 distance: 168 - 169: 32.683 distance: 168 - 171: 21.747 distance: 169 - 170: 17.599 distance: 169 - 173: 11.518 distance: 170 - 185: 23.411 distance: 171 - 172: 20.835 distance: 173 - 174: 33.019 distance: 174 - 175: 18.714 distance: 175 - 176: 31.846 distance: 175 - 177: 31.510 distance: 177 - 178: 20.431 distance: 178 - 179: 27.783 distance: 178 - 181: 32.418 distance: 179 - 180: 45.212 distance: 179 - 185: 15.549 distance: 181 - 182: 31.723 distance: 182 - 183: 14.147 distance: 182 - 184: 24.929