Starting phenix.real_space_refine on Sun Aug 24 01:25:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l8f_23232/08_2025/7l8f_23232.map" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 9855 2.51 5 N 2684 2.21 5 O 3199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15840 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 3523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3523 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 20, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 979 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "E" Number of atoms: 3508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3508 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 20, 'TRANS': 423} Chain breaks: 3 Chain: "F" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 980 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 1, 'TRANS': 121} Chain breaks: 1 Chain: "A" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3515 Classifications: {'peptide': 445} Link IDs: {'PTRANS': 20, 'TRANS': 424} Chain breaks: 3 Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 988 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "H" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 635 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 127} Link IDs: {'TRANS': 126} Unresolved non-hydrogen bonds: 254 Unresolved non-hydrogen angles: 381 Unresolved non-hydrogen dihedrals: 127 Planarities with less than four sites: {'UNK:plan-1': 127} Unresolved non-hydrogen planarities: 127 Chain: "L" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 535 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'TRANS': 106} Unresolved non-hydrogen bonds: 214 Unresolved non-hydrogen angles: 321 Unresolved non-hydrogen dihedrals: 107 Planarities with less than four sites: {'UNK:plan-1': 107} Unresolved non-hydrogen planarities: 107 Chain: "G" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.29, per 1000 atoms: 0.27 Number of scatterers: 15840 At special positions: 0 Unit cell: (143.17, 126.69, 134.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 3199 8.00 N 2684 7.00 C 9855 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.02 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.12 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.03 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.04 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.04 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.02 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 54 " - pdb=" SG CYS E 73 " distance=2.02 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.10 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.03 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.02 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.02 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.04 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.06 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.02 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA G 3 " - " MAN G 4 " " BMA K 3 " - " MAN K 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA G 3 " - " MAN G 5 " " BMA K 3 " - " MAN K 5 " " BMA Q 3 " - " MAN Q 5 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " 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-ASN " NAG A 701 " - " ASN A 160 " " NAG A 702 " - " ASN A 276 " " NAG A 703 " - " ASN A 386 " " NAG A 704 " - " ASN A 363 " " NAG A 705 " - " ASN A 234 " " NAG A 706 " - " ASN A 197 " " NAG A 707 " - " ASN A 133 " " NAG A 708 " - " ASN A 88 " " NAG A 709 " - " ASN A 241 " " NAG A 710 " - " ASN A 289 " " NAG A 711 " - " ASN A 339 " " NAG A 712 " - " ASN A 355 " " NAG A 713 " - " ASN A 392 " " NAG B 701 " - " ASN B 637 " " NAG B 702 " - " ASN B 618 " " NAG B 703 " - " ASN B 611 " " NAG C 701 " - " ASN C 448 " " NAG C 702 " - " ASN C 160 " " NAG C 703 " - " ASN C 276 " " NAG C 704 " - " ASN C 295 " " NAG C 705 " - " ASN C 386 " " NAG C 706 " - " ASN C 363 " " NAG C 707 " - " ASN C 234 " " NAG C 708 " - " ASN C 197 " " NAG C 709 " - " ASN C 133 " " NAG C 710 " - " ASN C 301 " " NAG C 711 " - " ASN C 88 " " NAG C 712 " - " ASN C 241 " " NAG C 713 " - " ASN C 289 " " NAG C 714 " - " ASN C 339 " " NAG C 715 " - " ASN C 392 " " NAG D 701 " - " ASN D 637 " " NAG D 702 " - " ASN D 618 " " NAG D 703 " - " ASN D 611 " " NAG E 701 " - " ASN E 448 " " NAG E 702 " - " ASN E 160 " " NAG E 703 " - " ASN E 276 " " NAG E 704 " - " ASN E 386 " " NAG E 705 " - " ASN E 363 " " NAG E 706 " - " ASN E 234 " " NAG E 707 " - " ASN E 133 " " NAG E 708 " - " ASN E 301 " " NAG E 709 " - " ASN E 88 " " NAG E 710 " - " ASN E 241 " " NAG E 711 " - " ASN E 289 " " NAG E 712 " - " ASN E 355 " " NAG E 713 " - " ASN E 392 " " NAG F 701 " - " ASN F 637 " " NAG F 702 " - " ASN F 611 " " NAG G 1 " - " ASN C 262 " " NAG I 1 " - " ASN C 156 " " NAG J 1 " - " ASN C 332 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 295 " " NAG N 1 " - " ASN E 197 " " NAG O 1 " - " ASN E 156 " " NAG P 1 " - " ASN E 332 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 448 " " NAG S 1 " - " ASN A 295 " " NAG T 1 " - " ASN A 156 " " NAG U 1 " - " ASN A 301 " " NAG V 1 " - " ASN A 332 " Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 624.2 milliseconds Enol-peptide restraints added in 1.2 microseconds 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3656 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 28 sheets defined 29.3% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.572A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE C 109 " --> pdb=" O HIS C 105 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ASP C 113 " --> pdb=" O ILE C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 335 through 351 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 475 through 484 removed outlier: 4.190A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 536 through 549 removed outlier: 3.505A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU D 544 " --> pdb=" O GLN D 540 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 545 " --> pdb=" O ALA D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 Processing helix chain 'D' and resid 618 through 623 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 661 Processing helix chain 'E' and resid 67 through 73 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.982A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 354 Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 392 removed outlier: 3.620A pdb=" N ASN E 392 " --> pdb=" O SER E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 475 through 484 removed outlier: 4.089A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 483 " --> pdb=" O TRP E 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 removed outlier: 3.519A pdb=" N MET F 535 " --> pdb=" O ALA F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 547 removed outlier: 3.871A pdb=" N GLN F 540 " --> pdb=" O THR F 536 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N LEU F 544 " --> pdb=" O GLN F 540 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N LEU F 545 " --> pdb=" O ALA F 541 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 625 Processing helix chain 'F' and resid 627 through 633 Processing helix chain 'F' and resid 634 through 636 No H-bonds generated for 'chain 'F' and resid 634 through 636' Processing helix chain 'F' and resid 638 through 654 Processing helix chain 'F' and resid 654 through 661 removed outlier: 4.280A pdb=" N GLN F 658 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP F 659 " --> pdb=" O LYS F 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.113A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 335 through 354 removed outlier: 3.996A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 476 through 484 removed outlier: 4.811A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 534 removed outlier: 3.500A pdb=" N SER B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.912A pdb=" N ASN B 543 " --> pdb=" O VAL B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 660 Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.426A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AA3, first strand: chain 'C' and resid 75 through 76 removed outlier: 4.197A pdb=" N VAL C 75 " --> pdb=" O CYS C 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.316A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AA8, first strand: chain 'C' and resid 374 through 378 removed outlier: 3.829A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER C 334 " --> pdb=" O GLN C 293 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 301 through 312 removed outlier: 7.180A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.414A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47 Processing sheet with id=AB3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AB6, first strand: chain 'E' and resid 202 through 203 removed outlier: 6.452A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 312 removed outlier: 6.673A pdb=" N ASN E 301 " --> pdb=" O ILE E 323 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ILE E 323 " --> pdb=" O ASN E 301 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY E 321 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLN E 315 " --> pdb=" O ILE E 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 315 through 323A current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AB8, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.371A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AC1, first strand: chain 'A' and resid 75 through 76 removed outlier: 5.610A pdb=" N VAL A 75 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'A' and resid 201 through 203 removed outlier: 6.514A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 283 through 312 removed outlier: 6.609A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 323A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 9 through 11 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 9 through 11 current: chain 'H' and resid 45 through 52 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 45 through 52 current: chain 'H' and resid 116 through 117 No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'H' and resid 102 through 104 Processing sheet with id=AC9, first strand: chain 'L' and resid 5 through 7 removed outlier: 4.077A pdb=" N UNK L 22 " --> pdb=" O UNK L 7 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.210A pdb=" N UNK L 33 " --> pdb=" O UNK L 49 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N UNK L 49 " --> pdb=" O UNK L 33 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N UNK L 35 " --> pdb=" O UNK L 47 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.80 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 3704 1.32 - 1.46: 5025 1.46 - 1.60: 7219 1.60 - 1.74: 35 1.74 - 1.88: 128 Bond restraints: 16111 Sorted by residual: bond pdb=" CB LEU B 661 " pdb=" CG LEU B 661 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB HIS C 374 " pdb=" CG HIS C 374 " ideal model delta sigma weight residual 1.497 1.406 0.091 1.40e-02 5.10e+03 4.18e+01 bond pdb=" CG GLN E 348 " pdb=" CD GLN E 348 " ideal model delta sigma weight residual 1.516 1.385 0.131 2.50e-02 1.60e+03 2.76e+01 bond pdb=" CB LEU F 520 " pdb=" CG LEU F 520 " ideal model delta sigma weight residual 1.530 1.629 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" CB LEU D 661 " pdb=" CG LEU D 661 " ideal model delta sigma weight residual 1.530 1.626 -0.096 2.00e-02 2.50e+03 2.32e+01 ... (remaining 16106 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 18217 2.16 - 4.32: 3122 4.32 - 6.48: 502 6.48 - 8.63: 68 8.63 - 10.79: 5 Bond angle restraints: 21914 Sorted by residual: angle pdb=" C GLU C 492 " pdb=" N PRO C 493 " pdb=" CA PRO C 493 " ideal model delta sigma weight residual 119.56 128.15 -8.59 1.02e+00 9.61e-01 7.09e+01 angle pdb=" C ARG C 298 " pdb=" N PRO C 299 " pdb=" CA PRO C 299 " ideal model delta sigma weight residual 119.56 127.85 -8.29 1.01e+00 9.80e-01 6.74e+01 angle pdb=" C GLU A 492 " pdb=" N PRO A 493 " pdb=" CA PRO A 493 " ideal model delta sigma weight residual 119.56 127.71 -8.15 1.02e+00 9.61e-01 6.38e+01 angle pdb=" C ARG A 298 " pdb=" N PRO A 299 " pdb=" CA PRO A 299 " ideal model delta sigma weight residual 119.56 127.48 -7.92 1.01e+00 9.80e-01 6.15e+01 angle pdb=" N PRO C 437 " pdb=" CA PRO C 437 " pdb=" C PRO C 437 " ideal model delta sigma weight residual 110.47 103.13 7.34 9.60e-01 1.09e+00 5.84e+01 ... (remaining 21909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.28: 10471 21.28 - 42.56: 208 42.56 - 63.85: 72 63.85 - 85.13: 33 85.13 - 106.41: 15 Dihedral angle restraints: 10799 sinusoidal: 5179 harmonic: 5620 Sorted by residual: dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 159.96 -66.96 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 157.43 -64.43 1 1.00e+01 1.00e-02 5.46e+01 dihedral pdb=" CB CYS E 126 " pdb=" SG CYS E 126 " pdb=" SG CYS E 196 " pdb=" CB CYS E 196 " ideal model delta sinusoidal sigma weight residual 93.00 146.06 -53.06 1 1.00e+01 1.00e-02 3.83e+01 ... (remaining 10796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 2031 0.127 - 0.255: 463 0.255 - 0.382: 197 0.382 - 0.509: 78 0.509 - 0.636: 6 Chirality restraints: 2775 Sorted by residual: chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.48e+02 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.64 0.24 2.00e-02 2.50e+03 1.40e+02 chirality pdb=" C1 NAG M 2 " pdb=" O4 NAG M 1 " pdb=" C2 NAG M 2 " pdb=" O5 NAG M 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.09e+02 ... (remaining 2772 not shown) Planarity restraints: 2759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 706 " 0.339 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG E 706 " -0.079 2.00e-02 2.50e+03 pdb=" C8 NAG E 706 " 0.073 2.00e-02 2.50e+03 pdb=" N2 NAG E 706 " -0.519 2.00e-02 2.50e+03 pdb=" O7 NAG E 706 " 0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 701 " 0.343 2.00e-02 2.50e+03 2.94e-01 1.08e+03 pdb=" C7 NAG D 701 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG D 701 " 0.159 2.00e-02 2.50e+03 pdb=" N2 NAG D 701 " -0.520 2.00e-02 2.50e+03 pdb=" O7 NAG D 701 " 0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 710 " 0.340 2.00e-02 2.50e+03 2.91e-01 1.06e+03 pdb=" C7 NAG E 710 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG E 710 " 0.158 2.00e-02 2.50e+03 pdb=" N2 NAG E 710 " -0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 710 " 0.103 2.00e-02 2.50e+03 ... (remaining 2756 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 500 2.67 - 3.23: 14641 3.23 - 3.79: 23344 3.79 - 4.34: 31977 4.34 - 4.90: 50384 Nonbonded interactions: 120846 Sorted by model distance: nonbonded pdb=" O ASP F 624 " pdb=" OD1 ASP F 624 " model vdw 2.118 3.040 nonbonded pdb=" O3 NAG B 703 " pdb=" O7 NAG B 703 " model vdw 2.244 3.040 nonbonded pdb=" OD2 ASP A 167 " pdb=" NZ LYS A 168 " model vdw 2.413 3.120 nonbonded pdb=" NZ LYS E 232 " pdb=" OE2 GLU E 269 " model vdw 2.418 3.120 nonbonded pdb=" CG2 ILE C 294 " pdb=" OG SER C 447 " model vdw 2.428 3.460 ... (remaining 120841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 33 through 505 or resid 701 through 713)) selection = (chain 'C' and (resid 33 through 64 or resid 66 through 397 or resid 411 through \ 505 or resid 702 through 714)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 521 through 548 or resid 568 through 702)) selection = (chain 'D' and (resid 521 through 548 or resid 568 through 702)) selection = (chain 'F' and resid 521 through 702) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'Q' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.410 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.138 16230 Z= 1.186 Angle : 1.725 10.793 22238 Z= 1.095 Chirality : 0.144 0.636 2775 Planarity : 0.017 0.294 2696 Dihedral : 11.247 106.409 7044 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.19), residues: 1669 helix: 0.21 (0.23), residues: 440 sheet: 0.91 (0.23), residues: 415 loop : 0.88 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 419 TYR 0.042 0.007 TYR F 638 PHE 0.026 0.006 PHE A 383 TRP 0.055 0.009 TRP A 479 HIS 0.014 0.002 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.02211 (16111) covalent geometry : angle 1.69172 (21914) SS BOND : bond 0.02167 ( 33) SS BOND : angle 3.11929 ( 66) hydrogen bonds : bond 0.17625 ( 541) hydrogen bonds : angle 7.30043 ( 1452) link_ALPHA1-3 : bond 0.09449 ( 3) link_ALPHA1-3 : angle 4.77589 ( 9) link_ALPHA1-6 : bond 0.05804 ( 3) link_ALPHA1-6 : angle 2.96085 ( 9) link_BETA1-4 : bond 0.07002 ( 17) link_BETA1-4 : angle 4.49834 ( 51) link_NAG-ASN : bond 0.07406 ( 63) link_NAG-ASN : angle 2.82680 ( 189) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 455 time to evaluate : 0.612 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: C 377 ASN cc_start: 0.8016 (t0) cc_final: 0.7579 (t0) REVERT: D 588 ARG cc_start: 0.8599 (ttp80) cc_final: 0.8209 (mtm-85) REVERT: D 591 GLN cc_start: 0.8907 (tt0) cc_final: 0.8542 (tp-100) REVERT: D 639 THR cc_start: 0.8233 (m) cc_final: 0.7517 (p) REVERT: A 125 LEU cc_start: 0.8607 (mt) cc_final: 0.8253 (mt) REVERT: A 153 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7224 (tp30) REVERT: A 207 LYS cc_start: 0.8654 (mmtt) cc_final: 0.8402 (mmtm) outliers start: 0 outliers final: 0 residues processed: 455 average time/residue: 0.1404 time to fit residues: 93.0475 Evaluate side-chains 226 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 130 GLN C 137 ASN C 352 HIS D 630 GLN ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 114 GLN E 170 GLN E 302 ASN E 352 HIS F 540 GLN F 607 ASN A 188 ASN A 425 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.140308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.113958 restraints weight = 26693.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.117629 restraints weight = 17295.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118248 restraints weight = 11121.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.118906 restraints weight = 9669.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119043 restraints weight = 8960.684| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16230 Z= 0.178 Angle : 0.813 10.938 22238 Z= 0.391 Chirality : 0.050 0.427 2775 Planarity : 0.005 0.051 2696 Dihedral : 8.860 81.672 3824 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.42 % Allowed : 9.40 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.20), residues: 1669 helix: 1.40 (0.25), residues: 414 sheet: 0.65 (0.21), residues: 484 loop : 0.28 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 617 TYR 0.020 0.002 TYR A 435 PHE 0.023 0.002 PHE E 391 TRP 0.022 0.002 TRP A 479 HIS 0.009 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00378 (16111) covalent geometry : angle 0.74907 (21914) SS BOND : bond 0.00306 ( 33) SS BOND : angle 1.72088 ( 66) hydrogen bonds : bond 0.06201 ( 541) hydrogen bonds : angle 5.38637 ( 1452) link_ALPHA1-3 : bond 0.01639 ( 3) link_ALPHA1-3 : angle 1.73690 ( 9) link_ALPHA1-6 : bond 0.00841 ( 3) link_ALPHA1-6 : angle 1.68788 ( 9) link_BETA1-4 : bond 0.00598 ( 17) link_BETA1-4 : angle 2.55166 ( 51) link_NAG-ASN : bond 0.00605 ( 63) link_NAG-ASN : angle 3.11491 ( 189) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 161 MET cc_start: 0.8530 (tpt) cc_final: 0.8018 (tpt) REVERT: C 207 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8477 (mmtm) REVERT: C 349 LEU cc_start: 0.8154 (mp) cc_final: 0.7921 (mp) REVERT: C 377 ASN cc_start: 0.8080 (t0) cc_final: 0.7718 (t0) REVERT: D 588 ARG cc_start: 0.8447 (ttp80) cc_final: 0.7807 (ttm-80) REVERT: D 617 ARG cc_start: 0.5258 (OUTLIER) cc_final: 0.4951 (tpt170) REVERT: D 632 ASP cc_start: 0.8502 (t0) cc_final: 0.8223 (t0) REVERT: E 233 PHE cc_start: 0.7837 (t80) cc_final: 0.6909 (t80) REVERT: F 591 GLN cc_start: 0.8379 (tt0) cc_final: 0.8142 (tt0) REVERT: F 647 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7310 (tm-30) REVERT: B 634 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7059 (mt-10) outliers start: 52 outliers final: 32 residues processed: 348 average time/residue: 0.1297 time to fit residues: 67.6740 Evaluate side-chains 245 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain D residue 617 ARG Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 467 THR Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain F residue 646 LEU Chi-restraints excluded: chain F residue 659 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 646 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 122 optimal weight: 0.0010 chunk 159 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 overall best weight: 1.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 300 ASN C 432 GLN D 630 GLN D 658 GLN E 114 GLN E 302 ASN F 653 GLN A 188 ASN B 625 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.134937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.107708 restraints weight = 27218.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.111042 restraints weight = 19405.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111999 restraints weight = 12023.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113543 restraints weight = 10216.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113573 restraints weight = 9416.287| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16230 Z= 0.195 Angle : 0.770 17.128 22238 Z= 0.375 Chirality : 0.049 0.410 2775 Planarity : 0.004 0.065 2696 Dihedral : 8.231 75.627 3824 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.42 % Allowed : 11.76 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.70 (0.20), residues: 1669 helix: 1.27 (0.26), residues: 424 sheet: 0.72 (0.22), residues: 457 loop : -0.05 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 503 TYR 0.025 0.002 TYR E 217 PHE 0.020 0.002 PHE A 53 TRP 0.023 0.002 TRP F 610 HIS 0.006 0.001 HIS D 585 Details of bonding type rmsd covalent geometry : bond 0.00447 (16111) covalent geometry : angle 0.70573 (21914) SS BOND : bond 0.00722 ( 33) SS BOND : angle 2.69978 ( 66) hydrogen bonds : bond 0.05487 ( 541) hydrogen bonds : angle 5.15946 ( 1452) link_ALPHA1-3 : bond 0.01588 ( 3) link_ALPHA1-3 : angle 1.48155 ( 9) link_ALPHA1-6 : bond 0.00798 ( 3) link_ALPHA1-6 : angle 1.83747 ( 9) link_BETA1-4 : bond 0.00712 ( 17) link_BETA1-4 : angle 2.09911 ( 51) link_NAG-ASN : bond 0.00631 ( 63) link_NAG-ASN : angle 2.82475 ( 189) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 223 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 207 LYS cc_start: 0.8587 (mmtt) cc_final: 0.8376 (mmtm) REVERT: C 349 LEU cc_start: 0.8229 (mp) cc_final: 0.7856 (mp) REVERT: C 377 ASN cc_start: 0.8301 (t0) cc_final: 0.8013 (t0) REVERT: D 530 MET cc_start: 0.7660 (mtp) cc_final: 0.7379 (mtt) REVERT: D 588 ARG cc_start: 0.8409 (ttp80) cc_final: 0.7813 (ttm-80) REVERT: E 233 PHE cc_start: 0.8166 (t80) cc_final: 0.7195 (t80) REVERT: B 530 MET cc_start: 0.7181 (mtt) cc_final: 0.5990 (mtt) REVERT: B 615 SER cc_start: 0.7460 (t) cc_final: 0.7259 (m) REVERT: B 631 TRP cc_start: 0.7867 (t-100) cc_final: 0.7306 (t-100) REVERT: B 636 SER cc_start: 0.7569 (p) cc_final: 0.7081 (m) outliers start: 52 outliers final: 32 residues processed: 266 average time/residue: 0.1304 time to fit residues: 52.0625 Evaluate side-chains 233 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 375 SER Chi-restraints excluded: chain C residue 419 ARG Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 595 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 ASN A 188 ASN A 203 GLN A 425 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.131921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.104771 restraints weight = 27182.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.107720 restraints weight = 19638.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.108254 restraints weight = 12975.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.108947 restraints weight = 11542.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.109115 restraints weight = 10680.117| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16230 Z= 0.186 Angle : 0.726 13.907 22238 Z= 0.348 Chirality : 0.048 0.394 2775 Planarity : 0.004 0.068 2696 Dihedral : 7.813 69.664 3824 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.61 % Allowed : 12.61 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.20), residues: 1669 helix: 1.30 (0.26), residues: 419 sheet: 0.57 (0.23), residues: 443 loop : -0.21 (0.21), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 480 TYR 0.013 0.002 TYR C 217 PHE 0.019 0.002 PHE A 53 TRP 0.032 0.002 TRP F 610 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00438 (16111) covalent geometry : angle 0.66744 (21914) SS BOND : bond 0.00454 ( 33) SS BOND : angle 2.36416 ( 66) hydrogen bonds : bond 0.05033 ( 541) hydrogen bonds : angle 5.03507 ( 1452) link_ALPHA1-3 : bond 0.01363 ( 3) link_ALPHA1-3 : angle 1.91705 ( 9) link_ALPHA1-6 : bond 0.00681 ( 3) link_ALPHA1-6 : angle 1.97085 ( 9) link_BETA1-4 : bond 0.00573 ( 17) link_BETA1-4 : angle 1.80389 ( 51) link_NAG-ASN : bond 0.00529 ( 63) link_NAG-ASN : angle 2.67610 ( 189) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 206 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7482 (mm-40) REVERT: C 349 LEU cc_start: 0.8282 (mp) cc_final: 0.7859 (mp) REVERT: D 530 MET cc_start: 0.7931 (mtp) cc_final: 0.7632 (mtt) REVERT: D 588 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7798 (ttm-80) REVERT: E 419 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8289 (mtp85) REVERT: F 591 GLN cc_start: 0.8611 (tt0) cc_final: 0.8163 (tt0) REVERT: B 530 MET cc_start: 0.7231 (mtt) cc_final: 0.6258 (mtt) REVERT: B 548 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6871 (mt) REVERT: B 616 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6719 (m-40) REVERT: B 631 TRP cc_start: 0.7690 (t-100) cc_final: 0.7196 (t-100) outliers start: 55 outliers final: 39 residues processed: 245 average time/residue: 0.1311 time to fit residues: 48.4491 Evaluate side-chains 226 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 184 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 372 THR Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain D residue 612 SER Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 419 ARG Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 612 SER Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 136 ASN Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 166 ARG Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 425 ASN Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 172 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 23 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 114 GLN ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.126669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.099064 restraints weight = 27535.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.102630 restraints weight = 19945.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.103804 restraints weight = 12231.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.104372 restraints weight = 9937.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.104530 restraints weight = 9358.266| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 16230 Z= 0.278 Angle : 0.821 12.835 22238 Z= 0.395 Chirality : 0.052 0.462 2775 Planarity : 0.005 0.068 2696 Dihedral : 8.254 68.979 3824 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.14 % Allowed : 13.01 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.20), residues: 1669 helix: 0.98 (0.26), residues: 426 sheet: 0.11 (0.23), residues: 450 loop : -0.50 (0.20), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 480 TYR 0.024 0.002 TYR C 217 PHE 0.019 0.003 PHE A 53 TRP 0.049 0.002 TRP F 610 HIS 0.006 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00667 (16111) covalent geometry : angle 0.76928 (21914) SS BOND : bond 0.00547 ( 33) SS BOND : angle 2.05369 ( 66) hydrogen bonds : bond 0.05580 ( 541) hydrogen bonds : angle 5.28383 ( 1452) link_ALPHA1-3 : bond 0.01496 ( 3) link_ALPHA1-3 : angle 1.83995 ( 9) link_ALPHA1-6 : bond 0.00491 ( 3) link_ALPHA1-6 : angle 1.89964 ( 9) link_BETA1-4 : bond 0.00578 ( 17) link_BETA1-4 : angle 1.92856 ( 51) link_NAG-ASN : bond 0.00572 ( 63) link_NAG-ASN : angle 2.80116 ( 189) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 211 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 82 GLN cc_start: 0.7840 (tm-30) cc_final: 0.7634 (tm-30) REVERT: D 588 ARG cc_start: 0.8390 (ttp80) cc_final: 0.7819 (ttm-80) REVERT: D 623 TRP cc_start: 0.8093 (m-10) cc_final: 0.7519 (m100) REVERT: E 125 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8730 (tt) REVERT: E 233 PHE cc_start: 0.8562 (t80) cc_final: 0.7815 (t80) REVERT: F 591 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: A 303 THR cc_start: 0.9224 (OUTLIER) cc_final: 0.8573 (p) REVERT: A 325 ASP cc_start: 0.7984 (t0) cc_final: 0.7673 (t0) REVERT: B 530 MET cc_start: 0.7210 (mtt) cc_final: 0.6607 (mtt) REVERT: B 548 ILE cc_start: 0.7626 (OUTLIER) cc_final: 0.7033 (mt) REVERT: B 616 ASN cc_start: 0.7299 (OUTLIER) cc_final: 0.6672 (m-40) REVERT: B 631 TRP cc_start: 0.7699 (t-100) cc_final: 0.7402 (t-100) outliers start: 63 outliers final: 37 residues processed: 255 average time/residue: 0.1310 time to fit residues: 50.2717 Evaluate side-chains 220 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 178 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 581 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 499 THR Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain F residue 614 TRP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 85 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 176 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114593 restraints weight = 25875.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117653 restraints weight = 18859.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118781 restraints weight = 14242.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.118999 restraints weight = 10926.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.119293 restraints weight = 10700.585| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16230 Z= 0.194 Angle : 0.717 10.231 22238 Z= 0.345 Chirality : 0.048 0.385 2775 Planarity : 0.004 0.056 2696 Dihedral : 7.787 61.742 3824 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 15.44 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.20), residues: 1669 helix: 1.13 (0.26), residues: 421 sheet: 0.06 (0.23), residues: 448 loop : -0.60 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 504 TYR 0.014 0.002 TYR C 217 PHE 0.017 0.002 PHE A 53 TRP 0.079 0.002 TRP F 610 HIS 0.003 0.001 HIS E 330 Details of bonding type rmsd covalent geometry : bond 0.00458 (16111) covalent geometry : angle 0.66470 (21914) SS BOND : bond 0.00585 ( 33) SS BOND : angle 2.00273 ( 66) hydrogen bonds : bond 0.04966 ( 541) hydrogen bonds : angle 5.00853 ( 1452) link_ALPHA1-3 : bond 0.01288 ( 3) link_ALPHA1-3 : angle 2.10810 ( 9) link_ALPHA1-6 : bond 0.00543 ( 3) link_ALPHA1-6 : angle 1.81945 ( 9) link_BETA1-4 : bond 0.00539 ( 17) link_BETA1-4 : angle 1.62790 ( 51) link_NAG-ASN : bond 0.00446 ( 63) link_NAG-ASN : angle 2.60582 ( 189) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3338 Ramachandran restraints generated. 1669 Oldfield, 0 Emsley, 1669 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 523 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8752 (mt) REVERT: D 588 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7818 (ttm-80) REVERT: E 233 PHE cc_start: 0.8523 (t80) cc_final: 0.7936 (t80) REVERT: F 591 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: B 548 ILE cc_start: 0.7385 (OUTLIER) cc_final: 0.6804 (mt) REVERT: B 616 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.6735 (m-40) REVERT: B 636 SER cc_start: 0.7382 (p) cc_final: 0.7006 (m) outliers start: 47 outliers final: 33 residues processed: 233 average time/residue: 0.1311 time to fit residues: 45.9752 Evaluate side-chains 222 residues out of total 1522 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 95 MET Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 172 VAL Chi-restraints excluded: chain C residue 205 CYS Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 443 ILE Chi-restraints excluded: chain D residue 523 LEU Chi-restraints excluded: chain D residue 595 ILE Chi-restraints excluded: chain D residue 605 CYS Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 111 LEU Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 218 CYS Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 320 THR Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain F residue 545 LEU Chi-restraints excluded: chain F residue 591 GLN Chi-restraints excluded: chain F residue 602 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain B residue 534 SER Chi-restraints excluded: chain B residue 538 THR Chi-restraints excluded: chain B residue 548 ILE Chi-restraints excluded: chain B residue 595 ILE Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain B residue 635 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/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-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 52.0464 > 50: distance: 15 - 161: 32.319 distance: 18 - 158: 29.367 distance: 27 - 149: 25.889 distance: 30 - 146: 29.291 distance: 40 - 138: 17.509 distance: 43 - 135: 22.735 distance: 98 - 103: 5.079 distance: 103 - 104: 14.315 distance: 104 - 105: 16.693 distance: 105 - 106: 6.092 distance: 105 - 111: 11.808 distance: 107 - 108: 15.368 distance: 107 - 109: 30.378 distance: 108 - 110: 12.226 distance: 111 - 112: 19.333 distance: 112 - 113: 6.033 distance: 112 - 115: 4.542 distance: 113 - 114: 4.598 distance: 113 - 120: 9.135 distance: 115 - 116: 11.318 distance: 116 - 117: 17.020 distance: 117 - 118: 34.480 distance: 117 - 119: 12.628 distance: 120 - 121: 26.640 distance: 120 - 126: 28.643 distance: 121 - 122: 4.526 distance: 121 - 124: 12.605 distance: 122 - 123: 3.365 distance: 122 - 127: 8.418 distance: 124 - 125: 33.102 distance: 125 - 126: 32.427 distance: 127 - 128: 7.134 distance: 128 - 129: 4.051 distance: 128 - 131: 3.592 distance: 129 - 130: 4.089 distance: 129 - 135: 17.611 distance: 131 - 132: 19.098 distance: 132 - 133: 38.928 distance: 132 - 134: 30.388 distance: 135 - 136: 15.779 distance: 136 - 137: 14.703 distance: 137 - 138: 25.533 distance: 137 - 139: 13.652 distance: 139 - 140: 11.100 distance: 140 - 141: 6.508 distance: 140 - 143: 28.309 distance: 141 - 142: 43.935 distance: 141 - 146: 12.972 distance: 143 - 144: 22.740 distance: 143 - 145: 48.665 distance: 146 - 147: 19.867 distance: 147 - 148: 27.118 distance: 147 - 150: 39.477 distance: 148 - 149: 38.070 distance: 148 - 151: 19.912 distance: 151 - 152: 14.089 distance: 151 - 157: 7.975 distance: 152 - 153: 9.782 distance: 152 - 155: 6.114 distance: 153 - 154: 19.023 distance: 153 - 158: 3.028 distance: 155 - 156: 10.575 distance: 156 - 157: 12.334 distance: 158 - 159: 42.507 distance: 159 - 162: 9.736 distance: 160 - 161: 4.374 distance: 160 - 165: 27.374 distance: 162 - 163: 6.690 distance: 165 - 166: 11.416 distance: 166 - 167: 12.886 distance: 167 - 168: 11.002 distance: 167 - 176: 29.235 distance: 169 - 170: 21.864 distance: 170 - 171: 11.473 distance: 171 - 172: 9.342 distance: 172 - 173: 15.036 distance: 173 - 174: 8.208 distance: 173 - 175: 21.480