Starting phenix.real_space_refine on Sat Sep 12 10:48:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2026/6ucv_20729.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 44 5.16 5 C 9682 2.51 5 N 2523 2.21 5 O 2851 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15102 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2399 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "C" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "E" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 2389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2389 Classifications: {'peptide': 311} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 9, 'TRANS': 301} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 411 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 53} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "L" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "M" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "a" Number of atoms: 2419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2419 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 9, 'TRANS': 307} Chain breaks: 1 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "b" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 397 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 50} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 267 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 33} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "i" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2369 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "j" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 1, 'TRANS': 48} Chain: "k" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 303 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "l" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 267 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 3, 'TRANS': 31} Chain: "m" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 393 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 45} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "I" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'MC3': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.49, per 1000 atoms: 0.23 Number of scatterers: 15102 At special positions: 0 Unit cell: (100.05, 120.75, 215.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 P 2 15.00 O 2851 8.00 N 2523 7.00 C 9682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 1.21 Conformation dependent library (CDL) restraints added in 634.2 milliseconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3644 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 4 sheets defined 37.5% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 55 removed outlier: 4.135A pdb=" N GLN A 47 " --> pdb=" O ASP A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.638A pdb=" N GLN A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 135 Proline residue: B 112 - end of helix Processing helix chain 'C' and resid 14 through 49 Proline residue: C 39 - end of helix Processing helix chain 'D' and resid 30 through 51 removed outlier: 3.638A pdb=" N THR D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 58 removed outlier: 3.917A pdb=" N ASP D 55 " --> pdb=" O SER D 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 31 Processing helix chain 'E' and resid 31 through 43 Processing helix chain 'E' and resid 49 through 55 removed outlier: 3.652A pdb=" N LEU E 54 " --> pdb=" O PHE E 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 46 through 56 removed outlier: 4.050A pdb=" N GLU I 56 " --> pdb=" O ARG I 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 364 through 373 removed outlier: 3.689A pdb=" N GLN I 372 " --> pdb=" O LEU I 368 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 135 Proline residue: J 112 - end of helix Processing helix chain 'K' and resid 14 through 49 Proline residue: K 39 - end of helix Processing helix chain 'L' and resid 30 through 51 removed outlier: 3.625A pdb=" N THR L 34 " --> pdb=" O SER L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 58 removed outlier: 3.913A pdb=" N ASP L 55 " --> pdb=" O SER L 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 31 Processing helix chain 'M' and resid 31 through 43 Processing helix chain 'M' and resid 49 through 55 removed outlier: 3.504A pdb=" N LEU M 54 " --> pdb=" O PHE M 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 40 through 54 Processing helix chain 'a' and resid 364 through 373 removed outlier: 3.754A pdb=" N GLN a 372 " --> pdb=" O LEU a 368 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 135 Proline residue: b 112 - end of helix Processing helix chain 'c' and resid 14 through 49 Proline residue: c 39 - end of helix Processing helix chain 'd' and resid 29 through 51 removed outlier: 4.031A pdb=" N THR d 34 " --> pdb=" O SER d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 51 through 58 removed outlier: 3.886A pdb=" N ASP d 55 " --> pdb=" O SER d 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 12 through 31 Processing helix chain 'e' and resid 31 through 43 removed outlier: 3.552A pdb=" N PHE e 35 " --> pdb=" O GLY e 31 " (cutoff:3.500A) Processing helix chain 'e' and resid 49 through 55 removed outlier: 3.692A pdb=" N LEU e 54 " --> pdb=" O PHE e 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 50 through 55 Processing helix chain 'i' and resid 67 through 72 removed outlier: 3.512A pdb=" N ARG i 72 " --> pdb=" O LYS i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 364 through 373 removed outlier: 3.581A pdb=" N GLN i 372 " --> pdb=" O LEU i 368 " (cutoff:3.500A) Processing helix chain 'j' and resid 87 through 135 Proline residue: j 112 - end of helix Processing helix chain 'k' and resid 14 through 49 Proline residue: k 39 - end of helix removed outlier: 3.512A pdb=" N TRP k 49 " --> pdb=" O VAL k 45 " (cutoff:3.500A) Processing helix chain 'l' and resid 30 through 51 removed outlier: 3.641A pdb=" N THR l 34 " --> pdb=" O SER l 30 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 57 removed outlier: 4.068A pdb=" N ASP l 55 " --> pdb=" O SER l 51 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 31 Processing helix chain 'm' and resid 31 through 43 Processing helix chain 'm' and resid 49 through 55 removed outlier: 3.512A pdb=" N LEU m 54 " --> pdb=" O PHE m 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 93 removed outlier: 6.971A pdb=" N PHE A 98 " --> pdb=" O PHE A 92 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N CYS A 165 " --> pdb=" O ASN A 184 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N THR A 194 " --> pdb=" O PRO A 185 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLY A 83 " --> pdb=" O CYS A 355 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU A 357 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG A 85 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N PHE A 359 " --> pdb=" O ARG A 85 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ASP A 87 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N THR A 361 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASN A 89 " --> pdb=" O THR A 361 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 83 through 93 removed outlier: 6.851A pdb=" N PHE I 98 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS I 165 " --> pdb=" O ASN I 184 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR I 194 " --> pdb=" O PRO I 185 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS I 323 " --> pdb=" O ASP I 319 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N GLY I 83 " --> pdb=" O CYS I 355 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N LEU I 357 " --> pdb=" O GLY I 83 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG I 85 " --> pdb=" O LEU I 357 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N PHE I 359 " --> pdb=" O ARG I 85 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASP I 87 " --> pdb=" O PHE I 359 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N THR I 361 " --> pdb=" O ASP I 87 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASN I 89 " --> pdb=" O THR I 361 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 85 through 93 removed outlier: 6.886A pdb=" N PHE a 98 " --> pdb=" O PHE a 92 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N CYS a 165 " --> pdb=" O ASN a 184 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N THR a 194 " --> pdb=" O PRO a 185 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS a 323 " --> pdb=" O ASP a 319 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ARG a 85 " --> pdb=" O LEU a 357 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N PHE a 359 " --> pdb=" O ARG a 85 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASP a 87 " --> pdb=" O PHE a 359 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR a 361 " --> pdb=" O ASP a 87 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ASN a 89 " --> pdb=" O THR a 361 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'i' and resid 83 through 93 removed outlier: 6.787A pdb=" N PHE i 98 " --> pdb=" O PHE i 92 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N CYS i 165 " --> pdb=" O ASN i 184 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR i 194 " --> pdb=" O PRO i 185 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS i 323 " --> pdb=" O ASP i 319 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLY i 83 " --> pdb=" O CYS i 355 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N LEU i 357 " --> pdb=" O GLY i 83 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG i 85 " --> pdb=" O LEU i 357 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N PHE i 359 " --> pdb=" O ARG i 85 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP i 87 " --> pdb=" O PHE i 359 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N THR i 361 " --> pdb=" O ASP i 87 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ASN i 89 " --> pdb=" O THR i 361 " (cutoff:3.500A) 1083 hydrogen bonds defined for protein. 3171 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: 2.90 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2487 1.30 - 1.43: 4065 1.43 - 1.56: 8770 1.56 - 1.69: 24 1.69 - 1.81: 72 Bond restraints: 15418 Sorted by residual: bond pdb=" C31 MC3 I 401 " pdb=" O2 MC3 I 401 " ideal model delta sigma weight residual 1.328 1.433 -0.105 2.00e-02 2.50e+03 2.76e+01 bond pdb=" C31 MC3 i 401 " pdb=" O2 MC3 i 401 " ideal model delta sigma weight residual 1.328 1.432 -0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C11 MC3 i 401 " pdb=" O3 MC3 i 401 " ideal model delta sigma weight residual 1.327 1.419 -0.092 2.00e-02 2.50e+03 2.11e+01 bond pdb=" C11 MC3 I 401 " pdb=" O3 MC3 I 401 " ideal model delta sigma weight residual 1.327 1.418 -0.091 2.00e-02 2.50e+03 2.06e+01 bond pdb=" N MC3 i 401 " pdb=" C8 MC3 i 401 " ideal model delta sigma weight residual 1.493 1.429 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 15413 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.76: 20685 3.76 - 7.53: 205 7.53 - 11.29: 21 11.29 - 15.05: 0 15.05 - 18.81: 4 Bond angle restraints: 20915 Sorted by residual: angle pdb=" O1P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O2P MC3 i 401 " ideal model delta sigma weight residual 119.69 100.88 18.81 3.00e+00 1.11e-01 3.93e+01 angle pdb=" O1P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O2P MC3 I 401 " ideal model delta sigma weight residual 119.69 101.69 18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" O3P MC3 I 401 " pdb=" P MC3 I 401 " pdb=" O4P MC3 I 401 " ideal model delta sigma weight residual 93.26 109.95 -16.69 3.00e+00 1.11e-01 3.10e+01 angle pdb=" O3P MC3 i 401 " pdb=" P MC3 i 401 " pdb=" O4P MC3 i 401 " ideal model delta sigma weight residual 93.26 109.81 -16.55 3.00e+00 1.11e-01 3.04e+01 angle pdb=" CA ASP a 134 " pdb=" CB ASP a 134 " pdb=" CG ASP a 134 " ideal model delta sigma weight residual 112.60 117.22 -4.62 1.00e+00 1.00e+00 2.13e+01 ... (remaining 20910 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.82: 8787 19.82 - 39.64: 255 39.64 - 59.46: 52 59.46 - 79.27: 2 79.27 - 99.09: 1 Dihedral angle restraints: 9097 sinusoidal: 3474 harmonic: 5623 Sorted by residual: dihedral pdb=" CA ASN i 95 " pdb=" C ASN i 95 " pdb=" N PRO i 96 " pdb=" CA PRO i 96 " ideal model delta harmonic sigma weight residual 180.00 139.35 40.65 0 5.00e+00 4.00e-02 6.61e+01 dihedral pdb=" CA ASN a 95 " pdb=" C ASN a 95 " pdb=" N PRO a 96 " pdb=" CA PRO a 96 " ideal model delta harmonic sigma weight residual 180.00 139.79 40.21 0 5.00e+00 4.00e-02 6.47e+01 dihedral pdb=" CA ASN I 95 " pdb=" C ASN I 95 " pdb=" N PRO I 96 " pdb=" CA PRO I 96 " ideal model delta harmonic sigma weight residual 180.00 140.83 39.17 0 5.00e+00 4.00e-02 6.14e+01 ... (remaining 9094 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 2100 0.078 - 0.156: 256 0.156 - 0.234: 18 0.234 - 0.312: 2 0.312 - 0.390: 4 Chirality restraints: 2380 Sorted by residual: chirality pdb=" CB ILE m 33 " pdb=" CA ILE m 33 " pdb=" CG1 ILE m 33 " pdb=" CG2 ILE m 33 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CB ILE M 33 " pdb=" CA ILE M 33 " pdb=" CG1 ILE M 33 " pdb=" CG2 ILE M 33 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" CB ILE e 33 " pdb=" CA ILE e 33 " pdb=" CG1 ILE e 33 " pdb=" CG2 ILE e 33 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.57e+00 ... (remaining 2377 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 206 " -0.044 5.00e-02 4.00e+02 6.67e-02 7.11e+00 pdb=" N PRO A 207 " 0.115 5.00e-02 4.00e+02 pdb=" CA PRO A 207 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 207 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR a 206 " -0.043 5.00e-02 4.00e+02 6.46e-02 6.67e+00 pdb=" N PRO a 207 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO a 207 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO a 207 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR I 206 " 0.043 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO I 207 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO I 207 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO I 207 " 0.036 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1409 2.75 - 3.29: 13753 3.29 - 3.82: 24101 3.82 - 4.36: 26697 4.36 - 4.90: 48932 Nonbonded interactions: 114892 Sorted by model distance: nonbonded pdb=" OD1 ASN a 179 " pdb=" OG SER a 200 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN A 179 " pdb=" OG SER A 200 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN I 179 " pdb=" OG SER I 200 " model vdw 2.233 3.040 nonbonded pdb=" OD1 ASN i 179 " pdb=" OG SER i 200 " model vdw 2.261 3.040 nonbonded pdb=" OG SER A 312 " pdb=" OG SER B 116 " model vdw 2.279 3.040 ... (remaining 114887 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 49 through 373) selection = (chain 'I' and resid 49 through 373) selection = (chain 'a' and resid 49 through 373) selection = (chain 'i' and resid 49 through 373) } ncs_group { reference = chain 'B' selection = (chain 'J' and resid 86 through 135) selection = (chain 'b' and resid 86 through 135) selection = chain 'j' } ncs_group { reference = chain 'C' selection = chain 'K' selection = chain 'c' selection = chain 'k' } ncs_group { reference = (chain 'D' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) selection = (chain 'L' and resid 27 through 61) selection = (chain 'd' and resid 27 through 61) selection = (chain 'l' and ((resid 27 through 28 and (name N or name CA or name C or name O \ or name CB )) or resid 29 through 61)) } ncs_group { reference = chain 'E' selection = chain 'M' selection = chain 'e' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.660 Find NCS groups from input model: 0.320 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 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 : 0.005 0.105 15418 Z= 0.255 Angle : 0.941 18.813 20915 Z= 0.481 Chirality : 0.053 0.390 2380 Planarity : 0.007 0.067 2661 Dihedral : 10.239 99.092 5453 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.88 % 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: -1.87 (0.17), residues: 1899 helix: -1.31 (0.14), residues: 724 sheet: -0.34 (0.18), residues: 808 loop : -2.50 (0.26), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 330 TYR 0.015 0.002 TYR E 30 PHE 0.025 0.002 PHE b 92 TRP 0.022 0.002 TRP J 100 HIS 0.005 0.001 HIS C 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.25 (15418) covalent geometry : angle 0.94119 / 0.48 (20915) hydrogen bonds : bond 0.11005 / 7.26 ( 1083) hydrogen bonds : angle 6.28007 / 4.31 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ILE cc_start: 0.9115 (tp) cc_final: 0.8830 (tp) REVERT: A 170 ASP cc_start: 0.8507 (t0) cc_final: 0.8263 (m-30) REVERT: A 171 TYR cc_start: 0.8367 (t80) cc_final: 0.8140 (t80) REVERT: I 369 MET cc_start: 0.8764 (mtp) cc_final: 0.8482 (tmm) REVERT: K 40 MET cc_start: 0.7006 (mpm) cc_final: 0.6411 (mpp) REVERT: M 54 LEU cc_start: 0.8884 (mp) cc_final: 0.8589 (tt) REVERT: a 303 ILE cc_start: 0.9077 (tt) cc_final: 0.8797 (mp) REVERT: e 38 TYR cc_start: 0.7540 (t80) cc_final: 0.6443 (m-80) REVERT: m 53 LEU cc_start: 0.8775 (tt) cc_final: 0.8465 (mt) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.0920 time to fit residues: 30.8773 Evaluate side-chains 84 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 65 ASN A 99 GLN C 17 HIS D 50 GLN E 29 HIS I 65 ASN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 17 HIS M 29 HIS M 52 ASN a 65 ASN a 99 GLN c 17 HIS e 52 ASN i 65 ASN i 99 GLN k 17 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.052160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.042227 restraints weight = 112321.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.043034 restraints weight = 66196.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.043214 restraints weight = 48391.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043375 restraints weight = 47640.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.043396 restraints weight = 42916.488| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15418 Z= 0.211 Angle : 0.648 7.741 20915 Z= 0.338 Chirality : 0.041 0.164 2380 Planarity : 0.005 0.057 2661 Dihedral : 6.506 61.196 2089 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.31 % Allowed : 2.88 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.41 % 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 (0.19), residues: 1899 helix: 1.33 (0.18), residues: 720 sheet: -0.26 (0.18), residues: 817 loop : -1.83 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG i 52 TYR 0.012 0.002 TYR a 307 PHE 0.025 0.002 PHE C 34 TRP 0.013 0.002 TRP c 36 HIS 0.007 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (15418) covalent geometry : angle 0.64769 / 0.34 (20915) hydrogen bonds : bond 0.03056 / 2.08 ( 1083) hydrogen bonds : angle 4.85620 / 3.33 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 101 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 PHE cc_start: 0.6856 (OUTLIER) cc_final: 0.6438 (m-10) REVERT: A 369 MET cc_start: 0.8008 (tpt) cc_final: 0.7691 (tpp) REVERT: J 130 PHE cc_start: 0.8960 (m-80) cc_final: 0.8731 (m-10) REVERT: J 132 LEU cc_start: 0.9550 (pp) cc_final: 0.9331 (pp) REVERT: M 54 LEU cc_start: 0.9197 (mp) cc_final: 0.8684 (tt) REVERT: c 40 MET cc_start: 0.8857 (mpp) cc_final: 0.8365 (mpp) outliers start: 5 outliers final: 1 residues processed: 106 average time/residue: 0.0887 time to fit residues: 15.6433 Evaluate side-chains 67 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 87 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 142 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN d 38 ASN e 29 HIS e 52 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.049085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.039379 restraints weight = 114804.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.039713 restraints weight = 70774.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.039938 restraints weight = 58928.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.040022 restraints weight = 54820.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.040112 restraints weight = 51186.623| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 15418 Z= 0.335 Angle : 0.760 8.266 20915 Z= 0.400 Chirality : 0.044 0.157 2380 Planarity : 0.005 0.059 2661 Dihedral : 7.047 67.431 2089 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.12 % Allowed : 4.25 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.34 (0.20), residues: 1899 helix: 1.87 (0.18), residues: 717 sheet: -0.34 (0.18), residues: 807 loop : -1.47 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 261 TYR 0.033 0.003 TYR E 30 PHE 0.023 0.002 PHE A 359 TRP 0.019 0.002 TRP I 145 HIS 0.011 0.002 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00716 / 0.34 (15418) covalent geometry : angle 0.76022 / 0.40 (20915) hydrogen bonds : bond 0.03547 / 2.41 ( 1083) hydrogen bonds : angle 5.12337 / 3.51 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8374 (mpp) cc_final: 0.8001 (mpp) REVERT: D 54 MET cc_start: 0.7709 (tpp) cc_final: 0.7436 (tpp) REVERT: I 369 MET cc_start: 0.8195 (tmm) cc_final: 0.7940 (tmm) REVERT: J 130 PHE cc_start: 0.8988 (m-80) cc_final: 0.8731 (m-10) REVERT: c 40 MET cc_start: 0.8969 (mpp) cc_final: 0.8767 (mpp) REVERT: j 126 MET cc_start: 0.8777 (tmm) cc_final: 0.8570 (tmm) outliers start: 2 outliers final: 1 residues processed: 73 average time/residue: 0.0955 time to fit residues: 11.9469 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 0 optimal weight: 40.0000 chunk 83 optimal weight: 7.9990 chunk 161 optimal weight: 0.0060 chunk 16 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 140 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 99 GLN I 172 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.049865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040355 restraints weight = 112910.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040761 restraints weight = 67803.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.041084 restraints weight = 53127.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041207 restraints weight = 48056.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041250 restraints weight = 44970.789| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15418 Z= 0.168 Angle : 0.609 8.016 20915 Z= 0.316 Chirality : 0.041 0.150 2380 Planarity : 0.004 0.056 2661 Dihedral : 6.393 68.237 2089 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 0.77 (0.20), residues: 1899 helix: 2.36 (0.19), residues: 723 sheet: -0.30 (0.18), residues: 809 loop : -1.13 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 315 TYR 0.017 0.001 TYR I 79 PHE 0.014 0.001 PHE C 34 TRP 0.014 0.001 TRP M 32 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (15418) covalent geometry : angle 0.60928 / 0.32 (20915) hydrogen bonds : bond 0.02946 / 1.99 ( 1083) hydrogen bonds : angle 4.64558 / 3.19 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7896 (tpt) cc_final: 0.7677 (tpp) REVERT: C 40 MET cc_start: 0.8224 (mpp) cc_final: 0.7755 (mpp) REVERT: D 54 MET cc_start: 0.7595 (tpp) cc_final: 0.7154 (tpp) REVERT: I 369 MET cc_start: 0.8045 (tmm) cc_final: 0.7768 (tmm) REVERT: J 130 PHE cc_start: 0.8993 (m-80) cc_final: 0.8630 (m-10) REVERT: K 40 MET cc_start: 0.8258 (mpp) cc_final: 0.7970 (mpp) REVERT: M 54 LEU cc_start: 0.9113 (mp) cc_final: 0.8679 (tt) REVERT: a 369 MET cc_start: 0.8053 (tpt) cc_final: 0.7838 (tpt) REVERT: c 40 MET cc_start: 0.8953 (mpp) cc_final: 0.8721 (mpp) REVERT: j 126 MET cc_start: 0.8710 (tmm) cc_final: 0.8482 (tmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0835 time to fit residues: 10.8180 Evaluate side-chains 57 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 95 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 46 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 97 optimal weight: 0.0470 chunk 78 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 99 GLN I 371 GLN M 52 ASN a 99 GLN ** a 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN i 99 GLN m 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.050439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.040907 restraints weight = 111708.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041342 restraints weight = 67374.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.041693 restraints weight = 53946.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.041753 restraints weight = 48791.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.041759 restraints weight = 45858.249| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15418 Z= 0.122 Angle : 0.577 7.865 20915 Z= 0.296 Chirality : 0.040 0.151 2380 Planarity : 0.004 0.054 2661 Dihedral : 5.766 67.076 2089 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.12 % Allowed : 2.00 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.07 (0.20), residues: 1899 helix: 2.68 (0.19), residues: 722 sheet: -0.25 (0.18), residues: 817 loop : -0.86 (0.37), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 315 TYR 0.010 0.001 TYR I 307 PHE 0.013 0.001 PHE A 359 TRP 0.011 0.001 TRP K 42 HIS 0.010 0.001 HIS i 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (15418) covalent geometry : angle 0.57721 / 0.30 (20915) hydrogen bonds : bond 0.02691 / 1.82 ( 1083) hydrogen bonds : angle 4.35717 / 2.99 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7960 (tpt) cc_final: 0.7740 (tpp) REVERT: B 127 GLU cc_start: 0.9250 (OUTLIER) cc_final: 0.8865 (pp20) REVERT: D 54 MET cc_start: 0.7702 (tpp) cc_final: 0.7278 (tpp) REVERT: I 369 MET cc_start: 0.8069 (tmm) cc_final: 0.7763 (tmm) REVERT: J 130 PHE cc_start: 0.9009 (m-80) cc_final: 0.8684 (m-10) REVERT: K 40 MET cc_start: 0.8228 (mpp) cc_final: 0.7994 (mmt) REVERT: M 54 LEU cc_start: 0.9113 (mp) cc_final: 0.8692 (tt) REVERT: a 369 MET cc_start: 0.8183 (tpt) cc_final: 0.7969 (tpt) REVERT: c 40 MET cc_start: 0.8941 (mpp) cc_final: 0.8711 (mpp) REVERT: j 102 LEU cc_start: 0.8982 (tp) cc_final: 0.8612 (tt) REVERT: j 126 MET cc_start: 0.8770 (tmm) cc_final: 0.8514 (tmm) outliers start: 2 outliers final: 0 residues processed: 79 average time/residue: 0.0804 time to fit residues: 11.1853 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 4 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 133 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 38 ASN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.050087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040675 restraints weight = 111586.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041124 restraints weight = 66705.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041238 restraints weight = 54712.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.041403 restraints weight = 50050.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.041456 restraints weight = 47258.599| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15418 Z= 0.153 Angle : 0.596 7.926 20915 Z= 0.305 Chirality : 0.040 0.149 2380 Planarity : 0.004 0.053 2661 Dihedral : 5.778 66.491 2089 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.16 (0.21), residues: 1899 helix: 2.78 (0.19), residues: 722 sheet: -0.23 (0.18), residues: 811 loop : -0.82 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 52 TYR 0.012 0.001 TYR I 307 PHE 0.012 0.001 PHE A 359 TRP 0.013 0.001 TRP m 41 HIS 0.006 0.001 HIS i 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (15418) covalent geometry : angle 0.59572 / 0.30 (20915) hydrogen bonds : bond 0.02724 / 1.84 ( 1083) hydrogen bonds : angle 4.37391 / 3.00 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7992 (tpt) cc_final: 0.7787 (tpp) REVERT: D 54 MET cc_start: 0.7650 (tpp) cc_final: 0.7344 (tpp) REVERT: I 369 MET cc_start: 0.8117 (tmm) cc_final: 0.7793 (tmm) REVERT: K 40 MET cc_start: 0.8302 (mpp) cc_final: 0.8070 (mmt) REVERT: M 54 LEU cc_start: 0.9088 (mp) cc_final: 0.8707 (tt) REVERT: a 369 MET cc_start: 0.8122 (tpt) cc_final: 0.7903 (tpt) REVERT: b 131 ASP cc_start: 0.8698 (m-30) cc_final: 0.8401 (m-30) REVERT: c 40 MET cc_start: 0.8933 (mpp) cc_final: 0.8680 (mpp) REVERT: j 126 MET cc_start: 0.8730 (tmm) cc_final: 0.8451 (tmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0825 time to fit residues: 10.7094 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 135 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 0 optimal weight: 40.0000 chunk 46 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 0.0980 chunk 176 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 HIS M 52 ASN a 99 GLN a 208 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.049642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.040160 restraints weight = 112152.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.040585 restraints weight = 66533.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040978 restraints weight = 52747.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041067 restraints weight = 48695.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041075 restraints weight = 44374.326| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15418 Z= 0.186 Angle : 0.619 7.936 20915 Z= 0.320 Chirality : 0.041 0.147 2380 Planarity : 0.004 0.053 2661 Dihedral : 5.856 66.292 2089 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.14 (0.21), residues: 1899 helix: 2.80 (0.19), residues: 722 sheet: -0.28 (0.18), residues: 810 loop : -0.79 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 315 TYR 0.018 0.001 TYR I 307 PHE 0.019 0.001 PHE A 359 TRP 0.015 0.001 TRP m 41 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (15418) covalent geometry : angle 0.61888 / 0.32 (20915) hydrogen bonds : bond 0.02862 / 1.94 ( 1083) hydrogen bonds : angle 4.47267 / 3.07 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8055 (tpt) cc_final: 0.7849 (tpp) REVERT: D 54 MET cc_start: 0.7700 (tpp) cc_final: 0.7386 (tpp) REVERT: I 369 MET cc_start: 0.8119 (tmm) cc_final: 0.7776 (tmm) REVERT: M 54 LEU cc_start: 0.9080 (mp) cc_final: 0.8762 (tt) REVERT: a 369 MET cc_start: 0.8199 (tpt) cc_final: 0.7976 (tpt) REVERT: j 126 MET cc_start: 0.8777 (tmm) cc_final: 0.8506 (tmm) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.0811 time to fit residues: 9.8657 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 108 optimal weight: 10.0000 chunk 177 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 29 HIS E 52 ASN I 99 GLN I 166 GLN M 52 ASN a 99 GLN a 208 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040709 restraints weight = 112919.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.041089 restraints weight = 64112.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041389 restraints weight = 50808.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.041499 restraints weight = 48285.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.041576 restraints weight = 44956.925| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15418 Z= 0.137 Angle : 0.596 7.811 20915 Z= 0.303 Chirality : 0.040 0.207 2380 Planarity : 0.004 0.054 2661 Dihedral : 5.612 65.089 2089 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.22 (0.21), residues: 1899 helix: 2.87 (0.19), residues: 722 sheet: -0.28 (0.18), residues: 811 loop : -0.64 (0.37), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 315 TYR 0.010 0.001 TYR e 38 PHE 0.010 0.001 PHE C 34 TRP 0.012 0.001 TRP m 41 HIS 0.004 0.001 HIS i 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (15418) covalent geometry : angle 0.59612 / 0.30 (20915) hydrogen bonds : bond 0.02684 / 1.81 ( 1083) hydrogen bonds : angle 4.32896 / 2.97 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8068 (tpt) cc_final: 0.7847 (tpp) REVERT: D 54 MET cc_start: 0.7657 (tpp) cc_final: 0.7338 (tpp) REVERT: I 369 MET cc_start: 0.8111 (tmm) cc_final: 0.7761 (tmm) REVERT: M 54 LEU cc_start: 0.9129 (mp) cc_final: 0.8815 (tt) REVERT: a 369 MET cc_start: 0.8174 (tpt) cc_final: 0.7954 (tpt) REVERT: j 126 MET cc_start: 0.8774 (tmm) cc_final: 0.8496 (tmm) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.0837 time to fit residues: 11.0463 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 63 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 2 optimal weight: 0.4980 chunk 18 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN E 52 ASN I 99 GLN M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.050236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.040814 restraints weight = 112057.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.041253 restraints weight = 64524.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.041773 restraints weight = 51116.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041795 restraints weight = 45677.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.041806 restraints weight = 42926.648| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15418 Z= 0.125 Angle : 0.593 7.829 20915 Z= 0.300 Chirality : 0.040 0.179 2380 Planarity : 0.004 0.053 2661 Dihedral : 5.444 64.131 2089 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.47 % 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: 1.36 (0.21), residues: 1899 helix: 2.93 (0.19), residues: 722 sheet: -0.19 (0.19), residues: 807 loop : -0.46 (0.38), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 315 TYR 0.008 0.001 TYR e 38 PHE 0.017 0.001 PHE b 130 TRP 0.013 0.001 TRP m 41 HIS 0.003 0.001 HIS a 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (15418) covalent geometry : angle 0.59330 / 0.30 (20915) hydrogen bonds : bond 0.02608 / 1.75 ( 1083) hydrogen bonds : angle 4.23781 / 2.91 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8021 (tpt) cc_final: 0.7810 (tpp) REVERT: D 54 MET cc_start: 0.7625 (tpp) cc_final: 0.7316 (tpp) REVERT: I 369 MET cc_start: 0.8130 (tmm) cc_final: 0.7758 (tmm) REVERT: M 54 LEU cc_start: 0.9127 (mp) cc_final: 0.8838 (tt) REVERT: j 126 MET cc_start: 0.8819 (tmm) cc_final: 0.8548 (tmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0828 time to fit residues: 10.7022 Evaluate side-chains 56 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 50 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 117 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 52 ASN i 99 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.049399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.039981 restraints weight = 114056.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040373 restraints weight = 66713.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.040744 restraints weight = 53508.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040815 restraints weight = 49605.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040836 restraints weight = 45987.628| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15418 Z= 0.202 Angle : 0.638 8.052 20915 Z= 0.329 Chirality : 0.041 0.181 2380 Planarity : 0.004 0.048 2661 Dihedral : 5.797 67.839 2089 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.16 (0.21), residues: 1899 helix: 2.82 (0.19), residues: 723 sheet: -0.33 (0.19), residues: 808 loop : -0.63 (0.37), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG i 52 TYR 0.022 0.001 TYR I 307 PHE 0.015 0.001 PHE d 41 TRP 0.018 0.001 TRP m 41 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (15418) covalent geometry : angle 0.63790 / 0.33 (20915) hydrogen bonds : bond 0.02894 / 1.94 ( 1083) hydrogen bonds : angle 4.48058 / 3.09 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.7873 (tpt) cc_final: 0.7658 (tpp) REVERT: D 54 MET cc_start: 0.7730 (tpp) cc_final: 0.7403 (tpp) REVERT: M 54 LEU cc_start: 0.9153 (mp) cc_final: 0.8886 (tt) REVERT: j 126 MET cc_start: 0.8788 (tmm) cc_final: 0.8513 (tmm) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0889 time to fit residues: 11.1940 Evaluate side-chains 53 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 187 random chunks: chunk 70 optimal weight: 10.0000 chunk 185 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 179 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN e 29 HIS e 52 ASN i 99 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.049245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.039831 restraints weight = 113455.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.040327 restraints weight = 67071.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040572 restraints weight = 52655.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040708 restraints weight = 49339.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040770 restraints weight = 45835.045| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15418 Z= 0.189 Angle : 0.624 8.058 20915 Z= 0.322 Chirality : 0.041 0.170 2380 Planarity : 0.004 0.048 2661 Dihedral : 5.754 67.718 2089 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.94 % 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: 1.11 (0.21), residues: 1899 helix: 2.77 (0.19), residues: 722 sheet: -0.35 (0.19), residues: 808 loop : -0.65 (0.37), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 235 TYR 0.013 0.001 TYR E 30 PHE 0.018 0.001 PHE A 359 TRP 0.017 0.001 TRP m 41 HIS 0.011 0.001 HIS i 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 (15418) covalent geometry : angle 0.62409 / 0.32 (20915) hydrogen bonds : bond 0.02864 / 1.92 ( 1083) hydrogen bonds : angle 4.48694 / 3.08 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1880.54 seconds wall clock time: 33 minutes 46.52 seconds (2026.52 seconds total)