Starting phenix.real_space_refine on Thu Sep 18 08:30:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ucv_20729/09_2025/6ucv_20729.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ucv_20729/09_2025/6ucv_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_2025/6ucv_20729.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2025/6ucv_20729.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2025/6ucv_20729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ucv_20729/09_2025/6ucv_20729.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.04, per 1000 atoms: 0.27 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: 1.22 Conformation dependent library (CDL) restraints added in 706.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.65 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: 2.87 Time building geometry restraints manager: 1.60 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: 8797 19.82 - 39.64: 259 39.64 - 59.46: 58 59.46 - 79.27: 2 79.27 - 99.09: 1 Dihedral angle restraints: 9117 sinusoidal: 3494 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 9114 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: 4.320 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: 0.320 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.480 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 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 : 10.415 99.092 5473 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 aren 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 covalent geometry : bond 0.00514 (15418) covalent geometry : angle 0.94119 (20915) hydrogen bonds : bond 0.11005 ( 1083) hydrogen bonds : angle 6.28007 ( 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 : 0.721 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: 0.8262 (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: 0.6412 (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: 0.1012 time to fit residues: 33.6812 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 : 0.608 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 65 ASN A 99 GLN C 17 HIS D 50 GLN E 29 HIS I 65 ASN I 99 GLN I 166 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN 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: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.051386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041557 restraints weight = 111125.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.042179 restraints weight = 64961.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.042494 restraints weight = 49369.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.042656 restraints weight = 46028.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.042683 restraints weight = 43822.378| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15418 Z= 0.211 Angle : 0.648 7.704 20915 Z= 0.338 Chirality : 0.041 0.160 2380 Planarity : 0.005 0.057 2661 Dihedral : 7.542 95.209 2109 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.31 % Allowed : 3.00 % Favored : 96.69 % 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 aren not related in a simple way. whole: -0.00 (0.19), residues: 1899 helix: 1.35 (0.18), residues: 720 sheet: -0.26 (0.18), residues: 817 loop : -1.81 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 235 TYR 0.013 0.002 TYR a 307 PHE 0.024 0.002 PHE C 34 TRP 0.013 0.002 TRP c 36 HIS 0.008 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00449 (15418) covalent geometry : angle 0.64801 (20915) hydrogen bonds : bond 0.03048 ( 1083) hydrogen bonds : angle 4.84260 ( 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 104 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 99 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 GLU cc_start: 0.8411 (pm20) cc_final: 0.8201 (pp20) REVERT: A 359 PHE cc_start: 0.6851 (OUTLIER) cc_final: 0.6409 (m-10) REVERT: A 369 MET cc_start: 0.7937 (tpt) cc_final: 0.7628 (tpp) REVERT: C 31 VAL cc_start: 0.9187 (t) cc_final: 0.8985 (p) REVERT: J 130 PHE cc_start: 0.9043 (m-80) cc_final: 0.8831 (m-10) REVERT: J 132 LEU cc_start: 0.9552 (pp) cc_final: 0.9345 (pp) REVERT: M 54 LEU cc_start: 0.9210 (mp) cc_final: 0.8658 (tt) REVERT: c 40 MET cc_start: 0.8819 (mpp) cc_final: 0.8322 (mpp) outliers start: 5 outliers final: 3 residues processed: 104 average time/residue: 0.1001 time to fit residues: 17.2873 Evaluate side-chains 69 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.538 ------------------------------------------------------------------------------- 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: 5.9990 chunk 57 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN M 52 ASN a 99 GLN d 38 ASN e 29 HIS e 52 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.040705 restraints weight = 113241.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.041186 restraints weight = 67243.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041565 restraints weight = 52536.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.041636 restraints weight = 47030.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.041670 restraints weight = 45466.781| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15418 Z= 0.254 Angle : 0.680 8.080 20915 Z= 0.357 Chirality : 0.043 0.153 2380 Planarity : 0.004 0.057 2661 Dihedral : 7.619 71.350 2109 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.06 % Allowed : 4.06 % Favored : 95.88 % 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 aren not related in a simple way. whole: 0.60 (0.20), residues: 1899 helix: 2.14 (0.19), residues: 718 sheet: -0.25 (0.18), residues: 809 loop : -1.34 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG i 310 TYR 0.025 0.002 TYR E 30 PHE 0.020 0.002 PHE A 359 TRP 0.016 0.002 TRP C 36 HIS 0.008 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00542 (15418) covalent geometry : angle 0.67952 (20915) hydrogen bonds : bond 0.03253 ( 1083) hydrogen bonds : angle 4.84438 ( 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 77 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: C 40 MET cc_start: 0.8184 (mpp) cc_final: 0.7759 (mpp) REVERT: D 54 MET cc_start: 0.7528 (tpp) cc_final: 0.7113 (tpp) REVERT: I 369 MET cc_start: 0.8072 (tmm) cc_final: 0.7817 (tmm) REVERT: J 130 PHE cc_start: 0.8940 (m-80) cc_final: 0.8654 (m-10) outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.1003 time to fit residues: 13.2487 Evaluate side-chains 58 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.653 ------------------------------------------------------------------------------- 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: 50.0000 chunk 83 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 160 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 140 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 145 optimal weight: 0.1980 chunk 153 optimal weight: 9.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 GLN 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 = 0.3486 r_free = 0.3486 target = 0.051253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.041154 restraints weight = 112112.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.042050 restraints weight = 68207.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.042625 restraints weight = 50779.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.042967 restraints weight = 42679.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.042967 restraints weight = 38679.458| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15418 Z= 0.136 Angle : 0.585 7.944 20915 Z= 0.300 Chirality : 0.040 0.146 2380 Planarity : 0.004 0.054 2661 Dihedral : 6.956 68.007 2109 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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 aren not related in a simple way. whole: 0.98 (0.20), residues: 1899 helix: 2.51 (0.19), residues: 723 sheet: -0.20 (0.18), residues: 809 loop : -0.96 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 315 TYR 0.015 0.001 TYR I 307 PHE 0.015 0.001 PHE i 359 TRP 0.012 0.001 TRP M 32 HIS 0.003 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00292 (15418) covalent geometry : angle 0.58478 (20915) hydrogen bonds : bond 0.02741 ( 1083) hydrogen bonds : angle 4.43701 ( 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 77 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.7756 (tpt) cc_final: 0.7527 (tpp) REVERT: D 54 MET cc_start: 0.7375 (tpp) cc_final: 0.6954 (tpp) REVERT: I 369 MET cc_start: 0.7906 (tmm) cc_final: 0.7632 (tmm) REVERT: J 130 PHE cc_start: 0.8774 (m-80) cc_final: 0.8486 (m-10) REVERT: c 40 MET cc_start: 0.8912 (mpp) cc_final: 0.8462 (mpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.0953 time to fit residues: 12.7243 Evaluate side-chains 60 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 0.4980 chunk 141 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 154 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 371 GLN M 52 ASN a 99 GLN e 52 ASN m 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.049846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.040299 restraints weight = 112231.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.040700 restraints weight = 67283.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.040869 restraints weight = 56186.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.040968 restraints weight = 51691.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.041034 restraints weight = 48596.109| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15418 Z= 0.184 Angle : 0.612 8.108 20915 Z= 0.318 Chirality : 0.041 0.150 2380 Planarity : 0.004 0.053 2661 Dihedral : 6.968 67.970 2109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.12 % Allowed : 2.25 % 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 aren not related in a simple way. whole: 1.05 (0.20), residues: 1899 helix: 2.60 (0.19), residues: 720 sheet: -0.23 (0.18), residues: 807 loop : -0.80 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 315 TYR 0.015 0.001 TYR E 30 PHE 0.017 0.001 PHE A 359 TRP 0.013 0.001 TRP M 32 HIS 0.010 0.001 HIS i 51 Details of bonding type rmsd covalent geometry : bond 0.00395 (15418) covalent geometry : angle 0.61247 (20915) hydrogen bonds : bond 0.02889 ( 1083) hydrogen bonds : angle 4.49688 ( 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 74 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 72 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.8045 (tpt) cc_final: 0.7830 (tpp) REVERT: B 127 GLU cc_start: 0.9247 (OUTLIER) cc_final: 0.8861 (pp20) REVERT: D 54 MET cc_start: 0.7707 (tpp) cc_final: 0.7248 (tpp) REVERT: I 369 MET cc_start: 0.8103 (tmm) cc_final: 0.7810 (tmm) REVERT: J 130 PHE cc_start: 0.9021 (m-80) cc_final: 0.8704 (m-10) REVERT: M 54 LEU cc_start: 0.9086 (mp) cc_final: 0.8738 (tt) REVERT: b 127 GLU cc_start: 0.9185 (pm20) cc_final: 0.8975 (pm20) REVERT: c 40 MET cc_start: 0.9033 (mpp) cc_final: 0.8541 (mpp) outliers start: 2 outliers final: 0 residues processed: 74 average time/residue: 0.0927 time to fit residues: 12.0778 Evaluate side-chains 58 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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: 7.9990 chunk 88 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 ASN I 99 GLN I 172 GLN ** I 203 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.049691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.040568 restraints weight = 112977.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.040894 restraints weight = 66136.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.041082 restraints weight = 58144.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.041191 restraints weight = 53240.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.041249 restraints weight = 48720.026| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15418 Z= 0.185 Angle : 0.610 7.976 20915 Z= 0.317 Chirality : 0.041 0.146 2380 Planarity : 0.004 0.051 2661 Dihedral : 6.976 68.085 2109 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.19 % Allowed : 2.19 % 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 aren not related in a simple way. whole: 1.07 (0.20), residues: 1899 helix: 2.67 (0.19), residues: 720 sheet: -0.24 (0.18), residues: 806 loop : -0.87 (0.36), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 315 TYR 0.020 0.001 TYR I 307 PHE 0.016 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 covalent geometry : bond 0.00398 (15418) covalent geometry : angle 0.61004 (20915) hydrogen bonds : bond 0.02893 ( 1083) hydrogen bonds : angle 4.48476 ( 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 76 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 369 MET cc_start: 0.8074 (tpt) cc_final: 0.7860 (tpp) REVERT: D 54 MET cc_start: 0.7696 (tpp) cc_final: 0.7384 (tpp) REVERT: I 369 MET cc_start: 0.8165 (tmm) cc_final: 0.7825 (tmm) REVERT: J 130 PHE cc_start: 0.8967 (m-80) cc_final: 0.8673 (m-10) REVERT: M 54 LEU cc_start: 0.9007 (mp) cc_final: 0.8702 (tt) REVERT: c 40 MET cc_start: 0.8980 (mpp) cc_final: 0.8679 (mpp) outliers start: 3 outliers final: 2 residues processed: 75 average time/residue: 0.0920 time to fit residues: 12.0443 Evaluate side-chains 60 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 58 time to evaluate : 0.623 ------------------------------------------------------------------------------- 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: 0.5980 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 46 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 52 ASN I 99 GLN ** I 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN a 99 GLN ** a 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3453 r_free = 0.3453 target = 0.049798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.040346 restraints weight = 112242.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.040699 restraints weight = 65997.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.040925 restraints weight = 57107.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.041022 restraints weight = 51903.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.041082 restraints weight = 47893.015| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15418 Z= 0.172 Angle : 0.620 8.470 20915 Z= 0.322 Chirality : 0.041 0.167 2380 Planarity : 0.004 0.052 2661 Dihedral : 6.916 67.234 2109 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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 aren not related in a simple way. whole: 1.16 (0.21), residues: 1899 helix: 2.76 (0.19), residues: 720 sheet: -0.24 (0.18), residues: 805 loop : -0.74 (0.36), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 315 TYR 0.014 0.001 TYR I 307 PHE 0.015 0.001 PHE A 359 TRP 0.014 0.001 TRP m 41 HIS 0.005 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00371 (15418) covalent geometry : angle 0.61992 (20915) hydrogen bonds : bond 0.02858 ( 1083) hydrogen bonds : angle 4.45706 ( 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 72 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.8095 (tpt) cc_final: 0.7888 (tpp) REVERT: D 54 MET cc_start: 0.7712 (tpp) cc_final: 0.7401 (tpp) REVERT: I 369 MET cc_start: 0.8167 (tmm) cc_final: 0.7822 (tmm) REVERT: J 130 PHE cc_start: 0.8976 (m-80) cc_final: 0.8684 (m-10) REVERT: M 54 LEU cc_start: 0.8989 (mp) cc_final: 0.8692 (tt) REVERT: c 40 MET cc_start: 0.9023 (mpp) cc_final: 0.8720 (mpp) REVERT: k 40 MET cc_start: 0.6967 (mpp) cc_final: 0.6651 (ttt) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0944 time to fit residues: 11.9986 Evaluate side-chains 58 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 155 optimal weight: 0.5980 chunk 49 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN E 29 HIS E 52 ASN I 99 GLN M 52 ASN a 99 GLN a 133 ASN 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 = 0.050245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.040838 restraints weight = 112111.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.041298 restraints weight = 64982.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.041512 restraints weight = 54305.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.041593 restraints weight = 51460.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.041656 restraints weight = 47056.291| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4831 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= 0.126 Angle : 0.596 8.124 20915 Z= 0.304 Chirality : 0.040 0.148 2380 Planarity : 0.004 0.053 2661 Dihedral : 6.646 64.936 2109 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 1.25 % Favored : 98.69 % 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 aren not related in a simple way. whole: 1.28 (0.21), residues: 1899 helix: 2.82 (0.19), residues: 722 sheet: -0.17 (0.18), residues: 805 loop : -0.60 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 315 TYR 0.012 0.001 TYR I 307 PHE 0.014 0.001 PHE b 130 TRP 0.011 0.001 TRP m 41 HIS 0.003 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00274 (15418) covalent geometry : angle 0.59578 (20915) hydrogen bonds : bond 0.02653 ( 1083) hydrogen bonds : angle 4.26764 ( 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 78 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.8118 (tpt) cc_final: 0.7902 (tpp) REVERT: D 54 MET cc_start: 0.7676 (tpp) cc_final: 0.7367 (tpp) REVERT: I 369 MET cc_start: 0.8166 (tmm) cc_final: 0.7787 (tmm) REVERT: J 130 PHE cc_start: 0.9000 (m-80) cc_final: 0.8705 (m-10) REVERT: M 54 LEU cc_start: 0.9032 (mp) cc_final: 0.8735 (tt) REVERT: c 40 MET cc_start: 0.9035 (mpp) cc_final: 0.8551 (mpp) REVERT: k 40 MET cc_start: 0.6926 (mpp) cc_final: 0.6681 (ttt) outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.0938 time to fit residues: 12.8443 Evaluate side-chains 59 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 7.9990 chunk 124 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 110 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 99 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.050234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.040331 restraints weight = 111532.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.041211 restraints weight = 67903.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.041780 restraints weight = 50493.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042004 restraints weight = 42494.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.042004 restraints weight = 39086.352| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4945 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= 0.130 Angle : 0.597 8.107 20915 Z= 0.304 Chirality : 0.040 0.148 2380 Planarity : 0.004 0.052 2661 Dihedral : 6.492 63.361 2109 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.21), residues: 1899 helix: 2.88 (0.19), residues: 722 sheet: -0.14 (0.19), residues: 805 loop : -0.51 (0.37), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 315 TYR 0.009 0.001 TYR E 30 PHE 0.012 0.001 PHE A 359 TRP 0.013 0.001 TRP m 41 HIS 0.004 0.001 HIS A 51 Details of bonding type rmsd covalent geometry : bond 0.00284 (15418) covalent geometry : angle 0.59724 (20915) hydrogen bonds : bond 0.02674 ( 1083) hydrogen bonds : angle 4.23671 ( 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 72 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.7945 (tpt) cc_final: 0.7732 (tpp) REVERT: D 54 MET cc_start: 0.7505 (tpp) cc_final: 0.7212 (tpp) REVERT: I 369 MET cc_start: 0.7958 (tmm) cc_final: 0.7406 (tmm) REVERT: J 130 PHE cc_start: 0.8868 (m-80) cc_final: 0.8607 (m-10) REVERT: M 54 LEU cc_start: 0.8991 (mp) cc_final: 0.8728 (tt) REVERT: c 40 MET cc_start: 0.8939 (mpp) cc_final: 0.8479 (mpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0928 time to fit residues: 11.8601 Evaluate side-chains 59 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 2.9990 chunk 151 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 105 optimal weight: 9.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 117 optimal weight: 8.9990 chunk 27 optimal weight: 3.9990 chunk 128 optimal weight: 7.9990 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** K 43 HIS M 52 ASN a 99 GLN 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 = 0.3453 r_free = 0.3453 target = 0.049787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.039914 restraints weight = 112532.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040764 restraints weight = 68702.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.041326 restraints weight = 51329.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.041434 restraints weight = 43277.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.041775 restraints weight = 41094.733| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15418 Z= 0.169 Angle : 0.627 9.330 20915 Z= 0.321 Chirality : 0.041 0.149 2380 Planarity : 0.004 0.051 2661 Dihedral : 6.607 64.177 2109 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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 aren not related in a simple way. whole: 1.31 (0.21), residues: 1899 helix: 2.85 (0.19), residues: 722 sheet: -0.17 (0.19), residues: 803 loop : -0.53 (0.37), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG i 52 TYR 0.012 0.001 TYR I 307 PHE 0.012 0.001 PHE d 41 TRP 0.015 0.001 TRP m 41 HIS 0.006 0.001 HIS i 51 Details of bonding type rmsd covalent geometry : bond 0.00367 (15418) covalent geometry : angle 0.62740 (20915) hydrogen bonds : bond 0.02785 ( 1083) hydrogen bonds : angle 4.37704 ( 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 76 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 369 MET cc_start: 0.7745 (tpt) cc_final: 0.7527 (tpp) REVERT: D 54 MET cc_start: 0.7529 (tpp) cc_final: 0.7227 (tpp) REVERT: I 369 MET cc_start: 0.7930 (tmm) cc_final: 0.7410 (tmm) REVERT: J 130 PHE cc_start: 0.8775 (m-80) cc_final: 0.8542 (m-10) REVERT: M 54 LEU cc_start: 0.8993 (mp) cc_final: 0.8755 (tt) REVERT: c 40 MET cc_start: 0.8907 (mpp) cc_final: 0.8654 (mpp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1001 time to fit residues: 13.0804 Evaluate side-chains 58 residues out of total 1668 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.637 ------------------------------------------------------------------------------- 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: 5.9990 chunk 185 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 140 optimal weight: 0.4980 chunk 145 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 115 optimal weight: 0.1980 chunk 150 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.049367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.039457 restraints weight = 114040.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.040296 restraints weight = 70528.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.040828 restraints weight = 52745.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.041144 restraints weight = 44829.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.041207 restraints weight = 40755.871| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.5343 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= 0.198 Angle : 0.645 9.563 20915 Z= 0.334 Chirality : 0.042 0.149 2380 Planarity : 0.004 0.050 2661 Dihedral : 6.820 66.525 2109 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % 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 aren not related in a simple way. whole: 1.20 (0.21), residues: 1899 helix: 2.81 (0.19), residues: 722 sheet: -0.24 (0.19), residues: 800 loop : -0.70 (0.37), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 235 TYR 0.024 0.001 TYR I 307 PHE 0.020 0.001 PHE A 359 TRP 0.017 0.001 TRP m 41 HIS 0.006 0.001 HIS A 102 Details of bonding type rmsd covalent geometry : bond 0.00427 (15418) covalent geometry : angle 0.64546 (20915) hydrogen bonds : bond 0.02936 ( 1083) hydrogen bonds : angle 4.49601 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2136.43 seconds wall clock time: 38 minutes 20.20 seconds (2300.20 seconds total)