Starting phenix.real_space_refine on Wed Feb 14 20:59:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze3_14682/02_2024/7ze3_14682_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 Mg 33 5.21 5 S 27 5.16 5 C 7274 2.51 5 N 1401 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10285 Number of models: 1 Model: "" Number of chains: 54 Chain: "A" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'TRANS': 87} Chain: "C" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 377 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 396 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'ZE0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 239 Unusual residues: {'BCL': 3, 'ZE0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'ZE0': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.55 Number of scatterers: 10285 At special positions: 0 Unit cell: (94.25, 103.35, 81.25, 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 27 16.00 Mg 33 11.99 O 1550 8.00 N 1401 7.00 C 7274 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 - 3.50 Amino acid : False - 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.68 Conformation dependent library (CDL) restraints added in 1.4 seconds 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1796 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 0 sheets defined 66.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 12 through 36 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'B' and resid 4 through 6 No H-bonds generated for 'chain 'B' and resid 4 through 6' Processing helix chain 'B' and resid 15 through 46 removed outlier: 3.507A pdb=" N HIS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 12 through 37 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'D' and resid 4 through 6 No H-bonds generated for 'chain 'D' and resid 4 through 6' Processing helix chain 'D' and resid 15 through 46 removed outlier: 3.700A pdb=" N HIS D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 8 removed outlier: 4.175A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 36 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'F' and resid 4 through 6 No H-bonds generated for 'chain 'F' and resid 4 through 6' Processing helix chain 'F' and resid 15 through 46 removed outlier: 3.600A pdb=" N HIS F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 4.109A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 36 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'H' and resid 4 through 6 No H-bonds generated for 'chain 'H' and resid 4 through 6' Processing helix chain 'H' and resid 15 through 46 removed outlier: 3.508A pdb=" N HIS H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 8 No H-bonds generated for 'chain 'I' and resid 6 through 8' Processing helix chain 'I' and resid 12 through 36 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'J' and resid 4 through 6 No H-bonds generated for 'chain 'J' and resid 4 through 6' Processing helix chain 'J' and resid 15 through 46 removed outlier: 3.590A pdb=" N HIS J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 8 No H-bonds generated for 'chain 'K' and resid 6 through 8' Processing helix chain 'K' and resid 12 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'L' and resid 4 through 6 No H-bonds generated for 'chain 'L' and resid 4 through 6' Processing helix chain 'L' and resid 15 through 46 removed outlier: 3.613A pdb=" N HIS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 8 No H-bonds generated for 'chain 'M' and resid 6 through 8' Processing helix chain 'M' and resid 12 through 37 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 40 through 46 Processing helix chain 'N' and resid 15 through 46 removed outlier: 3.602A pdb=" N HIS N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 9 removed outlier: 4.047A pdb=" N TRP O 7 " --> pdb=" O GLY O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 36 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'P' and resid 4 through 6 No H-bonds generated for 'chain 'P' and resid 4 through 6' Processing helix chain 'P' and resid 15 through 46 removed outlier: 3.589A pdb=" N HIS P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 4.128A pdb=" N TRP Q 7 " --> pdb=" O GLY Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 36 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'R' and resid 4 through 6 No H-bonds generated for 'chain 'R' and resid 4 through 6' Processing helix chain 'R' and resid 15 through 46 removed outlier: 3.578A pdb=" N HIS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1305 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: 2.39 Time building geometry restraints manager: 5.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 2952 1.37 - 1.57: 7600 1.57 - 1.78: 9 1.78 - 1.98: 45 1.98 - 2.18: 132 Bond restraints: 10738 Sorted by residual: bond pdb=" C35 ZE0 G 103 " pdb=" C36 ZE0 G 103 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.40e+01 bond pdb=" C35 ZE0 O 103 " pdb=" C36 ZE0 O 103 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.38e+01 bond pdb=" C35 ZE0 B 102 " pdb=" C36 ZE0 B 102 " ideal model delta sigma weight residual 1.340 1.534 -0.194 2.00e-02 2.50e+03 9.36e+01 bond pdb=" C35 ZE0 I 103 " pdb=" C36 ZE0 I 103 " ideal model delta sigma weight residual 1.340 1.533 -0.193 2.00e-02 2.50e+03 9.32e+01 bond pdb=" C35 ZE0 E 103 " pdb=" C36 ZE0 E 103 " ideal model delta sigma weight residual 1.340 1.533 -0.193 2.00e-02 2.50e+03 9.32e+01 ... (remaining 10733 not shown) Histogram of bond angle deviations from ideal: 84.75 - 100.16: 132 100.16 - 115.57: 7241 115.57 - 130.98: 7389 130.98 - 146.39: 243 146.39 - 161.79: 66 Bond angle restraints: 15071 Sorted by residual: angle pdb=" C29 ZE0 I 103 " pdb=" C28 ZE0 I 103 " pdb=" C30 ZE0 I 103 " ideal model delta sigma weight residual 68.22 117.98 -49.76 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C29 ZE0 E 103 " pdb=" C28 ZE0 E 103 " pdb=" C30 ZE0 E 103 " ideal model delta sigma weight residual 68.22 117.97 -49.75 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C29 ZE0 G 103 " pdb=" C28 ZE0 G 103 " pdb=" C30 ZE0 G 103 " ideal model delta sigma weight residual 68.22 117.96 -49.74 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C29 ZE0 B 102 " pdb=" C28 ZE0 B 102 " pdb=" C30 ZE0 B 102 " ideal model delta sigma weight residual 68.22 117.94 -49.72 3.00e+00 1.11e-01 2.75e+02 angle pdb=" C29 ZE0 M 104 " pdb=" C28 ZE0 M 104 " pdb=" C30 ZE0 M 104 " ideal model delta sigma weight residual 68.22 117.93 -49.71 3.00e+00 1.11e-01 2.75e+02 ... (remaining 15066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 5035 21.86 - 43.73: 254 43.73 - 65.59: 63 65.59 - 87.46: 36 87.46 - 109.32: 7 Dihedral angle restraints: 5395 sinusoidal: 2624 harmonic: 2771 Sorted by residual: dihedral pdb=" CA LEU S 61 " pdb=" C LEU S 61 " pdb=" N ILE S 62 " pdb=" CA ILE S 62 " ideal model delta harmonic sigma weight residual 180.00 158.25 21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA SER S 55 " pdb=" C SER S 55 " pdb=" N PHE S 56 " pdb=" CA PHE S 56 " ideal model delta harmonic sigma weight residual 180.00 158.68 21.32 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA LEU J 13 " pdb=" C LEU J 13 " pdb=" N THR J 14 " pdb=" CA THR J 14 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 5392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 876 0.030 - 0.061: 404 0.061 - 0.091: 137 0.091 - 0.121: 84 0.121 - 0.152: 15 Chirality restraints: 1516 Sorted by residual: chirality pdb=" CA MET A 26 " pdb=" N MET A 26 " pdb=" C MET A 26 " pdb=" CB MET A 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.75e-01 chirality pdb=" CA MET Q 26 " pdb=" N MET Q 26 " pdb=" C MET Q 26 " pdb=" CB MET Q 26 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA MET I 26 " pdb=" N MET I 26 " pdb=" C MET I 26 " pdb=" CB MET I 26 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1513 not shown) Planarity restraints: 1826 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL S1702 " 0.094 3.00e-02 1.11e+03 8.06e-02 3.61e+01 pdb=" CBA BCL S1702 " 0.083 3.00e-02 1.11e+03 pdb=" CGA BCL S1702 " -0.062 3.00e-02 1.11e+03 pdb=" O1A BCL S1702 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL S1702 " -0.114 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C21 ZE0 I 103 " 0.059 2.00e-02 2.50e+03 4.91e-02 3.02e+01 pdb=" C22 ZE0 I 103 " -0.073 2.00e-02 2.50e+03 pdb=" C23 ZE0 I 103 " -0.031 2.00e-02 2.50e+03 pdb=" C24 ZE0 I 103 " -0.004 2.00e-02 2.50e+03 pdb=" C25 ZE0 I 103 " 0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S1703 " 0.082 3.00e-02 1.11e+03 7.07e-02 2.78e+01 pdb=" CBA BCL S1703 " 0.073 3.00e-02 1.11e+03 pdb=" CGA BCL S1703 " -0.057 3.00e-02 1.11e+03 pdb=" O1A BCL S1703 " -0.001 3.00e-02 1.11e+03 pdb=" O2A BCL S1703 " -0.098 3.00e-02 1.11e+03 ... (remaining 1823 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1372 2.77 - 3.30: 8966 3.30 - 3.83: 18502 3.83 - 4.37: 22312 4.37 - 4.90: 37141 Nonbonded interactions: 88293 Sorted by model distance: nonbonded pdb=" O TRP J 49 " pdb=" O HOH J 201 " model vdw 2.231 2.440 nonbonded pdb=" O TRP P 49 " pdb=" O HOH P 201 " model vdw 2.266 2.440 nonbonded pdb=" O THR I 38 " pdb=" O HOH I 201 " model vdw 2.284 2.440 nonbonded pdb=" O TRP R 49 " pdb=" O HOH R 201 " model vdw 2.304 2.440 nonbonded pdb=" O PHE M 44 " pdb=" O HOH M 201 " model vdw 2.307 2.440 ... (remaining 88288 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'C' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'E' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'G' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'I' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'M' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'O' and (resid 1 through 48 or resid 101 through 102)) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 3 through 51) selection = (chain 'D' and resid 3 through 51) selection = (chain 'F' and resid 3 through 51) selection = (chain 'H' and resid 3 through 51) selection = (chain 'J' and resid 3 through 51) selection = (chain 'L' and resid 3 through 51) selection = chain 'N' selection = (chain 'P' and resid 3 through 51) selection = (chain 'R' and resid 3 through 51) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.960 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 30.840 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:12.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 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 : 0.014 0.194 10738 Z= 0.685 Angle : 4.251 49.757 15071 Z= 1.440 Chirality : 0.044 0.152 1516 Planarity : 0.009 0.081 1826 Dihedral : 16.340 109.320 3599 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.24), residues: 920 helix: 1.13 (0.18), residues: 603 sheet: None (None), residues: 0 loop : -0.65 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP Q 7 HIS 0.008 0.001 HIS A 37 PHE 0.012 0.001 PHE C 28 TYR 0.017 0.003 TYR S 40 ARG 0.015 0.003 ARG D 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 1.232 Fit side-chains REVERT: B 19 GLU cc_start: 0.7555 (mt-10) cc_final: 0.7224 (mm-30) REVERT: C 5 ARG cc_start: 0.7960 (mtt180) cc_final: 0.7725 (mtt90) REVERT: C 11 LYS cc_start: 0.8516 (mtmt) cc_final: 0.8141 (mttm) REVERT: G 11 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7982 (mttt) REVERT: I 43 LYS cc_start: 0.8001 (tttt) cc_final: 0.7679 (ttmt) REVERT: K 48 LYS cc_start: 0.7383 (tttt) cc_final: 0.7093 (mmtm) REVERT: M 5 ARG cc_start: 0.7462 (mtt180) cc_final: 0.7082 (mtp180) REVERT: M 11 LYS cc_start: 0.8180 (mtmt) cc_final: 0.7844 (mttp) REVERT: O 11 LYS cc_start: 0.8202 (mtmt) cc_final: 0.7983 (mttt) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 1.3675 time to fit residues: 228.7116 Evaluate side-chains 126 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.0980 chunk 34 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN S 49 GLN E 3 GLN E 37 HIS G 3 GLN ** I 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10738 Z= 0.161 Angle : 2.224 24.316 15071 Z= 0.750 Chirality : 0.039 0.130 1516 Planarity : 0.004 0.029 1826 Dihedral : 16.641 103.737 1925 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.74 % Allowed : 5.76 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.26), residues: 920 helix: 3.32 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.34 (0.29), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 40 HIS 0.006 0.001 HIS M 37 PHE 0.013 0.001 PHE C 28 TYR 0.009 0.001 TYR S 53 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 127 time to evaluate : 1.078 Fit side-chains REVERT: C 11 LYS cc_start: 0.8541 (mtmt) cc_final: 0.8231 (mttm) REVERT: F 20 GLU cc_start: 0.7631 (tp30) cc_final: 0.7419 (tp30) REVERT: G 11 LYS cc_start: 0.8268 (mtmt) cc_final: 0.7990 (mttt) REVERT: I 43 LYS cc_start: 0.7905 (tttt) cc_final: 0.7671 (mptt) REVERT: K 48 LYS cc_start: 0.7365 (tttt) cc_final: 0.7101 (tppt) REVERT: M 11 LYS cc_start: 0.8205 (mtmt) cc_final: 0.7840 (mttp) REVERT: O 11 LYS cc_start: 0.8214 (mtmt) cc_final: 0.8001 (mttt) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 1.3827 time to fit residues: 190.3489 Evaluate side-chains 117 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain L residue 29 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN A 37 HIS S 49 GLN I 2 ASN I 3 GLN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 3 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10738 Z= 0.358 Angle : 2.293 27.980 15071 Z= 0.777 Chirality : 0.047 0.183 1516 Planarity : 0.005 0.029 1826 Dihedral : 17.195 112.521 1925 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.10 % Allowed : 7.11 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.25), residues: 920 helix: 2.45 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.39 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 40 HIS 0.008 0.002 HIS C 37 PHE 0.022 0.003 PHE C 28 TYR 0.011 0.002 TYR J 46 ARG 0.003 0.001 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.026 Fit side-chains REVERT: C 11 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8200 (mttm) REVERT: F 20 GLU cc_start: 0.7814 (tp30) cc_final: 0.7565 (tp30) REVERT: G 11 LYS cc_start: 0.8326 (mtmt) cc_final: 0.8031 (mttt) REVERT: I 43 LYS cc_start: 0.8143 (tttt) cc_final: 0.7879 (mptt) REVERT: K 48 LYS cc_start: 0.7455 (tttt) cc_final: 0.7027 (tptp) REVERT: L 23 LYS cc_start: 0.8684 (ttmm) cc_final: 0.8129 (mtmm) REVERT: M 5 ARG cc_start: 0.7609 (mtt180) cc_final: 0.7181 (mtp180) REVERT: O 11 LYS cc_start: 0.8189 (mtmt) cc_final: 0.7901 (mttt) outliers start: 9 outliers final: 4 residues processed: 123 average time/residue: 1.5219 time to fit residues: 199.2266 Evaluate side-chains 120 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 116 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain L residue 29 SER Chi-restraints excluded: chain M residue 14 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 2 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10738 Z= 0.235 Angle : 2.229 26.429 15071 Z= 0.750 Chirality : 0.042 0.156 1516 Planarity : 0.004 0.031 1826 Dihedral : 16.911 107.587 1925 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.23 % Allowed : 7.60 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.25), residues: 920 helix: 2.68 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.57 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 40 HIS 0.005 0.001 HIS C 37 PHE 0.016 0.002 PHE M 28 TYR 0.008 0.001 TYR R 44 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.922 Fit side-chains REVERT: C 11 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8238 (mttm) REVERT: G 11 LYS cc_start: 0.8340 (mtmt) cc_final: 0.8048 (mttt) REVERT: I 43 LYS cc_start: 0.8083 (tttt) cc_final: 0.7852 (mptt) REVERT: K 48 LYS cc_start: 0.7433 (tttt) cc_final: 0.7153 (tppt) REVERT: L 23 LYS cc_start: 0.8639 (ttmm) cc_final: 0.8176 (mtmm) REVERT: O 11 LYS cc_start: 0.8199 (mtmt) cc_final: 0.7907 (mttt) outliers start: 10 outliers final: 5 residues processed: 123 average time/residue: 1.4413 time to fit residues: 189.0197 Evaluate side-chains 121 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 116 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain Q residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 3 GLN G 37 HIS I 2 ASN ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10738 Z= 0.140 Angle : 2.157 23.989 15071 Z= 0.724 Chirality : 0.038 0.140 1516 Planarity : 0.004 0.031 1826 Dihedral : 16.591 100.753 1925 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.98 % Allowed : 9.31 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.26), residues: 920 helix: 3.14 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.43 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.004 0.001 HIS C 37 PHE 0.014 0.001 PHE P 41 TYR 0.008 0.001 TYR S 53 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 129 time to evaluate : 1.160 Fit side-chains REVERT: S 30 ILE cc_start: 0.8132 (OUTLIER) cc_final: 0.7775 (pp) REVERT: C 11 LYS cc_start: 0.8609 (mtmt) cc_final: 0.8245 (mttt) REVERT: G 11 LYS cc_start: 0.8335 (mtmt) cc_final: 0.8028 (mttt) REVERT: K 48 LYS cc_start: 0.7393 (tttt) cc_final: 0.7141 (tppt) REVERT: L 23 LYS cc_start: 0.8571 (ttmm) cc_final: 0.8202 (mtmm) REVERT: O 11 LYS cc_start: 0.8233 (mtmt) cc_final: 0.7926 (mttt) REVERT: O 43 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.7921 (mttm) outliers start: 8 outliers final: 3 residues processed: 132 average time/residue: 1.4506 time to fit residues: 204.5199 Evaluate side-chains 130 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 125 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain O residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 8.9990 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10738 Z= 0.399 Angle : 2.266 27.470 15071 Z= 0.767 Chirality : 0.048 0.183 1516 Planarity : 0.005 0.034 1826 Dihedral : 17.397 112.132 1925 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.72 % Allowed : 10.17 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 920 helix: 2.25 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.50 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP M 40 HIS 0.007 0.002 HIS C 37 PHE 0.019 0.003 PHE Q 28 TYR 0.011 0.002 TYR S 37 ARG 0.003 0.001 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.006 Fit side-chains REVERT: C 5 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7779 (mtt90) REVERT: C 11 LYS cc_start: 0.8611 (mtmt) cc_final: 0.8183 (mttm) REVERT: G 11 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8041 (mttt) REVERT: L 23 LYS cc_start: 0.8656 (ttmm) cc_final: 0.8351 (mttp) REVERT: M 11 LYS cc_start: 0.8430 (mtpp) cc_final: 0.7882 (mttp) REVERT: O 11 LYS cc_start: 0.8160 (mtmt) cc_final: 0.7857 (mttt) outliers start: 14 outliers final: 7 residues processed: 129 average time/residue: 1.3802 time to fit residues: 189.9712 Evaluate side-chains 127 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain I residue 14 VAL Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10738 Z= 0.163 Angle : 2.134 24.722 15071 Z= 0.716 Chirality : 0.039 0.130 1516 Planarity : 0.004 0.029 1826 Dihedral : 16.848 102.640 1925 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.86 % Allowed : 11.40 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.26), residues: 920 helix: 2.93 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.58 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.004 0.001 HIS N 40 PHE 0.009 0.001 PHE M 28 TYR 0.007 0.001 TYR S 53 ARG 0.002 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.009 Fit side-chains REVERT: S 30 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7785 (pp) REVERT: C 5 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7785 (mtt90) REVERT: C 11 LYS cc_start: 0.8638 (mtmt) cc_final: 0.8253 (mttm) REVERT: G 11 LYS cc_start: 0.8343 (mtmt) cc_final: 0.8032 (mttt) REVERT: L 23 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8173 (mtmm) REVERT: O 11 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7905 (mttt) outliers start: 7 outliers final: 4 residues processed: 123 average time/residue: 1.5237 time to fit residues: 200.1252 Evaluate side-chains 123 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 117 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 61 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10738 Z= 0.173 Angle : 2.133 24.750 15071 Z= 0.717 Chirality : 0.039 0.129 1516 Planarity : 0.004 0.030 1826 Dihedral : 16.597 103.866 1925 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.86 % Allowed : 12.01 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.26), residues: 920 helix: 3.01 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.55 (0.30), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.004 0.001 HIS N 40 PHE 0.012 0.001 PHE M 28 TYR 0.006 0.001 TYR S 53 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.982 Fit side-chains REVERT: S 30 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7775 (pp) REVERT: C 5 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7781 (mtt90) REVERT: C 11 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8236 (mttt) REVERT: G 11 LYS cc_start: 0.8354 (mtmt) cc_final: 0.8045 (mttt) REVERT: L 23 LYS cc_start: 0.8591 (ttmm) cc_final: 0.8202 (mtmm) REVERT: O 11 LYS cc_start: 0.8195 (mtmt) cc_final: 0.7880 (mttt) outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 1.4143 time to fit residues: 185.3223 Evaluate side-chains 124 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 117 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10738 Z= 0.454 Angle : 2.270 27.750 15071 Z= 0.769 Chirality : 0.051 0.171 1516 Planarity : 0.005 0.033 1826 Dihedral : 17.606 113.218 1925 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.98 % Allowed : 12.01 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.25), residues: 920 helix: 2.02 (0.19), residues: 585 sheet: None (None), residues: 0 loop : -0.58 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 40 HIS 0.009 0.002 HIS B 24 PHE 0.023 0.003 PHE M 28 TYR 0.013 0.002 TYR J 46 ARG 0.004 0.001 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.932 Fit side-chains REVERT: C 5 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7767 (mtt90) REVERT: C 11 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8219 (mttm) REVERT: G 11 LYS cc_start: 0.8358 (mtmt) cc_final: 0.8047 (mttt) REVERT: L 23 LYS cc_start: 0.8653 (ttmm) cc_final: 0.8337 (mttp) REVERT: M 11 LYS cc_start: 0.8432 (mtpp) cc_final: 0.7882 (mttp) REVERT: O 11 LYS cc_start: 0.8159 (mtmt) cc_final: 0.7864 (mttt) outliers start: 8 outliers final: 6 residues processed: 125 average time/residue: 1.4488 time to fit residues: 192.8283 Evaluate side-chains 125 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 118 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain M residue 14 VAL Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10738 Z= 0.201 Angle : 2.131 25.624 15071 Z= 0.717 Chirality : 0.040 0.140 1516 Planarity : 0.004 0.031 1826 Dihedral : 17.088 105.120 1925 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.74 % Allowed : 12.01 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.26), residues: 920 helix: 2.66 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.70 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.005 0.001 HIS N 40 PHE 0.014 0.001 PHE M 28 TYR 0.007 0.001 TYR R 46 ARG 0.002 0.000 ARG G 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1840 Ramachandran restraints generated. 920 Oldfield, 0 Emsley, 920 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 119 time to evaluate : 1.018 Fit side-chains REVERT: C 5 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7791 (mtt90) REVERT: C 11 LYS cc_start: 0.8646 (mtmt) cc_final: 0.8250 (mttm) REVERT: G 11 LYS cc_start: 0.8349 (mtmt) cc_final: 0.8039 (mttt) REVERT: L 23 LYS cc_start: 0.8592 (ttmm) cc_final: 0.8206 (mttm) REVERT: O 11 LYS cc_start: 0.8222 (mtmt) cc_final: 0.7918 (mttt) outliers start: 6 outliers final: 5 residues processed: 124 average time/residue: 1.4049 time to fit residues: 185.6077 Evaluate side-chains 124 residues out of total 816 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 49 GLN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain N residue 29 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 3 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.124863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.102287 restraints weight = 9742.928| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.28 r_work: 0.2779 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10738 Z= 0.218 Angle : 2.137 25.788 15071 Z= 0.719 Chirality : 0.040 0.140 1516 Planarity : 0.004 0.029 1826 Dihedral : 16.955 106.155 1925 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.86 % Allowed : 12.25 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.26), residues: 920 helix: 2.73 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.68 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 40 HIS 0.005 0.001 HIS N 40 PHE 0.014 0.002 PHE M 28 TYR 0.008 0.001 TYR R 44 ARG 0.002 0.000 ARG K 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3583.95 seconds wall clock time: 64 minutes 40.09 seconds (3880.09 seconds total)