Starting phenix.real_space_refine on Fri Jan 19 03:26:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/01_2024/7zdi_14650_updated.pdb" } resolution = 2.9 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= 0.013 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 9 5.16 5 C 7274 2.51 5 N 1401 2.21 5 O 1567 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-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 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: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, '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: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 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, 'IRM': 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, 'IRM': 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" 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: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 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: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 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} Time building chain proxies: 5.71, per 1000 atoms: 0.56 Number of scatterers: 10284 At special positions: 0 Unit cell: (96.2, 102.7, 80.6, 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 9 16.00 Mg 33 11.99 O 1567 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: 4.42 Conformation dependent library (CDL) restraints added in 1.4 seconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 64.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.944A pdb=" N TRP A 7 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 37 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'B' and resid 15 through 46 removed outlier: 3.951A pdb=" N HIS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.950A pdb=" N TRP C 7 " --> pdb=" O GLY C 4 " (cutoff:3.500A) 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 15 through 46 removed outlier: 3.945A pdb=" N HIS D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 8 removed outlier: 3.965A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 37 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'F' and resid 15 through 46 removed outlier: 4.006A pdb=" N HIS F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 3.979A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'H' and resid 15 through 46 removed outlier: 3.935A pdb=" N HIS H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.997A pdb=" N TRP I 7 " --> pdb=" O GLY I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'J' and resid 15 through 46 removed outlier: 3.965A pdb=" N HIS J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.928A pdb=" N TRP K 7 " --> pdb=" O GLY K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'L' and resid 15 through 46 removed outlier: 3.938A pdb=" N HIS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.927A pdb=" N TRP M 7 " --> pdb=" O GLY M 4 " (cutoff:3.500A) 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: 3.894A pdb=" N HIS N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 8 removed outlier: 3.907A pdb=" N TRP O 7 " --> pdb=" O GLY O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 37 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'P' and resid 15 through 46 removed outlier: 3.884A pdb=" N HIS P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 3.884A pdb=" N TRP Q 7 " --> pdb=" O GLY Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 37 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'R' and resid 15 through 46 removed outlier: 3.904A pdb=" N HIS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1317 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: 2.47 Time building geometry restraints manager: 4.64 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: 2950 1.37 - 1.57: 7692 1.57 - 1.77: 9 1.77 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10792 Sorted by residual: bond pdb=" SD CXM C 1 " pdb=" CE CXM C 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.27e+00 bond pdb=" SD CXM Q 1 " pdb=" CE CXM Q 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" SD CXM K 1 " pdb=" CE CXM K 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" SD CXM E 1 " pdb=" CE CXM E 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.04e+00 bond pdb=" SD CXM O 1 " pdb=" CE CXM O 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.01e+00 ... (remaining 10787 not shown) Histogram of bond angle deviations from ideal: 84.94 - 99.98: 132 99.98 - 115.03: 7014 115.03 - 130.07: 7644 130.07 - 145.11: 317 145.11 - 160.15: 99 Bond angle restraints: 15206 Sorted by residual: angle pdb=" C1 BCL A 101 " pdb=" C2 BCL A 101 " pdb=" C3 BCL A 101 " ideal model delta sigma weight residual 123.38 144.55 -21.17 4.41e+00 5.14e-02 2.31e+01 angle pdb=" C1 BCL E 101 " pdb=" C2 BCL E 101 " pdb=" C3 BCL E 101 " ideal model delta sigma weight residual 123.38 143.67 -20.30 4.41e+00 5.14e-02 2.12e+01 angle pdb=" C1 BCL C 102 " pdb=" C2 BCL C 102 " pdb=" C3 BCL C 102 " ideal model delta sigma weight residual 123.38 140.54 -17.16 4.41e+00 5.14e-02 1.51e+01 angle pdb=" C1 BCL S1702 " pdb=" O2A BCL S1702 " pdb=" CGA BCL S1702 " ideal model delta sigma weight residual 116.11 124.93 -8.81 4.27e+00 5.48e-02 4.26e+00 angle pdb=" N GLY M 4 " pdb=" CA GLY M 4 " pdb=" C GLY M 4 " ideal model delta sigma weight residual 113.27 115.81 -2.54 1.33e+00 5.65e-01 3.64e+00 ... (remaining 15201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5215 24.18 - 48.37: 193 48.37 - 72.55: 11 72.55 - 96.73: 0 96.73 - 120.92: 12 Dihedral angle restraints: 5431 sinusoidal: 2651 harmonic: 2780 Sorted by residual: dihedral pdb=" C3 BCL M 102 " pdb=" C5 BCL M 102 " pdb=" C6 BCL M 102 " pdb=" C7 BCL M 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.83 -56.83 3 9.00e+00 1.23e-02 2.62e+01 dihedral pdb=" C3 BCL K 102 " pdb=" C5 BCL K 102 " pdb=" C6 BCL K 102 " pdb=" C7 BCL K 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.57 -56.57 3 9.00e+00 1.23e-02 2.61e+01 dihedral pdb=" C3 BCL Q 102 " pdb=" C5 BCL Q 102 " pdb=" C6 BCL Q 102 " pdb=" C7 BCL Q 102 " ideal model delta sinusoidal sigma weight residual 60.00 114.36 -54.36 3 9.00e+00 1.23e-02 2.58e+01 ... (remaining 5428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 942 0.029 - 0.058: 333 0.058 - 0.086: 108 0.086 - 0.115: 96 0.115 - 0.144: 28 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA PRO J 10 " pdb=" N PRO J 10 " pdb=" C PRO J 10 " pdb=" CB PRO J 10 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA PRO N 10 " pdb=" N PRO N 10 " pdb=" C PRO N 10 " pdb=" CB PRO N 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA PRO L 10 " pdb=" N PRO L 10 " pdb=" C PRO L 10 " pdb=" CB PRO L 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1504 not shown) Planarity restraints: 1853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL A 101 " -0.056 1.50e-02 4.44e+03 4.85e-02 5.23e+01 pdb=" C2 BCL A 101 " 0.086 1.50e-02 4.44e+03 pdb=" C3 BCL A 101 " 0.006 1.50e-02 4.44e+03 pdb=" C4 BCL A 101 " -0.000 1.50e-02 4.44e+03 pdb=" C5 BCL A 101 " -0.036 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.055 1.50e-02 4.44e+03 4.82e-02 5.16e+01 pdb=" C2 BCL E 101 " -0.084 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.008 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.037 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL C 102 " 0.053 1.50e-02 4.44e+03 4.60e-02 4.69e+01 pdb=" C2 BCL C 102 " -0.078 1.50e-02 4.44e+03 pdb=" C3 BCL C 102 " -0.014 1.50e-02 4.44e+03 pdb=" C4 BCL C 102 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL C 102 " 0.038 1.50e-02 4.44e+03 ... (remaining 1850 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2968 2.88 - 3.39: 9484 3.39 - 3.89: 18326 3.89 - 4.40: 21774 4.40 - 4.90: 35403 Nonbonded interactions: 87955 Sorted by model distance: nonbonded pdb=" OH TYR S 5 " pdb=" OD2 ASP J 27 " model vdw 2.378 2.440 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 22 " model vdw 2.385 2.520 nonbonded pdb=" OE1 GLU B 19 " pdb=" ND2 ASN S 96 " model vdw 2.415 2.520 nonbonded pdb=" N LEU S 15 " pdb=" O CXM I 1 " model vdw 2.449 2.520 nonbonded pdb=" OH TYR S 37 " pdb=" OD2 ASP N 27 " model vdw 2.467 2.440 ... (remaining 87950 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 49 or resid 101 through 102)) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'M' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'O' and (resid 1 through 49 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' and resid 3 through 51) 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: 1.150 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: 5.940 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 29.650 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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:11.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 0.046 10792 Z= 0.265 Angle : 0.933 21.170 15206 Z= 0.360 Chirality : 0.042 0.144 1507 Planarity : 0.009 0.087 1853 Dihedral : 13.216 120.917 3653 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.10 (0.24), residues: 929 helix: 1.39 (0.18), residues: 603 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 7 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE G 41 TYR 0.016 0.004 TYR K 32 ARG 0.016 0.003 ARG R 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 1.016 Fit side-chains REVERT: J 46 TYR cc_start: 0.8424 (m-80) cc_final: 0.8128 (m-80) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.4773 time to fit residues: 130.8728 Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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: 6.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10792 Z= 0.185 Angle : 0.772 9.312 15206 Z= 0.268 Chirality : 0.040 0.118 1507 Planarity : 0.005 0.031 1853 Dihedral : 13.162 113.685 2033 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 0.37 % Allowed : 4.34 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.36 (0.25), residues: 929 helix: 3.14 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.46 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 45 HIS 0.004 0.001 HIS P 24 PHE 0.007 0.001 PHE B 32 TYR 0.009 0.001 TYR K 32 ARG 0.000 0.000 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.892 Fit side-chains REVERT: C 43 LYS cc_start: 0.8030 (tttm) cc_final: 0.7208 (ttmt) REVERT: Q 43 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7818 (tptp) outliers start: 3 outliers final: 1 residues processed: 58 average time/residue: 1.3848 time to fit residues: 86.4137 Evaluate side-chains 50 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 10792 Z= 0.332 Angle : 0.889 11.458 15206 Z= 0.305 Chirality : 0.045 0.143 1507 Planarity : 0.005 0.037 1853 Dihedral : 13.656 113.595 2033 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.50 % Allowed : 6.07 % Favored : 93.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.78 (0.25), residues: 929 helix: 2.52 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.63 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 40 HIS 0.003 0.001 HIS P 24 PHE 0.008 0.002 PHE R 32 TYR 0.011 0.002 TYR Q 32 ARG 0.002 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.018 Fit side-chains REVERT: O 43 LYS cc_start: 0.8162 (tttp) cc_final: 0.7959 (tttp) REVERT: P 20 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7944 (mm-30) outliers start: 4 outliers final: 2 residues processed: 58 average time/residue: 1.4356 time to fit residues: 89.6227 Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 55 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 SER Chi-restraints excluded: chain S residue 25 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 6.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.0020 chunk 65 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10792 Z= 0.148 Angle : 0.713 10.172 15206 Z= 0.241 Chirality : 0.038 0.116 1507 Planarity : 0.004 0.035 1853 Dihedral : 13.240 99.988 2033 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 0.25 % Allowed : 7.06 % Favored : 92.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.61 (0.25), residues: 929 helix: 3.23 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.89 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.004 0.001 PHE B 32 TYR 0.004 0.001 TYR I 32 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.990 Fit side-chains REVERT: P 20 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7903 (mm-30) outliers start: 2 outliers final: 2 residues processed: 60 average time/residue: 1.2416 time to fit residues: 81.2049 Evaluate side-chains 52 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER 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: 9.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10792 Z= 0.202 Angle : 0.751 9.902 15206 Z= 0.256 Chirality : 0.040 0.121 1507 Planarity : 0.004 0.034 1853 Dihedral : 13.197 98.565 2033 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.25 % Allowed : 7.43 % Favored : 92.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.52 (0.25), residues: 929 helix: 3.11 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.96 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE R 32 TYR 0.006 0.001 TYR Q 32 ARG 0.001 0.000 ARG E 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.970 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.2560 time to fit residues: 72.3776 Evaluate side-chains 52 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN B 24 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 10792 Z= 0.527 Angle : 1.056 16.573 15206 Z= 0.360 Chirality : 0.053 0.183 1507 Planarity : 0.006 0.046 1853 Dihedral : 13.999 112.054 2033 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.50 % Allowed : 7.93 % Favored : 91.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.22 (0.24), residues: 929 helix: 1.99 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.67 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 45 HIS 0.005 0.001 HIS P 40 PHE 0.010 0.002 PHE R 32 TYR 0.012 0.002 TYR N 46 ARG 0.002 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 0.993 Fit side-chains REVERT: G 43 LYS cc_start: 0.8065 (tttp) cc_final: 0.7507 (ttmt) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 1.3868 time to fit residues: 89.5436 Evaluate side-chains 58 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain I residue 36 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10792 Z= 0.185 Angle : 0.762 10.496 15206 Z= 0.257 Chirality : 0.039 0.113 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.392 99.244 2033 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 0.50 % Allowed : 8.05 % Favored : 91.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.19 (0.25), residues: 929 helix: 2.84 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.87 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.004 0.001 PHE R 32 TYR 0.006 0.001 TYR J 46 ARG 0.001 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 56 time to evaluate : 1.011 Fit side-chains REVERT: A 43 LYS cc_start: 0.8376 (OUTLIER) cc_final: 0.8093 (tttp) outliers start: 4 outliers final: 3 residues processed: 59 average time/residue: 1.2167 time to fit residues: 78.8693 Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 53 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LYS Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain I residue 36 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 9.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 61 optimal weight: 0.1980 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10792 Z= 0.216 Angle : 0.782 12.044 15206 Z= 0.263 Chirality : 0.040 0.115 1507 Planarity : 0.005 0.038 1853 Dihedral : 13.278 98.351 2033 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.37 % Allowed : 8.67 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.28 (0.25), residues: 929 helix: 2.90 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.91 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.006 0.001 PHE R 32 TYR 0.007 0.001 TYR J 46 ARG 0.001 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.965 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 57 average time/residue: 1.2582 time to fit residues: 78.1258 Evaluate side-chains 56 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain I residue 36 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 65 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 10792 Z= 0.309 Angle : 0.857 13.630 15206 Z= 0.290 Chirality : 0.043 0.128 1507 Planarity : 0.005 0.039 1853 Dihedral : 13.410 99.442 2033 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.37 % Allowed : 8.55 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.97 (0.24), residues: 929 helix: 2.62 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.88 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.007 0.002 PHE R 32 TYR 0.009 0.001 TYR J 46 ARG 0.001 0.000 ARG J 30 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 1.005 Fit side-chains REVERT: O 43 LYS cc_start: 0.8433 (tttp) cc_final: 0.8221 (tptt) outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 1.2618 time to fit residues: 80.7014 Evaluate side-chains 58 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain I residue 36 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 6.9990 chunk 74 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 49 optimal weight: 0.0050 chunk 39 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10792 Z= 0.172 Angle : 0.742 10.283 15206 Z= 0.249 Chirality : 0.038 0.113 1507 Planarity : 0.004 0.038 1853 Dihedral : 13.193 98.468 2033 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.37 % Allowed : 8.55 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.54 (0.25), residues: 929 helix: 3.18 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.93 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE A 41 TYR 0.005 0.001 TYR H 46 ARG 0.001 0.000 ARG J 30 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.936 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 1.1472 time to fit residues: 74.0159 Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASN Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain I residue 36 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: 5.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 chunk 11 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.106221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.081518 restraints weight = 11334.032| |-----------------------------------------------------------------------------| r_work (start): 0.2720 rms_B_bonded: 1.43 r_work: 0.2536 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2403 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 10792 Z= 0.202 Angle : 0.759 10.892 15206 Z= 0.256 Chirality : 0.039 0.116 1507 Planarity : 0.004 0.037 1853 Dihedral : 13.161 98.122 2033 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.37 % Allowed : 8.67 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.44 (0.25), residues: 929 helix: 3.04 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.94 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 40 HIS 0.003 0.001 HIS N 24 PHE 0.005 0.001 PHE R 32 TYR 0.006 0.001 TYR H 46 ARG 0.001 0.000 ARG J 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.22 seconds wall clock time: 46 minutes 19.47 seconds (2779.47 seconds total)