Starting phenix.real_space_refine (version: 1.21rc1) on Wed Jul 5 06:13:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z23_14456/07_2023/7z23_14456.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 6198 2.51 5 N 1446 2.21 5 O 1554 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 42": "OE1" <-> "OE2" Residue "E PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 104": "OE1" <-> "OE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 42": "OE1" <-> "OE2" Residue "B PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 104": "OE1" <-> "OE2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 227": "OE1" <-> "OE2" Residue "B PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 227": "OE1" <-> "OE2" Residue "C PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 104": "OE1" <-> "OE2" Residue "D PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 42": "OE1" <-> "OE2" Residue "F PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 227": "OE1" <-> "OE2" Residue "F PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 9246 Number of models: 1 Model: "" Number of chains: 6 Chain: "E" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "B" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "D" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.51 Number of scatterers: 9246 At special positions: 0 Unit cell: (101.37, 105.294, 86.328, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1554 8.00 N 1446 7.00 C 6198 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 3.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 77.8% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'E' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU E 42 " --> pdb=" O GLY E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 103 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'A' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 103 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 4.298A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 52 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 103 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VAL C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 103 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL D 41 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU D 42 " --> pdb=" O GLY D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 103 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 4.297A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 45 removed outlier: 4.404A pdb=" N TRP F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N GLU F 42 " --> pdb=" O GLY F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 52 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 103 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 Processing helix chain 'F' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'E' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE E 199 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A 199 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE B 199 " --> pdb=" O ARG B 53 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE C 199 " --> pdb=" O ARG C 53 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE D 199 " --> pdb=" O ARG D 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 4.532A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE F 199 " --> pdb=" O ARG F 53 " (cutoff:3.500A) 684 hydrogen bonds defined for protein. 2034 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: 2.51 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2676 1.34 - 1.46: 2079 1.46 - 1.58: 4689 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 9504 Sorted by residual: bond pdb=" C VAL D 87 " pdb=" N PRO D 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.72e+00 bond pdb=" C VAL E 87 " pdb=" N PRO E 88 " ideal model delta sigma weight residual 1.335 1.359 -0.025 1.28e-02 6.10e+03 3.68e+00 bond pdb=" C ASP C 190 " pdb=" N PRO C 191 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.19e-02 7.06e+03 3.58e+00 bond pdb=" C VAL C 87 " pdb=" N PRO C 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.54e+00 bond pdb=" C VAL F 87 " pdb=" N PRO F 88 " ideal model delta sigma weight residual 1.335 1.359 -0.024 1.28e-02 6.10e+03 3.50e+00 ... (remaining 9499 not shown) Histogram of bond angle deviations from ideal: 99.92 - 106.74: 204 106.74 - 113.56: 5156 113.56 - 120.39: 3823 120.39 - 127.21: 3602 127.21 - 134.04: 115 Bond angle restraints: 12900 Sorted by residual: angle pdb=" N ARG D 76 " pdb=" CA ARG D 76 " pdb=" C ARG D 76 " ideal model delta sigma weight residual 111.36 107.02 4.34 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N ARG B 76 " pdb=" CA ARG B 76 " pdb=" C ARG B 76 " ideal model delta sigma weight residual 111.36 107.05 4.31 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" C ARG A 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.56e+01 angle pdb=" N ARG E 76 " pdb=" CA ARG E 76 " pdb=" C ARG E 76 " ideal model delta sigma weight residual 111.36 107.06 4.30 1.09e+00 8.42e-01 1.55e+01 angle pdb=" N ARG C 76 " pdb=" CA ARG C 76 " pdb=" C ARG C 76 " ideal model delta sigma weight residual 111.36 107.07 4.29 1.09e+00 8.42e-01 1.55e+01 ... (remaining 12895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 4824 15.94 - 31.87: 564 31.87 - 47.81: 114 47.81 - 63.75: 18 63.75 - 79.68: 12 Dihedral angle restraints: 5532 sinusoidal: 2196 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS A 61 " pdb=" SG CYS A 61 " pdb=" SG CYS A 192 " pdb=" CB CYS A 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.11 57.89 1 1.00e+01 1.00e-02 4.50e+01 dihedral pdb=" CB CYS D 61 " pdb=" SG CYS D 61 " pdb=" SG CYS D 192 " pdb=" CB CYS D 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 dihedral pdb=" CB CYS B 61 " pdb=" SG CYS B 61 " pdb=" SG CYS B 192 " pdb=" CB CYS B 192 " ideal model delta sinusoidal sigma weight residual 93.00 35.13 57.87 1 1.00e+01 1.00e-02 4.49e+01 ... (remaining 5529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1168 0.049 - 0.097: 236 0.097 - 0.146: 57 0.146 - 0.194: 4 0.194 - 0.243: 11 Chirality restraints: 1476 Sorted by residual: chirality pdb=" CA TRP C 78 " pdb=" N TRP C 78 " pdb=" C TRP C 78 " pdb=" CB TRP C 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP F 78 " pdb=" N TRP F 78 " pdb=" C TRP F 78 " pdb=" CB TRP F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CA TRP D 78 " pdb=" N TRP D 78 " pdb=" C TRP D 78 " pdb=" CB TRP D 78 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1473 not shown) Planarity restraints: 1548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 212 " 0.020 2.00e-02 2.50e+03 1.93e-02 6.51e+00 pdb=" CG PHE C 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE C 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE C 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE C 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 212 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 212 " 0.021 2.00e-02 2.50e+03 1.93e-02 6.49e+00 pdb=" CG PHE B 212 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE B 212 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 212 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE B 212 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 212 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 212 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 212 " -0.021 2.00e-02 2.50e+03 1.92e-02 6.44e+00 pdb=" CG PHE D 212 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE D 212 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE D 212 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 212 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE D 212 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 212 " -0.002 2.00e-02 2.50e+03 ... (remaining 1545 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2502 2.80 - 3.33: 10130 3.33 - 3.85: 15635 3.85 - 4.38: 16709 4.38 - 4.90: 27744 Nonbonded interactions: 72720 Sorted by model distance: nonbonded pdb=" NH1 ARG B 76 " pdb=" O ALA C 40 " model vdw 2.280 2.520 nonbonded pdb=" NH1 ARG E 76 " pdb=" O ALA A 40 " model vdw 2.283 2.520 nonbonded pdb=" O SER B 86 " pdb=" OG1 THR B 89 " model vdw 2.283 2.440 nonbonded pdb=" O SER F 86 " pdb=" OG1 THR F 89 " model vdw 2.284 2.440 nonbonded pdb=" O SER D 86 " pdb=" OG1 THR D 89 " model vdw 2.284 2.440 ... (remaining 72715 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 12.230 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 25.590 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 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 : 0.004 0.033 9504 Z= 0.224 Angle : 0.922 7.456 12900 Z= 0.559 Chirality : 0.047 0.243 1476 Planarity : 0.006 0.055 1548 Dihedral : 14.001 79.684 3318 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.34 (0.25), residues: 1110 helix: 0.28 (0.18), residues: 864 sheet: 0.15 (0.69), residues: 60 loop : -2.31 (0.36), residues: 186 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2648 time to fit residues: 115.1543 Evaluate side-chains 250 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 9504 Z= 0.248 Angle : 0.818 8.947 12900 Z= 0.420 Chirality : 0.046 0.180 1476 Planarity : 0.005 0.043 1548 Dihedral : 4.566 14.445 1218 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.24), residues: 1110 helix: 0.51 (0.17), residues: 870 sheet: 0.87 (0.63), residues: 60 loop : -2.35 (0.35), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 293 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 295 average time/residue: 0.2606 time to fit residues: 99.4600 Evaluate side-chains 248 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 242 time to evaluate : 1.085 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0815 time to fit residues: 2.3528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 33 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN A 63 ASN A 95 HIS B 63 ASN B 95 HIS C 63 ASN C 95 HIS D 63 ASN F 63 ASN F 95 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9504 Z= 0.256 Angle : 0.816 10.788 12900 Z= 0.423 Chirality : 0.044 0.182 1476 Planarity : 0.005 0.035 1548 Dihedral : 4.335 15.027 1218 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.30 (0.24), residues: 1110 helix: 0.68 (0.17), residues: 870 sheet: 1.24 (0.65), residues: 60 loop : -2.25 (0.35), residues: 180 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 256 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 11 residues processed: 270 average time/residue: 0.2355 time to fit residues: 84.6727 Evaluate side-chains 252 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 241 time to evaluate : 1.057 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0970 time to fit residues: 3.3356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 7.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 95 HIS ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9504 Z= 0.225 Angle : 0.798 11.266 12900 Z= 0.414 Chirality : 0.044 0.162 1476 Planarity : 0.004 0.031 1548 Dihedral : 4.243 16.179 1218 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 23.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.73 (0.24), residues: 1110 helix: 1.02 (0.17), residues: 864 sheet: 0.95 (0.62), residues: 60 loop : -2.03 (0.35), residues: 186 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 288 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 8 residues processed: 297 average time/residue: 0.2576 time to fit residues: 100.5048 Evaluate side-chains 260 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 252 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0961 time to fit residues: 2.7908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 6.9990 chunk 59 optimal weight: 0.0370 chunk 1 optimal weight: 0.2980 chunk 77 optimal weight: 9.9990 chunk 43 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 63 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 9504 Z= 0.226 Angle : 0.853 12.964 12900 Z= 0.437 Chirality : 0.045 0.220 1476 Planarity : 0.005 0.058 1548 Dihedral : 4.311 17.882 1218 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 23.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.79 (0.24), residues: 1110 helix: 1.03 (0.17), residues: 864 sheet: 0.92 (0.59), residues: 60 loop : -1.77 (0.38), residues: 186 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 288 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 0 residues processed: 294 average time/residue: 0.2554 time to fit residues: 97.7762 Evaluate side-chains 253 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 253 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 9504 Z= 0.225 Angle : 0.855 13.431 12900 Z= 0.446 Chirality : 0.045 0.185 1476 Planarity : 0.005 0.055 1548 Dihedral : 4.306 16.701 1218 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 25.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.24), residues: 1110 helix: 1.10 (0.17), residues: 864 sheet: 0.91 (0.57), residues: 60 loop : -1.67 (0.38), residues: 186 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 275 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 279 average time/residue: 0.2719 time to fit residues: 98.2236 Evaluate side-chains 240 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 232 time to evaluate : 1.095 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0957 time to fit residues: 2.7699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN C 15 GLN D 15 GLN F 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.5762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 9504 Z= 0.272 Angle : 0.879 13.469 12900 Z= 0.465 Chirality : 0.047 0.236 1476 Planarity : 0.005 0.077 1548 Dihedral : 4.451 20.283 1218 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 31.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.24), residues: 1110 helix: 1.01 (0.17), residues: 864 sheet: 0.85 (0.58), residues: 60 loop : -1.64 (0.39), residues: 186 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 258 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 261 average time/residue: 0.2532 time to fit residues: 87.1820 Evaluate side-chains 240 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 1.140 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 20.0000 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 99 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: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9504 Z= 0.255 Angle : 0.949 13.339 12900 Z= 0.500 Chirality : 0.050 0.247 1476 Planarity : 0.006 0.058 1548 Dihedral : 4.444 21.019 1218 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 29.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.24), residues: 1110 helix: 1.02 (0.17), residues: 864 sheet: 0.88 (0.57), residues: 60 loop : -1.49 (0.40), residues: 186 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 263 time to evaluate : 1.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 264 average time/residue: 0.2548 time to fit residues: 88.9616 Evaluate side-chains 248 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 246 time to evaluate : 1.039 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0808 time to fit residues: 1.7223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.1980 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 9504 Z= 0.263 Angle : 0.985 14.548 12900 Z= 0.521 Chirality : 0.050 0.238 1476 Planarity : 0.005 0.060 1548 Dihedral : 4.500 19.748 1218 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 32.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer Outliers : 0.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.24), residues: 1110 helix: 0.86 (0.17), residues: 864 sheet: 0.91 (0.58), residues: 60 loop : -1.44 (0.40), residues: 186 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 270 time to evaluate : 1.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 270 average time/residue: 0.2474 time to fit residues: 89.3481 Evaluate side-chains 251 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 250 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0797 time to fit residues: 1.4802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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: 0.8326 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 9504 Z= 0.258 Angle : 1.092 17.426 12900 Z= 0.564 Chirality : 0.052 0.223 1476 Planarity : 0.005 0.062 1548 Dihedral : 4.531 19.336 1218 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.51 (0.24), residues: 1110 helix: 0.79 (0.17), residues: 858 sheet: 1.06 (0.58), residues: 60 loop : -1.66 (0.40), residues: 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 263 average time/residue: 0.2501 time to fit residues: 86.8335 Evaluate side-chains 247 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.068 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 10.0000 chunk 26 optimal weight: 0.0980 chunk 79 optimal weight: 0.0070 chunk 12 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.0770 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 63 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.056861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.045950 restraints weight = 59003.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.046997 restraints weight = 43689.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.047768 restraints weight = 34566.642| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.6629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 9504 Z= 0.259 Angle : 1.143 17.287 12900 Z= 0.591 Chirality : 0.053 0.258 1476 Planarity : 0.006 0.069 1548 Dihedral : 4.575 22.766 1218 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 30.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.25 (0.24), residues: 1110 helix: 0.57 (0.17), residues: 858 sheet: 1.26 (0.60), residues: 60 loop : -1.69 (0.40), residues: 192 =============================================================================== Job complete usr+sys time: 2351.39 seconds wall clock time: 43 minutes 24.79 seconds (2604.79 seconds total)