Starting phenix.real_space_refine on Sat Aug 3 10:18:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izf_35863/08_2024/8izf_35863.cif" } resolution = 3.85 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= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 5088 2.51 5 N 1202 2.21 5 O 1264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 76": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ASP 122": "OD1" <-> "OD2" Residue "A TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 132": "OD1" <-> "OD2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 209": "NH1" <-> "NH2" Residue "A ASP 248": "OD1" <-> "OD2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 381": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B ARG 25": "NH1" <-> "NH2" Residue "B PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 76": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 147": "NH1" <-> "NH2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ASP 248": "OD1" <-> "OD2" Residue "C GLU 251": "OE1" <-> "OE2" Residue "C PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 381": "NH1" <-> "NH2" Residue "C ARG 385": "NH1" <-> "NH2" Residue "D ARG 25": "NH1" <-> "NH2" Residue "D PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "D GLU 136": "OE1" <-> "OE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 7594 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1087 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 2670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2670 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 306} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1087 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'6PL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 12 Time building chain proxies: 4.73, per 1000 atoms: 0.62 Number of scatterers: 7594 At special positions: 0 Unit cell: (110.416, 101.84, 100.768, 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 38 16.00 P 2 15.00 O 1264 8.00 N 1202 7.00 C 5088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 102 " - pdb=" SG CYS B 142 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 75 " distance=2.03 Simple disulfide: pdb=" SG CYS D 102 " - pdb=" SG CYS D 142 " 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: 3.27 Conformation dependent library (CDL) restraints added in 1.4 seconds 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1708 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 2 sheets defined 67.0% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 71 through 82 removed outlier: 3.530A pdb=" N PHE A 75 " --> pdb=" O ILE A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 Processing helix chain 'A' and resid 109 through 115 Processing helix chain 'A' and resid 130 through 162 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 167 through 196 Proline residue: A 188 - end of helix Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 217 through 241 Processing helix chain 'A' and resid 249 through 269 Processing helix chain 'A' and resid 275 through 298 removed outlier: 3.786A pdb=" N LEU A 288 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 335 removed outlier: 3.947A pdb=" N TYR A 320 " --> pdb=" O TYR A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 384 removed outlier: 3.881A pdb=" N ILE A 356 " --> pdb=" O ILE A 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 47 Processing helix chain 'B' and resid 48 through 52 removed outlier: 3.736A pdb=" N HIS B 52 " --> pdb=" O TYR B 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 48 through 52' Processing helix chain 'B' and resid 76 through 92 removed outlier: 3.541A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 142 removed outlier: 3.523A pdb=" N VAL B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 82 Processing helix chain 'C' and resid 84 through 100 Processing helix chain 'C' and resid 109 through 115 Processing helix chain 'C' and resid 130 through 162 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 167 through 196 Proline residue: C 188 - end of helix Processing helix chain 'C' and resid 205 through 209 Processing helix chain 'C' and resid 217 through 241 Processing helix chain 'C' and resid 249 through 269 Processing helix chain 'C' and resid 275 through 298 removed outlier: 3.786A pdb=" N LEU C 288 " --> pdb=" O VAL C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 335 removed outlier: 3.946A pdb=" N TYR C 320 " --> pdb=" O TYR C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 384 removed outlier: 3.881A pdb=" N ILE C 356 " --> pdb=" O ILE C 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 47 Processing helix chain 'D' and resid 48 through 52 removed outlier: 3.736A pdb=" N HIS D 52 " --> pdb=" O TYR D 48 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 48 through 52' Processing helix chain 'D' and resid 76 through 92 removed outlier: 3.541A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 142 removed outlier: 3.524A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL B 129 " --> pdb=" O ILE B 65 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 59 removed outlier: 3.616A pdb=" N VAL D 129 " --> pdb=" O ILE D 65 " (cutoff:3.500A) 486 hydrogen bonds defined for protein. 1434 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: 2.09 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1096 1.32 - 1.44: 2532 1.44 - 1.57: 4158 1.57 - 1.70: 2 1.70 - 1.83: 58 Bond restraints: 7846 Sorted by residual: bond pdb=" C31 6PL D 201 " pdb=" O2 6PL D 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C31 6PL B 201 " pdb=" O2 6PL B 201 " ideal model delta sigma weight residual 1.330 1.430 -0.100 2.00e-02 2.50e+03 2.51e+01 bond pdb=" C11 6PL D 201 " pdb=" O3 6PL D 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C11 6PL B 201 " pdb=" O3 6PL B 201 " ideal model delta sigma weight residual 1.327 1.426 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" CA PHE A 343 " pdb=" CB PHE A 343 " ideal model delta sigma weight residual 1.530 1.462 0.068 1.69e-02 3.50e+03 1.62e+01 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 98.18 - 105.38: 129 105.38 - 112.59: 3941 112.59 - 119.79: 2706 119.79 - 126.99: 3766 126.99 - 134.19: 110 Bond angle restraints: 10652 Sorted by residual: angle pdb=" N PHE C 343 " pdb=" CA PHE C 343 " pdb=" C PHE C 343 " ideal model delta sigma weight residual 110.80 130.12 -19.32 2.13e+00 2.20e-01 8.23e+01 angle pdb=" N PHE A 343 " pdb=" CA PHE A 343 " pdb=" C PHE A 343 " ideal model delta sigma weight residual 110.80 130.08 -19.28 2.13e+00 2.20e-01 8.20e+01 angle pdb=" N LYS C 247 " pdb=" CA LYS C 247 " pdb=" C LYS C 247 " ideal model delta sigma weight residual 110.24 98.33 11.91 1.41e+00 5.03e-01 7.13e+01 angle pdb=" N LYS A 247 " pdb=" CA LYS A 247 " pdb=" C LYS A 247 " ideal model delta sigma weight residual 110.24 98.35 11.89 1.41e+00 5.03e-01 7.11e+01 angle pdb=" N MET A 140 " pdb=" CA MET A 140 " pdb=" C MET A 140 " ideal model delta sigma weight residual 111.36 103.42 7.94 1.09e+00 8.42e-01 5.31e+01 ... (remaining 10647 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 3954 18.05 - 36.09: 412 36.09 - 54.14: 100 54.14 - 72.19: 16 72.19 - 90.24: 16 Dihedral angle restraints: 4498 sinusoidal: 1834 harmonic: 2664 Sorted by residual: dihedral pdb=" CA GLU D 118 " pdb=" C GLU D 118 " pdb=" N ASP D 119 " pdb=" CA ASP D 119 " ideal model delta harmonic sigma weight residual 180.00 158.66 21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" CA GLU B 118 " pdb=" C GLU B 118 " pdb=" N ASP B 119 " pdb=" CA ASP B 119 " ideal model delta harmonic sigma weight residual 180.00 158.70 21.30 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA CYS B 53 " pdb=" CB CYS B 53 " pdb=" SG CYS B 53 " pdb=" SG CYS B 75 " ideal model delta sinusoidal sigma weight residual -73.00 2.17 -75.17 1 2.00e+01 2.50e-03 1.79e+01 ... (remaining 4495 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 1107 0.118 - 0.236: 27 0.236 - 0.354: 2 0.354 - 0.472: 0 0.472 - 0.590: 2 Chirality restraints: 1138 Sorted by residual: chirality pdb=" CA PHE C 343 " pdb=" N PHE C 343 " pdb=" C PHE C 343 " pdb=" CB PHE C 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.71e+00 chirality pdb=" CA PHE A 343 " pdb=" N PHE A 343 " pdb=" C PHE A 343 " pdb=" CB PHE A 343 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" CA LYS C 247 " pdb=" N LYS C 247 " pdb=" C LYS C 247 " pdb=" CB LYS C 247 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1135 not shown) Planarity restraints: 1296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 139 " -0.019 2.00e-02 2.50e+03 3.87e-02 1.49e+01 pdb=" C TYR A 139 " 0.067 2.00e-02 2.50e+03 pdb=" O TYR A 139 " -0.026 2.00e-02 2.50e+03 pdb=" N MET A 140 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 139 " 0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C TYR C 139 " -0.067 2.00e-02 2.50e+03 pdb=" O TYR C 139 " 0.026 2.00e-02 2.50e+03 pdb=" N MET C 140 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 77 " -0.016 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS D 77 " 0.057 2.00e-02 2.50e+03 pdb=" O LYS D 77 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 78 " -0.019 2.00e-02 2.50e+03 ... (remaining 1293 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 65 2.54 - 3.13: 6462 3.13 - 3.72: 12006 3.72 - 4.31: 15506 4.31 - 4.90: 25341 Nonbonded interactions: 59380 Sorted by model distance: nonbonded pdb=" O ILE B 103 " pdb=" OH TYR D 148 " model vdw 1.945 3.040 nonbonded pdb=" OH TYR B 148 " pdb=" O ILE D 103 " model vdw 1.952 3.040 nonbonded pdb=" O LYS A 244 " pdb=" O PRO A 245 " model vdw 2.010 3.040 nonbonded pdb=" O LYS C 244 " pdb=" O PRO C 245 " model vdw 2.011 3.040 nonbonded pdb=" OG SER A 186 " pdb=" OD2 ASP A 283 " model vdw 2.168 3.040 ... (remaining 59375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.870 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: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 23.760 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.006 0.100 7846 Z= 0.383 Angle : 1.095 19.322 10652 Z= 0.624 Chirality : 0.057 0.590 1138 Planarity : 0.006 0.063 1296 Dihedral : 16.149 90.235 2778 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.68 % Allowed : 9.48 % Favored : 89.84 % Rotamer: Outliers : 2.73 % Allowed : 1.74 % Favored : 95.53 % 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: -1.59 (0.27), residues: 886 helix: 0.25 (0.20), residues: 562 sheet: -1.68 (0.58), residues: 58 loop : -3.81 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 50 HIS 0.008 0.001 HIS A 249 PHE 0.020 0.002 PHE A 271 TYR 0.032 0.002 TYR C 279 ARG 0.011 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 294 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.8276 (p-90) cc_final: 0.7844 (p-90) REVERT: A 168 HIS cc_start: 0.7148 (OUTLIER) cc_final: 0.6197 (m90) REVERT: A 174 MET cc_start: 0.8632 (mmt) cc_final: 0.8164 (mmt) REVERT: A 182 TYR cc_start: 0.7918 (p90) cc_final: 0.7554 (t80) REVERT: A 236 CYS cc_start: 0.8676 (p) cc_final: 0.8464 (p) REVERT: A 251 GLU cc_start: 0.7857 (pm20) cc_final: 0.7460 (pm20) REVERT: A 289 LEU cc_start: 0.8881 (tp) cc_final: 0.8583 (tt) REVERT: A 334 ARG cc_start: 0.7006 (tmt170) cc_final: 0.6782 (tpt170) REVERT: A 343 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7782 (t80) REVERT: A 346 GLN cc_start: 0.8589 (mp10) cc_final: 0.8219 (mp10) REVERT: C 84 TRP cc_start: 0.8268 (p-90) cc_final: 0.7829 (p-90) REVERT: C 168 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6175 (m90) REVERT: C 174 MET cc_start: 0.8753 (mmt) cc_final: 0.8269 (mmt) REVERT: C 236 CYS cc_start: 0.8675 (p) cc_final: 0.8460 (p) REVERT: C 251 GLU cc_start: 0.7866 (pm20) cc_final: 0.7509 (pm20) REVERT: C 334 ARG cc_start: 0.6939 (tmt170) cc_final: 0.6230 (ttt180) REVERT: C 343 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.7799 (t80) REVERT: C 346 GLN cc_start: 0.8577 (mp10) cc_final: 0.8175 (mp10) REVERT: D 65 ILE cc_start: 0.9318 (pt) cc_final: 0.9083 (pt) outliers start: 22 outliers final: 4 residues processed: 306 average time/residue: 0.1767 time to fit residues: 74.3922 Evaluate side-chains 212 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 204 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 364 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7846 Z= 0.215 Angle : 0.723 13.409 10652 Z= 0.372 Chirality : 0.043 0.140 1138 Planarity : 0.005 0.056 1296 Dihedral : 9.685 54.833 1084 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 4.34 % Allowed : 16.00 % Favored : 79.65 % 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: -0.88 (0.28), residues: 886 helix: 0.93 (0.21), residues: 544 sheet: -1.69 (0.57), residues: 58 loop : -3.48 (0.35), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 68 HIS 0.005 0.001 HIS A 82 PHE 0.032 0.002 PHE A 158 TYR 0.030 0.002 TYR C 182 ARG 0.003 0.000 ARG B 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 249 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 TRP cc_start: 0.8115 (p-90) cc_final: 0.7815 (p-90) REVERT: A 139 TYR cc_start: 0.8145 (m-80) cc_final: 0.7939 (m-80) REVERT: A 140 MET cc_start: 0.8420 (tpp) cc_final: 0.7828 (tpp) REVERT: A 168 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6596 (m90) REVERT: A 332 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7587 (mt0) REVERT: A 334 ARG cc_start: 0.6139 (tmt170) cc_final: 0.5482 (ttt180) REVERT: A 343 PHE cc_start: 0.8391 (OUTLIER) cc_final: 0.7924 (t80) REVERT: A 357 VAL cc_start: 0.7664 (t) cc_final: 0.7449 (p) REVERT: B 28 PHE cc_start: 0.8704 (t80) cc_final: 0.8494 (t80) REVERT: B 148 TYR cc_start: 0.7761 (m-80) cc_final: 0.7467 (m-80) REVERT: C 84 TRP cc_start: 0.8103 (p-90) cc_final: 0.7803 (p-90) REVERT: C 168 HIS cc_start: 0.7403 (OUTLIER) cc_final: 0.6576 (m90) REVERT: C 332 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: C 334 ARG cc_start: 0.6135 (tmt170) cc_final: 0.5506 (ttt180) REVERT: C 343 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7928 (t80) REVERT: C 357 VAL cc_start: 0.7698 (t) cc_final: 0.7496 (p) REVERT: C 370 TYR cc_start: 0.7902 (t80) cc_final: 0.7652 (t80) REVERT: D 65 ILE cc_start: 0.9213 (pt) cc_final: 0.8949 (pt) outliers start: 35 outliers final: 23 residues processed: 266 average time/residue: 0.1576 time to fit residues: 58.7908 Evaluate side-chains 233 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 175 GLU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 332 GLN Chi-restraints excluded: chain A residue 339 TYR Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 175 GLU Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 332 GLN Chi-restraints excluded: chain C residue 339 TYR Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 66 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 79 optimal weight: 0.9990 chunk 27 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS A 332 GLN ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS C 332 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7846 Z= 0.202 Angle : 0.684 9.459 10652 Z= 0.354 Chirality : 0.043 0.250 1138 Planarity : 0.005 0.052 1296 Dihedral : 8.986 57.550 1082 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 4.96 % Allowed : 19.73 % Favored : 75.31 % 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: -0.74 (0.28), residues: 886 helix: 0.98 (0.21), residues: 546 sheet: -0.95 (0.60), residues: 54 loop : -3.46 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 72 HIS 0.009 0.001 HIS A 82 PHE 0.027 0.001 PHE A 158 TYR 0.022 0.002 TYR C 279 ARG 0.003 0.000 ARG B 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 238 time to evaluate : 0.907 Fit side-chains REVERT: A 168 HIS cc_start: 0.7390 (OUTLIER) cc_final: 0.6768 (m90) REVERT: A 224 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7086 (t80) REVERT: A 248 ASP cc_start: 0.7364 (t70) cc_final: 0.6620 (t0) REVERT: A 323 LEU cc_start: 0.8555 (mm) cc_final: 0.8346 (tp) REVERT: A 334 ARG cc_start: 0.6215 (tmt170) cc_final: 0.5558 (ttt180) REVERT: A 343 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7899 (t80) REVERT: A 357 VAL cc_start: 0.7644 (t) cc_final: 0.7426 (p) REVERT: B 28 PHE cc_start: 0.8678 (t80) cc_final: 0.8378 (t80) REVERT: B 38 GLU cc_start: 0.8032 (tp30) cc_final: 0.7826 (tp30) REVERT: B 148 TYR cc_start: 0.7921 (m-80) cc_final: 0.7587 (m-80) REVERT: C 168 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.6772 (m90) REVERT: C 174 MET cc_start: 0.8463 (mmt) cc_final: 0.8262 (mmp) REVERT: C 224 TYR cc_start: 0.8384 (OUTLIER) cc_final: 0.7039 (t80) REVERT: C 334 ARG cc_start: 0.6121 (tmt170) cc_final: 0.5508 (ttt180) REVERT: C 343 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7889 (t80) REVERT: C 357 VAL cc_start: 0.7603 (t) cc_final: 0.7384 (p) REVERT: D 92 TYR cc_start: 0.8311 (m-10) cc_final: 0.7958 (m-10) outliers start: 40 outliers final: 22 residues processed: 262 average time/residue: 0.1652 time to fit residues: 60.4565 Evaluate side-chains 242 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 HIS Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 67 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain C residue 82 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 67 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.0030 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 7846 Z= 0.254 Angle : 0.702 10.544 10652 Z= 0.364 Chirality : 0.044 0.216 1138 Planarity : 0.005 0.050 1296 Dihedral : 8.628 59.070 1082 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.92 % Favored : 91.08 % Rotamer: Outliers : 5.71 % Allowed : 23.20 % Favored : 71.09 % 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: -0.78 (0.28), residues: 886 helix: 0.98 (0.21), residues: 552 sheet: -0.95 (0.60), residues: 56 loop : -3.66 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 72 HIS 0.013 0.002 HIS C 82 PHE 0.029 0.002 PHE C 158 TYR 0.025 0.002 TYR C 182 ARG 0.006 0.001 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 0.923 Fit side-chains REVERT: A 168 HIS cc_start: 0.7334 (OUTLIER) cc_final: 0.6808 (m90) REVERT: A 224 TYR cc_start: 0.8554 (OUTLIER) cc_final: 0.7062 (t80) REVERT: A 233 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: A 248 ASP cc_start: 0.7359 (t70) cc_final: 0.6805 (t0) REVERT: A 251 GLU cc_start: 0.7656 (pm20) cc_final: 0.7375 (pm20) REVERT: A 334 ARG cc_start: 0.6312 (tmt170) cc_final: 0.5572 (ttt180) REVERT: A 343 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.7833 (t80) REVERT: A 357 VAL cc_start: 0.7710 (t) cc_final: 0.7481 (p) REVERT: B 28 PHE cc_start: 0.8693 (t80) cc_final: 0.8434 (t80) REVERT: B 149 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6908 (p90) REVERT: C 168 HIS cc_start: 0.7351 (m170) cc_final: 0.6835 (m90) REVERT: C 224 TYR cc_start: 0.8542 (OUTLIER) cc_final: 0.7052 (t80) REVERT: C 248 ASP cc_start: 0.7477 (t0) cc_final: 0.7036 (t0) REVERT: C 251 GLU cc_start: 0.7706 (pm20) cc_final: 0.7486 (pm20) REVERT: C 334 ARG cc_start: 0.6277 (tmt170) cc_final: 0.5526 (ttt180) REVERT: C 343 PHE cc_start: 0.8485 (OUTLIER) cc_final: 0.7835 (t80) REVERT: D 149 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6809 (p90) outliers start: 46 outliers final: 31 residues processed: 253 average time/residue: 0.1452 time to fit residues: 52.4675 Evaluate side-chains 239 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 200 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 168 HIS Chi-restraints excluded: chain A residue 194 MET Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 237 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS C 82 HIS C 234 GLN ** D 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7846 Z= 0.205 Angle : 0.686 9.334 10652 Z= 0.353 Chirality : 0.042 0.165 1138 Planarity : 0.005 0.049 1296 Dihedral : 8.063 59.334 1080 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 5.21 % Allowed : 26.05 % Favored : 68.73 % 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: -0.72 (0.27), residues: 886 helix: 1.06 (0.21), residues: 550 sheet: -0.87 (0.60), residues: 56 loop : -3.69 (0.31), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 84 HIS 0.004 0.001 HIS A 82 PHE 0.031 0.002 PHE C 158 TYR 0.020 0.001 TYR D 42 ARG 0.004 0.000 ARG D 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1772 Ramachandran restraints generated. 886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 0.891 Fit side-chains REVERT: A 168 HIS cc_start: 0.7333 (m170) cc_final: 0.6887 (m90) REVERT: A 224 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.6926 (t80) REVERT: A 233 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.7689 (tt0) REVERT: A 248 ASP cc_start: 0.7364 (t70) cc_final: 0.6678 (t0) REVERT: A 251 GLU cc_start: 0.7436 (pm20) cc_final: 0.6995 (pm20) REVERT: A 334 ARG cc_start: 0.6304 (tmt170) cc_final: 0.5511 (ttt180) REVERT: A 343 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7849 (t80) REVERT: B 28 PHE cc_start: 0.8682 (t80) cc_final: 0.8436 (t80) REVERT: B 149 HIS cc_start: 0.7338 (OUTLIER) cc_final: 0.6898 (p90) REVERT: C 168 HIS cc_start: 0.7380 (OUTLIER) cc_final: 0.6966 (m90) REVERT: C 224 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.6986 (t80) REVERT: C 248 ASP cc_start: 0.7345 (t0) cc_final: 0.6634 (t0) REVERT: C 251 GLU cc_start: 0.7550 (pm20) cc_final: 0.7218 (pm20) REVERT: C 334 ARG cc_start: 0.6189 (tmt170) cc_final: 0.5481 (ttt180) REVERT: C 343 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7851 (t80) REVERT: D 149 HIS cc_start: 0.7344 (OUTLIER) cc_final: 0.6889 (p90) outliers start: 42 outliers final: 28 residues processed: 255 average time/residue: 0.1482 time to fit residues: 54.3936 Evaluate side-chains 254 residues out of total 808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 218 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 224 TYR Chi-restraints excluded: chain A residue 233 GLN Chi-restraints excluded: chain A residue 236 CYS Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 263 ILE Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 343 PHE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 27 CYS Chi-restraints excluded: chain B residue 37 VAL Chi-restraints excluded: chain B residue 53 CYS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 149 HIS Chi-restraints excluded: chain C residue 113 PHE Chi-restraints excluded: chain C residue 168 HIS Chi-restraints excluded: chain C residue 219 LEU Chi-restraints excluded: chain C residue 224 TYR Chi-restraints excluded: chain C residue 236 CYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 343 PHE Chi-restraints excluded: chain C residue 364 LEU Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain D residue 27 CYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 53 CYS Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 149 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.1835 > 50: distance: 41 - 45: 22.012 distance: 45 - 46: 29.658 distance: 46 - 47: 10.885 distance: 46 - 49: 3.026 distance: 47 - 48: 29.104 distance: 47 - 51: 41.858 distance: 49 - 50: 9.089 distance: 51 - 52: 37.650 distance: 52 - 53: 9.866 distance: 52 - 55: 5.227 distance: 53 - 54: 32.408 distance: 53 - 65: 27.711 distance: 55 - 56: 20.342 distance: 56 - 57: 9.768 distance: 56 - 58: 16.040 distance: 57 - 59: 22.297 distance: 58 - 60: 17.479 distance: 58 - 61: 4.912 distance: 59 - 60: 8.077 distance: 60 - 62: 21.590 distance: 61 - 63: 23.374 distance: 62 - 64: 7.828 distance: 63 - 64: 18.988 distance: 65 - 66: 18.227 distance: 66 - 67: 6.142 distance: 66 - 69: 7.635 distance: 67 - 68: 3.682 distance: 67 - 73: 18.707 distance: 69 - 71: 13.124 distance: 70 - 72: 28.745 distance: 73 - 74: 37.208 distance: 74 - 75: 43.894 distance: 74 - 77: 15.721 distance: 75 - 76: 16.372 distance: 75 - 79: 15.061 distance: 76 - 102: 32.272 distance: 79 - 80: 8.556 distance: 80 - 81: 18.262 distance: 80 - 83: 23.536 distance: 81 - 82: 28.346 distance: 82 - 109: 28.437 distance: 83 - 84: 29.300 distance: 84 - 85: 16.073 distance: 84 - 86: 40.674 distance: 87 - 88: 36.217 distance: 87 - 93: 25.105 distance: 88 - 89: 16.733 distance: 88 - 91: 19.854 distance: 89 - 90: 16.293 distance: 89 - 94: 10.559 distance: 90 - 120: 7.999 distance: 91 - 92: 15.195 distance: 92 - 93: 36.456 distance: 94 - 95: 20.210 distance: 95 - 96: 7.682 distance: 95 - 98: 21.879 distance: 96 - 97: 11.263 distance: 96 - 102: 20.641 distance: 97 - 127: 28.646 distance: 98 - 99: 18.899 distance: 98 - 100: 40.358 distance: 99 - 101: 57.387 distance: 102 - 103: 8.262 distance: 103 - 104: 12.779 distance: 103 - 106: 18.467 distance: 104 - 109: 7.183 distance: 105 - 135: 8.436 distance: 106 - 107: 17.296 distance: 106 - 108: 3.265 distance: 109 - 110: 9.740 distance: 110 - 111: 12.827 distance: 110 - 113: 6.541 distance: 111 - 112: 6.328 distance: 111 - 120: 10.817 distance: 112 - 142: 29.342 distance: 113 - 114: 9.551 distance: 114 - 115: 16.147 distance: 114 - 116: 3.565 distance: 115 - 117: 11.095 distance: 116 - 118: 10.265 distance: 117 - 119: 5.614 distance: 118 - 119: 12.792 distance: 120 - 121: 18.763 distance: 121 - 122: 19.553 distance: 121 - 124: 12.477 distance: 122 - 123: 4.288 distance: 122 - 127: 19.753 distance: 123 - 146: 26.084 distance: 124 - 125: 9.163 distance: 124 - 126: 11.662 distance: 130 - 150: 3.019