Starting phenix.real_space_refine on Sat Mar 16 09:37:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/03_2024/7pm4_13520_updated.pdb" } resolution = 2.49 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 40 5.16 5 C 9276 2.51 5 N 2340 2.21 5 O 2632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "B PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B GLU 315": "OE1" <-> "OE2" Residue "B GLU 362": "OE1" <-> "OE2" Residue "C PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "D PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 315": "OE1" <-> "OE2" Residue "D GLU 362": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 14288 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3533 Classifications: {'peptide': 431} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 30, 'TRANS': 400} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'DFU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Time building chain proxies: 7.55, per 1000 atoms: 0.53 Number of scatterers: 14288 At special positions: 0 Unit cell: (159.408, 113.488, 59.696, 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 40 16.00 O 2632 8.00 N 2340 7.00 C 9276 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS B 266 " - pdb=" SG CYS B 274 " distance=2.03 Simple disulfide: pdb=" SG CYS C 266 " - pdb=" SG CYS C 274 " distance=2.03 Simple disulfide: pdb=" SG CYS D 266 " - pdb=" SG CYS D 274 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 236 " " NAG B 501 " - " ASN B 236 " " NAG C 501 " - " ASN C 236 " " NAG D 501 " - " ASN D 236 " Time building additional restraints: 6.00 Conformation dependent library (CDL) restraints added in 2.6 seconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 12 sheets defined 30.3% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 36 through 41 removed outlier: 3.906A pdb=" N SER A 41 " --> pdb=" O PRO A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 61 through 65 Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 82 through 91 Processing helix chain 'A' and resid 99 through 104 Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 112 through 121 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.661A pdb=" N ARG A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 232 through 235 No H-bonds generated for 'chain 'A' and resid 232 through 235' Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'A' and resid 313 through 325 Processing helix chain 'A' and resid 344 through 363 removed outlier: 3.668A pdb=" N ILE A 359 " --> pdb=" O LYS A 355 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 41 removed outlier: 3.906A pdb=" N SER B 41 " --> pdb=" O PRO B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 51 Processing helix chain 'B' and resid 61 through 65 Proline residue: B 65 - end of helix Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 98 through 104 Proline residue: B 103 - end of helix Processing helix chain 'B' and resid 112 through 121 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.661A pdb=" N ARG B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 193 Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 206 through 215 Processing helix chain 'B' and resid 232 through 235 No H-bonds generated for 'chain 'B' and resid 232 through 235' Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'B' and resid 313 through 325 Processing helix chain 'B' and resid 344 through 363 removed outlier: 3.668A pdb=" N ILE B 359 " --> pdb=" O LYS B 355 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA B 363 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 41 removed outlier: 3.906A pdb=" N SER C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 51 Processing helix chain 'C' and resid 61 through 65 Proline residue: C 65 - end of helix Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 82 through 91 Processing helix chain 'C' and resid 99 through 104 Proline residue: C 103 - end of helix Processing helix chain 'C' and resid 112 through 121 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.661A pdb=" N ARG C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 193 Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 232 through 235 No H-bonds generated for 'chain 'C' and resid 232 through 235' Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'C' and resid 313 through 325 Processing helix chain 'C' and resid 344 through 363 removed outlier: 3.668A pdb=" N ILE C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA C 363 " --> pdb=" O ILE C 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 41 removed outlier: 3.906A pdb=" N SER D 41 " --> pdb=" O PRO D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 46 through 51 Processing helix chain 'D' and resid 61 through 65 Proline residue: D 65 - end of helix Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 82 through 91 Processing helix chain 'D' and resid 98 through 104 Proline residue: D 103 - end of helix Processing helix chain 'D' and resid 112 through 121 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.661A pdb=" N ARG D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 193 Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'D' and resid 206 through 215 Processing helix chain 'D' and resid 232 through 235 No H-bonds generated for 'chain 'D' and resid 232 through 235' Processing helix chain 'D' and resid 237 through 246 Processing helix chain 'D' and resid 313 through 325 Processing helix chain 'D' and resid 344 through 363 removed outlier: 3.668A pdb=" N ILE D 359 " --> pdb=" O LYS D 355 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLU D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA D 363 " --> pdb=" O ILE D 359 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 221 through 225 removed outlier: 7.448A pdb=" N SER A 179 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR A 126 " --> pdb=" O PHE A 53 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR A 330 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE A 56 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU A 332 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 381 through 386 Processing sheet with id= C, first strand: chain 'A' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS A 426 " --> pdb=" O SER A 438 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 221 through 225 removed outlier: 7.448A pdb=" N SER B 179 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 126 " --> pdb=" O PHE B 53 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR B 330 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 56 " --> pdb=" O TYR B 330 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU B 332 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 381 through 386 Processing sheet with id= F, first strand: chain 'B' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS B 426 " --> pdb=" O SER B 438 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 221 through 225 removed outlier: 7.448A pdb=" N SER C 179 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 126 " --> pdb=" O PHE C 53 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR C 330 " --> pdb=" O GLY C 54 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE C 56 " --> pdb=" O TYR C 330 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU C 332 " --> pdb=" O PHE C 56 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 381 through 386 Processing sheet with id= I, first strand: chain 'C' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS C 426 " --> pdb=" O SER C 438 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 221 through 225 removed outlier: 7.448A pdb=" N SER D 179 " --> pdb=" O THR D 131 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR D 126 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR D 330 " --> pdb=" O GLY D 54 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE D 56 " --> pdb=" O TYR D 330 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N LEU D 332 " --> pdb=" O PHE D 56 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 381 through 386 Processing sheet with id= L, first strand: chain 'D' and resid 402 through 405 removed outlier: 4.371A pdb=" N LYS D 426 " --> pdb=" O SER D 438 " (cutoff:3.500A) 406 hydrogen bonds defined for protein. 1140 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: 4.08 Time building geometry restraints manager: 6.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4368 1.34 - 1.46: 4052 1.46 - 1.58: 6300 1.58 - 1.69: 0 1.69 - 1.81: 60 Bond restraints: 14780 Sorted by residual: bond pdb=" C1 DFU A 502 " pdb=" N5 DFU A 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU B 502 " pdb=" N5 DFU B 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C1 DFU C 502 " pdb=" N5 DFU C 502 " ideal model delta sigma weight residual 1.459 1.503 -0.044 2.00e-02 2.50e+03 4.74e+00 bond pdb=" C5 DFU D 502 " pdb=" N5 DFU D 502 " ideal model delta sigma weight residual 1.465 1.500 -0.035 2.00e-02 2.50e+03 3.10e+00 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 100.66 - 107.34: 828 107.34 - 114.02: 7880 114.02 - 120.70: 5972 120.70 - 127.39: 5168 127.39 - 134.07: 372 Bond angle restraints: 20220 Sorted by residual: angle pdb=" C THR D 410 " pdb=" N THR D 411 " pdb=" CA THR D 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR B 410 " pdb=" N THR B 411 " pdb=" CA THR B 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR C 410 " pdb=" N THR C 411 " pdb=" CA THR C 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" C THR A 410 " pdb=" N THR A 411 " pdb=" CA THR A 411 " ideal model delta sigma weight residual 122.44 117.91 4.53 1.19e+00 7.06e-01 1.45e+01 angle pdb=" CG LYS D 426 " pdb=" CD LYS D 426 " pdb=" CE LYS D 426 " ideal model delta sigma weight residual 111.30 117.30 -6.00 2.30e+00 1.89e-01 6.80e+00 ... (remaining 20215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 7388 17.61 - 35.21: 748 35.21 - 52.82: 228 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8464 sinusoidal: 3468 harmonic: 4996 Sorted by residual: dihedral pdb=" CB CYS D 266 " pdb=" SG CYS D 266 " pdb=" SG CYS D 274 " pdb=" CB CYS D 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS C 266 " pdb=" SG CYS C 266 " pdb=" SG CYS C 274 " pdb=" CB CYS C 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 dihedral pdb=" CB CYS B 266 " pdb=" SG CYS B 266 " pdb=" SG CYS B 274 " pdb=" CB CYS B 274 " ideal model delta sinusoidal sigma weight residual 93.00 161.31 -68.31 1 1.00e+01 1.00e-02 6.05e+01 ... (remaining 8461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1172 0.029 - 0.058: 540 0.058 - 0.087: 196 0.087 - 0.115: 124 0.115 - 0.144: 20 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA ILE C 455 " pdb=" N ILE C 455 " pdb=" C ILE C 455 " pdb=" CB ILE C 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE B 455 " pdb=" N ILE B 455 " pdb=" C ILE B 455 " pdb=" CB ILE B 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 chirality pdb=" CA ILE A 455 " pdb=" N ILE A 455 " pdb=" C ILE A 455 " pdb=" CB ILE A 455 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 2049 not shown) Planarity restraints: 2552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET A 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET A 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU A 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 418 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET C 418 " -0.031 2.00e-02 2.50e+03 pdb=" O MET C 418 " 0.012 2.00e-02 2.50e+03 pdb=" N LEU C 419 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 418 " -0.009 2.00e-02 2.50e+03 1.80e-02 3.25e+00 pdb=" C MET B 418 " 0.031 2.00e-02 2.50e+03 pdb=" O MET B 418 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 419 " -0.010 2.00e-02 2.50e+03 ... (remaining 2549 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2544 2.77 - 3.30: 13436 3.30 - 3.83: 26552 3.83 - 4.37: 33134 4.37 - 4.90: 53008 Nonbonded interactions: 128674 Sorted by model distance: nonbonded pdb=" OG1 THR C 378 " pdb=" N THR C 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR D 378 " pdb=" N THR D 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR A 378 " pdb=" N THR A 379 " model vdw 2.237 2.520 nonbonded pdb=" OG1 THR B 378 " pdb=" N THR B 379 " model vdw 2.237 2.520 nonbonded pdb=" O SER B 445 " pdb=" OG SER B 445 " model vdw 2.253 2.440 ... (remaining 128669 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 19.350 Check model and map are aligned: 0.280 Set scattering table: 0.140 Process input model: 40.870 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 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 : 0.003 0.044 14780 Z= 0.201 Angle : 0.560 6.924 20220 Z= 0.287 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.861 88.029 5252 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 1.06 % Allowed : 16.22 % Favored : 82.71 % 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: 0.76 (0.21), residues: 1716 helix: 1.44 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.23 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 223 HIS 0.002 0.000 HIS A 286 PHE 0.010 0.001 PHE A 394 TYR 0.010 0.001 TYR D 177 ARG 0.001 0.000 ARG C 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 1.760 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.2489 time to fit residues: 161.0751 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 428 SER Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 428 SER Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain D residue 247 ASP Chi-restraints excluded: chain D residue 428 SER Chi-restraints excluded: chain D residue 447 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 72 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.0670 chunk 69 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14780 Z= 0.187 Angle : 0.523 5.924 20220 Z= 0.268 Chirality : 0.044 0.143 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.974 37.648 2024 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 13.56 % Favored : 84.04 % 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: 0.75 (0.21), residues: 1716 helix: 1.43 (0.23), residues: 512 sheet: 0.10 (0.29), residues: 284 loop : 0.21 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 223 HIS 0.001 0.000 HIS B 286 PHE 0.010 0.002 PHE A 96 TYR 0.010 0.001 TYR A 177 ARG 0.002 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 2.167 Fit side-chains REVERT: A 315 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: B 315 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7478 (tp30) REVERT: C 315 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7479 (tp30) REVERT: D 315 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7476 (tp30) outliers start: 36 outliers final: 12 residues processed: 124 average time/residue: 1.1748 time to fit residues: 162.0584 Evaluate side-chains 112 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.0469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14780 Z= 0.284 Angle : 0.580 6.158 20220 Z= 0.300 Chirality : 0.046 0.148 2052 Planarity : 0.005 0.035 2548 Dihedral : 5.014 37.846 2012 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.93 % Allowed : 13.30 % Favored : 83.78 % 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: 0.56 (0.21), residues: 1716 helix: 1.21 (0.23), residues: 512 sheet: -0.03 (0.29), residues: 284 loop : 0.13 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 260 HIS 0.002 0.001 HIS C 286 PHE 0.012 0.002 PHE A 96 TYR 0.011 0.001 TYR B 92 ARG 0.003 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 1.761 Fit side-chains REVERT: A 400 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6977 (p0) REVERT: B 400 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.6972 (p0) REVERT: C 400 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6972 (p0) REVERT: D 400 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6979 (p0) outliers start: 44 outliers final: 20 residues processed: 132 average time/residue: 1.2268 time to fit residues: 179.2208 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Chi-restraints excluded: chain D residue 461 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 chunk 81 optimal weight: 0.0570 chunk 17 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 44 optimal weight: 0.0060 overall best weight: 1.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 ASN B 273 ASN C 273 ASN D 273 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14780 Z= 0.317 Angle : 0.601 6.197 20220 Z= 0.313 Chirality : 0.047 0.149 2052 Planarity : 0.005 0.037 2548 Dihedral : 5.154 38.267 2012 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.72 % Allowed : 11.97 % Favored : 84.31 % 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: 0.44 (0.21), residues: 1716 helix: 1.17 (0.23), residues: 512 sheet: -0.10 (0.30), residues: 284 loop : 0.03 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 260 HIS 0.002 0.001 HIS C 286 PHE 0.012 0.002 PHE B 109 TYR 0.012 0.002 TYR C 92 ARG 0.003 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 104 time to evaluate : 1.553 Fit side-chains REVERT: A 315 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7472 (tp30) REVERT: A 400 ASN cc_start: 0.7340 (OUTLIER) cc_final: 0.6968 (p0) REVERT: B 315 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: B 400 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6963 (p0) REVERT: C 315 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: C 400 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6963 (p0) REVERT: D 315 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: D 400 ASN cc_start: 0.7339 (OUTLIER) cc_final: 0.6966 (p0) outliers start: 56 outliers final: 27 residues processed: 144 average time/residue: 1.2858 time to fit residues: 204.1359 Evaluate side-chains 135 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 100 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 400 ASN Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 400 ASN Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 141 optimal weight: 0.8980 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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: 0.8632 moved from start: 0.0568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14780 Z= 0.263 Angle : 0.573 6.094 20220 Z= 0.297 Chirality : 0.046 0.146 2052 Planarity : 0.005 0.037 2548 Dihedral : 4.998 37.842 2012 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.53 % Allowed : 13.70 % Favored : 83.78 % 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: 0.50 (0.21), residues: 1716 helix: 1.23 (0.23), residues: 512 sheet: -0.12 (0.30), residues: 284 loop : 0.07 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 260 HIS 0.002 0.001 HIS B 286 PHE 0.011 0.002 PHE A 96 TYR 0.011 0.001 TYR C 92 ARG 0.003 0.001 ARG D 108 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 96 time to evaluate : 1.687 Fit side-chains REVERT: A 315 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7484 (tp30) REVERT: B 315 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7483 (tp30) REVERT: C 315 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: D 315 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7483 (tp30) outliers start: 38 outliers final: 26 residues processed: 122 average time/residue: 1.2502 time to fit residues: 168.8762 Evaluate side-chains 122 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 92 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 216 SER Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.2980 chunk 160 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8613 moved from start: 0.0447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14780 Z= 0.194 Angle : 0.531 5.940 20220 Z= 0.273 Chirality : 0.044 0.143 2052 Planarity : 0.005 0.036 2548 Dihedral : 4.700 36.178 2012 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.13 % Allowed : 13.83 % Favored : 84.04 % 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: 0.63 (0.21), residues: 1716 helix: 1.34 (0.23), residues: 512 sheet: -0.08 (0.29), residues: 284 loop : 0.16 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.001 0.000 HIS B 286 PHE 0.011 0.002 PHE C 96 TYR 0.009 0.001 TYR C 177 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.688 Fit side-chains REVERT: A 315 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: B 315 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 315 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7466 (tp30) REVERT: D 315 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7464 (tp30) outliers start: 32 outliers final: 24 residues processed: 124 average time/residue: 1.4372 time to fit residues: 195.8832 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 104 time to evaluate : 1.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 263 ASN Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 461 LYS Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 216 SER Chi-restraints excluded: chain B residue 263 ASN Chi-restraints excluded: chain B residue 305 MET Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 461 LYS Chi-restraints excluded: chain C residue 153 VAL Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 315 GLU Chi-restraints excluded: chain C residue 447 VAL Chi-restraints excluded: chain C residue 450 GLU Chi-restraints excluded: chain C residue 461 LYS Chi-restraints excluded: chain D residue 153 VAL Chi-restraints excluded: chain D residue 263 ASN Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 315 GLU Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 71.5916 > 50: distance: 43 - 73: 31.438 distance: 57 - 81: 23.600 distance: 68 - 73: 32.231 distance: 73 - 74: 10.977 distance: 74 - 75: 9.783 distance: 74 - 77: 33.356 distance: 75 - 76: 5.137 distance: 75 - 81: 43.826 distance: 77 - 78: 34.194 distance: 78 - 80: 39.690 distance: 81 - 82: 54.446 distance: 82 - 83: 42.714 distance: 83 - 84: 35.281 distance: 83 - 85: 28.504 distance: 85 - 86: 34.473 distance: 86 - 87: 12.947 distance: 86 - 89: 21.585 distance: 87 - 88: 35.416 distance: 87 - 94: 7.443 distance: 89 - 90: 22.858 distance: 90 - 91: 35.560 distance: 91 - 92: 46.604 distance: 91 - 93: 25.378 distance: 94 - 95: 19.329 distance: 95 - 96: 21.839 distance: 95 - 98: 25.476 distance: 96 - 97: 30.227 distance: 96 - 99: 14.560 distance: 99 - 100: 33.574 distance: 100 - 101: 20.399 distance: 100 - 103: 10.446 distance: 101 - 102: 24.585 distance: 101 - 107: 15.296 distance: 103 - 104: 37.225 distance: 103 - 105: 46.840 distance: 104 - 106: 36.268 distance: 107 - 108: 14.040 distance: 108 - 109: 35.677 distance: 108 - 111: 37.954 distance: 109 - 110: 8.876 distance: 109 - 119: 35.947 distance: 111 - 112: 15.005 distance: 112 - 113: 6.761 distance: 112 - 114: 8.219 distance: 113 - 115: 18.483 distance: 114 - 116: 14.170 distance: 115 - 117: 21.250 distance: 116 - 117: 15.784 distance: 117 - 118: 22.910 distance: 119 - 120: 14.769 distance: 120 - 121: 22.132 distance: 120 - 123: 47.453 distance: 121 - 122: 35.590 distance: 121 - 124: 39.728 distance: 124 - 125: 40.298 distance: 125 - 126: 40.886 distance: 125 - 128: 48.661 distance: 126 - 127: 40.190 distance: 126 - 130: 39.196 distance: 128 - 129: 47.172 distance: 130 - 131: 40.938 distance: 131 - 132: 51.500 distance: 131 - 134: 47.521 distance: 132 - 133: 22.851 distance: 132 - 139: 43.582 distance: 134 - 135: 29.387 distance: 135 - 136: 6.277 distance: 136 - 137: 40.763 distance: 137 - 138: 37.852 distance: 139 - 140: 29.715 distance: 139 - 145: 40.044 distance: 140 - 141: 47.733 distance: 140 - 143: 31.119 distance: 141 - 142: 5.066 distance: 141 - 146: 33.238 distance: 144 - 145: 49.619