Starting phenix.real_space_refine on Sun Dec 10 11:19:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_13520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/12_2023/7pm4_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.65, per 1000 atoms: 0.54 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: 5.91 Conformation dependent library (CDL) restraints added in 2.5 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: 2.99 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: 4.19 Time building geometry restraints manager: 6.25 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 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG D 501 " pdb=" O5 NAG D 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C1 NAG C 501 " pdb=" O5 NAG C 501 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.44e+00 bond pdb=" C5 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+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: 7352 17.61 - 35.21: 740 35.21 - 52.82: 228 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8420 sinusoidal: 3424 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 8417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1184 0.029 - 0.058: 528 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: 3.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 18.110 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 40.360 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.060 ------------------------------------------------------------------------------- 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 0.024 14780 Z= 0.179 Angle : 0.546 6.737 20220 Z= 0.284 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 16.895 88.029 5208 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 : 1.662 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.2254 time to fit residues: 157.9458 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.579 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.1436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 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: 0.0198 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 : 0.522 5.926 20220 Z= 0.267 Chirality : 0.044 0.143 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.394 21.831 1964 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.19 % Allowed : 13.03 % 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: 0.75 (0.21), residues: 1716 helix: 1.43 (0.23), residues: 512 sheet: 0.09 (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 B 223 HIS 0.001 0.000 HIS D 286 PHE 0.010 0.002 PHE C 96 TYR 0.010 0.001 TYR C 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 148 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 100 time to evaluate : 1.753 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 136 average time/residue: 1.1955 time to fit residues: 180.9625 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.660 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 0.9932 time to fit residues: 11.1004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 169 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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: 0.8617 moved from start: 0.0334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14780 Z= 0.220 Angle : 0.541 6.006 20220 Z= 0.279 Chirality : 0.045 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.433 16.541 1964 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.46 % Allowed : 12.43 % Favored : 84.11 % 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: 0.69 (0.21), residues: 1716 helix: 1.33 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.21 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 260 HIS 0.002 0.001 HIS B 286 PHE 0.011 0.002 PHE A 96 TYR 0.011 0.001 TYR D 177 ARG 0.002 0.000 ARG C 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 152 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 100 time to evaluate : 1.722 Fit side-chains outliers start: 52 outliers final: 28 residues processed: 144 average time/residue: 1.2694 time to fit residues: 202.2380 Evaluate side-chains 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 1.688 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 20 residues processed: 8 average time/residue: 1.0062 time to fit residues: 11.1138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 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: 5.9990 chunk 82 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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: 0.8652 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 14780 Z= 0.436 Angle : 0.662 6.433 20220 Z= 0.347 Chirality : 0.051 0.152 2052 Planarity : 0.006 0.042 2548 Dihedral : 5.028 22.986 1964 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.19 % Allowed : 12.77 % 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: 0.30 (0.21), residues: 1716 helix: 1.02 (0.22), residues: 512 sheet: -0.20 (0.30), residues: 284 loop : -0.03 (0.22), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 260 HIS 0.002 0.001 HIS D 111 PHE 0.015 0.003 PHE C 109 TYR 0.015 0.002 TYR B 92 ARG 0.005 0.001 ARG B 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 152 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 104 time to evaluate : 1.523 Fit side-chains outliers start: 48 outliers final: 28 residues processed: 136 average time/residue: 1.3216 time to fit residues: 199.1797 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 20 residues processed: 8 average time/residue: 1.5010 time to fit residues: 15.1326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.0670 chunk 141 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 overall best weight: 0.9322 ------------------------------------------------------------------------------- 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: 0.8615 moved from start: 0.0489 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= 0.192 Angle : 0.532 5.920 20220 Z= 0.275 Chirality : 0.044 0.142 2052 Planarity : 0.005 0.036 2548 Dihedral : 4.477 16.764 1964 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.66 % Allowed : 13.56 % 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: 1.27 (0.23), residues: 512 sheet: -0.12 (0.29), residues: 284 loop : 0.14 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 183 HIS 0.002 0.000 HIS C 286 PHE 0.011 0.002 PHE C 96 TYR 0.010 0.001 TYR D 177 ARG 0.002 0.000 ARG A 42 *********************** 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 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 104 time to evaluate : 1.704 Fit side-chains outliers start: 40 outliers final: 36 residues processed: 136 average time/residue: 1.2210 time to fit residues: 184.8537 Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.777 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.8688 time to fit residues: 10.2406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 160 optimal weight: 0.8980 overall best weight: 1.3362 ------------------------------------------------------------------------------- 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: 0.8628 moved from start: 0.0567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14780 Z= 0.251 Angle : 0.564 6.092 20220 Z= 0.293 Chirality : 0.045 0.145 2052 Planarity : 0.005 0.037 2548 Dihedral : 4.593 16.983 1964 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % 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: 0.52 (0.21), residues: 1716 helix: 1.22 (0.23), residues: 512 sheet: -0.11 (0.30), residues: 284 loop : 0.11 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 223 HIS 0.002 0.001 HIS A 286 PHE 0.011 0.002 PHE A 96 TYR 0.011 0.001 TYR C 177 ARG 0.002 0.001 ARG A 108 *********************** 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 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.666 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 132 average time/residue: 1.1852 time to fit residues: 174.0964 Evaluate side-chains 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 104 time to evaluate : 1.550 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.6951 time to fit residues: 8.6045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 121 optimal weight: 6.9990 chunk 140 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8618 moved from start: 0.0499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14780 Z= 0.208 Angle : 0.540 5.975 20220 Z= 0.278 Chirality : 0.044 0.144 2052 Planarity : 0.005 0.036 2548 Dihedral : 4.438 16.491 1964 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.13 % Allowed : 14.10 % 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: 0.62 (0.21), residues: 1716 helix: 1.30 (0.23), residues: 512 sheet: -0.06 (0.30), residues: 284 loop : 0.17 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 183 HIS 0.001 0.001 HIS D 286 PHE 0.011 0.002 PHE A 96 TYR 0.010 0.001 TYR D 177 ARG 0.002 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 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 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.754 Fit side-chains outliers start: 32 outliers final: 32 residues processed: 140 average time/residue: 1.3426 time to fit residues: 209.3414 Evaluate side-chains 144 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.525 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 1.2374 time to fit residues: 7.5688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 15 optimal weight: 0.5980 chunk 130 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 158 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.8590 moved from start: 0.0414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14780 Z= 0.145 Angle : 0.501 5.785 20220 Z= 0.256 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.125 15.574 1964 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.13 % Allowed : 14.36 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1716 helix: 1.43 (0.23), residues: 512 sheet: 0.02 (0.30), residues: 284 loop : 0.30 (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 0.010 0.001 PHE A 96 TYR 0.008 0.001 TYR A 177 ARG 0.001 0.000 ARG C 86 *********************** REFINEMENT MACRO_CYCLE 8 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 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 100 time to evaluate : 1.632 Fit side-chains outliers start: 32 outliers final: 32 residues processed: 128 average time/residue: 1.0491 time to fit residues: 151.7799 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.734 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 1.1359 time to fit residues: 7.2950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 1.9990 chunk 158 optimal weight: 0.9980 chunk 92 optimal weight: 0.1980 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8603 moved from start: 0.0428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14780 Z= 0.178 Angle : 0.523 5.915 20220 Z= 0.268 Chirality : 0.043 0.147 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.218 16.149 1964 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.39 % Allowed : 13.83 % 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: 0.78 (0.21), residues: 1716 helix: 1.41 (0.23), residues: 512 sheet: 0.05 (0.30), residues: 284 loop : 0.28 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 223 HIS 0.001 0.000 HIS C 286 PHE 0.010 0.001 PHE A 96 TYR 0.009 0.001 TYR A 177 ARG 0.001 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 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: 36 poor density : 104 time to evaluate : 1.635 Fit side-chains outliers start: 36 outliers final: 32 residues processed: 128 average time/residue: 1.2492 time to fit residues: 177.7836 Evaluate side-chains 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.605 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 20 residues processed: 12 average time/residue: 1.0735 time to fit residues: 16.4132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 0.2980 chunk 171 optimal weight: 0.3980 chunk 157 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 chunk 145 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8592 moved from start: 0.0419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14780 Z= 0.158 Angle : 0.519 7.232 20220 Z= 0.262 Chirality : 0.043 0.145 2052 Planarity : 0.004 0.036 2548 Dihedral : 4.112 15.745 1964 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.60 % Allowed : 14.63 % 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: 0.84 (0.21), residues: 1716 helix: 1.45 (0.23), residues: 512 sheet: 0.11 (0.30), residues: 284 loop : 0.32 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 183 HIS 0.001 0.000 HIS C 286 PHE 0.010 0.001 PHE A 96 TYR 0.008 0.001 TYR B 177 ARG 0.001 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 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 124 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.550 Fit side-chains outliers start: 24 outliers final: 20 residues processed: 124 average time/residue: 1.3077 time to fit residues: 179.5977 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 20 residues processed: 0 time to fit residues: 2.1032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 0.9980 chunk 125 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.085624 restraints weight = 15763.176| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.48 r_work: 0.2774 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2645 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.0467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14780 Z= 0.186 Angle : 0.537 7.145 20220 Z= 0.272 Chirality : 0.043 0.147 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.234 16.179 1964 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.86 % Allowed : 14.10 % 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: 0.79 (0.21), residues: 1716 helix: 1.38 (0.23), residues: 512 sheet: 0.12 (0.30), residues: 284 loop : 0.29 (0.23), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 223 HIS 0.001 0.000 HIS B 286 PHE 0.010 0.001 PHE C 96 TYR 0.009 0.001 TYR B 177 ARG 0.001 0.000 ARG C 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4402.31 seconds wall clock time: 79 minutes 53.92 seconds (4793.92 seconds total)