Starting phenix.real_space_refine on Thu Nov 16 04:57:32 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_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_13520/11_2023/7pm4_13520_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_2023/7pm4_13520_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pm4_13520/11_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-1.21rc1-5144/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 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 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 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 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: 7.73, 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: 5.66 Conformation dependent library (CDL) restraints added in 2.4 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: 2.97 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: 3.81 Time building geometry restraints manager: 6.17 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: 7276 17.61 - 35.21: 740 35.21 - 52.82: 220 52.82 - 70.42: 76 70.42 - 88.03: 24 Dihedral angle restraints: 8336 sinusoidal: 3340 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 8333 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: 3.750 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: 18.480 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 40.440 Find NCS groups from input model: 0.820 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: 0.000 Load rotamer database and sin/cos tables:12.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.660 ------------------------------------------------------------------------------- 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 : 16.953 88.029 5124 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 *********************** 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 : 1.668 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 116 average time/residue: 1.2005 time to fit residues: 154.7788 Evaluate side-chains 108 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.708 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 2.3204 ------------------------------------------------------------------------------- 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: 0.0202 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 5.921 20220 Z= 0.267 Chirality : 0.044 0.143 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.236 16.205 1880 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 3.06 % Allowed : 13.16 % 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: 1.42 (0.23), residues: 512 sheet: 0.09 (0.29), residues: 284 loop : 0.21 (0.23), residues: 920 *********************** 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 146 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 100 time to evaluate : 1.903 Fit side-chains outliers start: 46 outliers final: 22 residues processed: 134 average time/residue: 1.2022 time to fit residues: 179.4013 Evaluate side-chains 119 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 97 time to evaluate : 1.727 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 14 residues processed: 8 average time/residue: 1.0676 time to fit residues: 11.6342 ------------------------------------------------------------------------------- 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: 0.6980 chunk 129 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 169 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.8597 moved from start: 0.0206 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= 0.165 Angle : 0.504 5.887 20220 Z= 0.258 Chirality : 0.043 0.141 2052 Planarity : 0.004 0.033 2548 Dihedral : 4.161 15.918 1880 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.72 % Allowed : 12.50 % 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: 0.82 (0.21), residues: 1716 helix: 1.44 (0.23), residues: 512 sheet: 0.14 (0.29), residues: 284 loop : 0.28 (0.23), residues: 920 *********************** 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 160 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 104 time to evaluate : 1.578 Fit side-chains outliers start: 56 outliers final: 24 residues processed: 152 average time/residue: 1.1874 time to fit residues: 200.6693 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 104 time to evaluate : 1.575 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 16 residues processed: 8 average time/residue: 1.0203 time to fit residues: 11.2716 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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: 0.8630 moved from start: 0.0498 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= 0.282 Angle : 0.576 6.154 20220 Z= 0.299 Chirality : 0.046 0.149 2052 Planarity : 0.005 0.035 2548 Dihedral : 4.565 17.135 1880 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % 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: 0.59 (0.21), residues: 1716 helix: 1.23 (0.23), residues: 512 sheet: -0.00 (0.29), residues: 284 loop : 0.15 (0.23), residues: 920 *********************** 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 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 1.775 Fit side-chains outliers start: 36 outliers final: 24 residues processed: 120 average time/residue: 1.2932 time to fit residues: 172.3706 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.613 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 20 residues processed: 8 average time/residue: 1.9840 time to fit residues: 19.1399 ------------------------------------------------------------------------------- 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: 1.9990 chunk 94 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8643 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 14780 Z= 0.346 Angle : 0.616 6.247 20220 Z= 0.321 Chirality : 0.048 0.151 2052 Planarity : 0.005 0.036 2548 Dihedral : 4.765 17.722 1880 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.93 % Allowed : 12.83 % Favored : 84.24 % 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: 0.42 (0.21), residues: 1716 helix: 1.10 (0.23), residues: 512 sheet: -0.10 (0.30), residues: 284 loop : 0.04 (0.22), residues: 920 *********************** 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 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 96 time to evaluate : 1.678 Fit side-chains outliers start: 44 outliers final: 32 residues processed: 128 average time/residue: 1.2275 time to fit residues: 174.7809 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 96 time to evaluate : 1.867 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 24 residues processed: 8 average time/residue: 1.5610 time to fit residues: 15.7087 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 41 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 chunk 160 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8594 moved from start: 0.0393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 14780 Z= 0.146 Angle : 0.499 5.813 20220 Z= 0.256 Chirality : 0.043 0.140 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.162 15.812 1880 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % 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: 0.76 (0.21), residues: 1716 helix: 1.47 (0.23), residues: 512 sheet: -0.01 (0.30), residues: 284 loop : 0.24 (0.23), residues: 920 *********************** 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 : 1.649 Fit side-chains outliers start: 32 outliers final: 32 residues processed: 136 average time/residue: 1.2448 time to fit residues: 188.2936 Evaluate side-chains 120 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 88 time to evaluate : 1.692 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 32 residues processed: 0 time to fit residues: 2.3657 ------------------------------------------------------------------------------- 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: 2.9990 chunk 94 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 66 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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: 0.8612 moved from start: 0.0418 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= 0.202 Angle : 0.533 5.996 20220 Z= 0.274 Chirality : 0.044 0.145 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.326 16.438 1880 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.66 % Allowed : 14.10 % Favored : 83.24 % 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: 0.68 (0.21), residues: 1716 helix: 1.36 (0.23), residues: 512 sheet: 0.02 (0.30), residues: 284 loop : 0.19 (0.23), residues: 920 *********************** 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 140 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.660 Fit side-chains outliers start: 40 outliers final: 36 residues processed: 132 average time/residue: 1.2703 time to fit residues: 188.4351 Evaluate side-chains 132 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 96 time to evaluate : 2.075 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 8 average time/residue: 0.8293 time to fit residues: 10.4960 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 112 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 15 optimal weight: 0.5980 chunk 130 optimal weight: 0.0070 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.0381 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= 0.151 Angle : 0.503 5.824 20220 Z= 0.257 Chirality : 0.043 0.142 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.117 15.673 1880 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % 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: 1.42 (0.23), residues: 512 sheet: 0.08 (0.29), residues: 284 loop : 0.27 (0.23), residues: 920 *********************** 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 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 104 time to evaluate : 1.655 Fit side-chains outliers start: 32 outliers final: 28 residues processed: 132 average time/residue: 1.3084 time to fit residues: 191.2378 Evaluate side-chains 128 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.1958 time to fit residues: 7.5632 ------------------------------------------------------------------------------- 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: 2.9990 chunk 158 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 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: 0.6980 chunk 153 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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: 0.8614 moved from start: 0.0450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14780 Z= 0.213 Angle : 0.541 6.026 20220 Z= 0.278 Chirality : 0.044 0.149 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.341 16.536 1880 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.39 % Allowed : 14.89 % 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: 0.68 (0.21), residues: 1716 helix: 1.32 (0.23), residues: 512 sheet: 0.05 (0.29), residues: 284 loop : 0.21 (0.23), residues: 920 *********************** 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 136 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 100 time to evaluate : 1.744 Fit side-chains outliers start: 36 outliers final: 28 residues processed: 132 average time/residue: 1.2014 time to fit residues: 177.1223 Evaluate side-chains 125 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 97 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.1511 time to fit residues: 7.2384 ------------------------------------------------------------------------------- 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: 5.9990 chunk 113 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 157 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8608 moved from start: 0.0435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14780 Z= 0.194 Angle : 0.532 5.954 20220 Z= 0.273 Chirality : 0.044 0.148 2052 Planarity : 0.004 0.035 2548 Dihedral : 4.293 16.254 1880 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.86 % Allowed : 15.69 % Favored : 82.45 % 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: 0.70 (0.21), residues: 1716 helix: 1.32 (0.23), residues: 512 sheet: 0.06 (0.29), residues: 284 loop : 0.23 (0.23), residues: 920 ********************** 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 127 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 99 time to evaluate : 1.817 Fit side-chains outliers start: 28 outliers final: 28 residues processed: 123 average time/residue: 1.1563 time to fit residues: 159.3359 Evaluate side-chains 126 residues out of total 1520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.571 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 24 residues processed: 4 average time/residue: 1.1746 time to fit residues: 7.3491 ------------------------------------------------------------------------------- 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: 0.7980 chunk 125 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 57 optimal weight: 0.0670 chunk 140 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3350 r_free = 0.3350 target = 0.116555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.086292 restraints weight = 15834.571| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 1.48 r_work: 0.2789 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.0392 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= 0.159 Angle : 0.519 7.363 20220 Z= 0.262 Chirality : 0.043 0.144 2052 Planarity : 0.004 0.034 2548 Dihedral : 4.120 15.679 1880 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.86 % Allowed : 15.43 % 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: 0.80 (0.21), residues: 1716 helix: 1.41 (0.23), residues: 512 sheet: 0.10 (0.29), residues: 284 loop : 0.29 (0.23), residues: 920 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4394.41 seconds wall clock time: 80 minutes 6.09 seconds (4806.09 seconds total)