Starting phenix.real_space_refine on Fri Feb 16 06:56:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6o_23702/02_2024/7m6o_23702_updated.pdb" } resolution = 2.84 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 9555 2.51 5 N 2380 2.21 5 O 2635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 2893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2893 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 16, 'TRANS': 340} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'NAG': 1, 'TCI': 1} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.13, per 1000 atoms: 0.55 Number of scatterers: 14670 At special positions: 0 Unit cell: (93.16, 91.8, 137.36, 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 100 16.00 O 2635 8.00 N 2380 7.00 C 9555 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 162 " - pdb=" SG CYS A 176 " distance=2.04 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 176 " distance=2.04 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 176 " distance=2.04 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 176 " distance=2.04 Simple disulfide: pdb=" SG CYS E 162 " - pdb=" SG CYS E 176 " distance=2.04 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 62 " " NAG B 802 " - " ASN B 62 " " NAG C 802 " - " ASN C 62 " " NAG D 802 " - " ASN D 62 " " NAG E 802 " - " ASN E 62 " Time building additional restraints: 5.62 Conformation dependent library (CDL) restraints added in 2.8 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 20 sheets defined 36.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.598A pdb=" N MET A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 263 removed outlier: 3.725A pdb=" N ILE A 249 " --> pdb=" O GLY A 245 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 274 through 294 Processing helix chain 'A' and resid 306 through 339 removed outlier: 3.679A pdb=" N LEU A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 441 Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.598A pdb=" N MET B 42 " --> pdb=" O LEU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 263 removed outlier: 3.726A pdb=" N ILE B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE B 253 " --> pdb=" O ILE B 249 " (cutoff:3.500A) Proline residue: B 254 - end of helix Processing helix chain 'B' and resid 274 through 294 Processing helix chain 'B' and resid 306 through 339 removed outlier: 3.679A pdb=" N LEU B 322 " --> pdb=" O VAL B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 441 Proline residue: B 419 - end of helix Processing helix chain 'C' and resid 34 through 42 removed outlier: 3.598A pdb=" N MET C 42 " --> pdb=" O LEU C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 245 through 263 removed outlier: 3.726A pdb=" N ILE C 249 " --> pdb=" O GLY C 245 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE C 253 " --> pdb=" O ILE C 249 " (cutoff:3.500A) Proline residue: C 254 - end of helix Processing helix chain 'C' and resid 274 through 294 Processing helix chain 'C' and resid 306 through 339 removed outlier: 3.678A pdb=" N LEU C 322 " --> pdb=" O VAL C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 441 Proline residue: C 419 - end of helix Processing helix chain 'D' and resid 34 through 42 removed outlier: 3.598A pdb=" N MET D 42 " --> pdb=" O LEU D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 263 removed outlier: 3.725A pdb=" N ILE D 249 " --> pdb=" O GLY D 245 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ILE D 253 " --> pdb=" O ILE D 249 " (cutoff:3.500A) Proline residue: D 254 - end of helix Processing helix chain 'D' and resid 274 through 294 Processing helix chain 'D' and resid 306 through 339 removed outlier: 3.679A pdb=" N LEU D 322 " --> pdb=" O VAL D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 441 Proline residue: D 419 - end of helix Processing helix chain 'E' and resid 34 through 42 removed outlier: 3.598A pdb=" N MET E 42 " --> pdb=" O LEU E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 245 through 263 removed outlier: 3.725A pdb=" N ILE E 249 " --> pdb=" O GLY E 245 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Proline residue: E 254 - end of helix Processing helix chain 'E' and resid 274 through 294 Processing helix chain 'E' and resid 306 through 339 removed outlier: 3.679A pdb=" N LEU E 322 " --> pdb=" O VAL E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 396 through 441 Proline residue: E 419 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 192 through 194 removed outlier: 5.889A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 67 through 69 Processing sheet with id= C, first strand: chain 'A' and resid 106 through 108 Processing sheet with id= D, first strand: chain 'A' and resid 173 through 181 Processing sheet with id= E, first strand: chain 'B' and resid 192 through 194 removed outlier: 5.890A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 67 through 69 Processing sheet with id= G, first strand: chain 'B' and resid 106 through 108 Processing sheet with id= H, first strand: chain 'B' and resid 173 through 181 Processing sheet with id= I, first strand: chain 'C' and resid 192 through 194 removed outlier: 5.890A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 67 through 69 Processing sheet with id= K, first strand: chain 'C' and resid 106 through 108 Processing sheet with id= L, first strand: chain 'C' and resid 173 through 181 Processing sheet with id= M, first strand: chain 'D' and resid 192 through 194 removed outlier: 5.890A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 67 through 69 Processing sheet with id= O, first strand: chain 'D' and resid 106 through 108 Processing sheet with id= P, first strand: chain 'D' and resid 173 through 181 Processing sheet with id= Q, first strand: chain 'E' and resid 192 through 194 removed outlier: 5.890A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 5.162A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 67 through 69 Processing sheet with id= S, first strand: chain 'E' and resid 106 through 108 Processing sheet with id= T, first strand: chain 'E' and resid 173 through 181 680 hydrogen bonds defined for protein. 2025 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.08 Time building geometry restraints manager: 6.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4325 1.34 - 1.46: 3271 1.46 - 1.58: 7264 1.58 - 1.70: 0 1.70 - 1.82: 170 Bond restraints: 15030 Sorted by residual: bond pdb=" SD MET B 287 " pdb=" CE MET B 287 " ideal model delta sigma weight residual 1.791 1.729 0.062 2.50e-02 1.60e+03 6.07e+00 bond pdb=" SD MET E 287 " pdb=" CE MET E 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 6.03e+00 bond pdb=" SD MET D 287 " pdb=" CE MET D 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.96e+00 bond pdb=" SD MET A 287 " pdb=" CE MET A 287 " ideal model delta sigma weight residual 1.791 1.730 0.061 2.50e-02 1.60e+03 5.92e+00 bond pdb=" SD MET C 287 " pdb=" CE MET C 287 " ideal model delta sigma weight residual 1.791 1.731 0.060 2.50e-02 1.60e+03 5.84e+00 ... (remaining 15025 not shown) Histogram of bond angle deviations from ideal: 95.03 - 102.89: 131 102.89 - 110.74: 4539 110.74 - 118.60: 7264 118.60 - 126.46: 8236 126.46 - 134.31: 220 Bond angle restraints: 20390 Sorted by residual: angle pdb=" CA TRP E 263 " pdb=" CB TRP E 263 " pdb=" CG TRP E 263 " ideal model delta sigma weight residual 113.60 124.11 -10.51 1.90e+00 2.77e-01 3.06e+01 angle pdb=" CA TRP A 263 " pdb=" CB TRP A 263 " pdb=" CG TRP A 263 " ideal model delta sigma weight residual 113.60 124.08 -10.48 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP B 263 " pdb=" CB TRP B 263 " pdb=" CG TRP B 263 " ideal model delta sigma weight residual 113.60 124.07 -10.47 1.90e+00 2.77e-01 3.04e+01 angle pdb=" CA TRP C 263 " pdb=" CB TRP C 263 " pdb=" CG TRP C 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 angle pdb=" CA TRP D 263 " pdb=" CB TRP D 263 " pdb=" CG TRP D 263 " ideal model delta sigma weight residual 113.60 124.06 -10.46 1.90e+00 2.77e-01 3.03e+01 ... (remaining 20385 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.73: 8385 16.73 - 33.46: 610 33.46 - 50.19: 90 50.19 - 66.92: 25 66.92 - 83.65: 10 Dihedral angle restraints: 9120 sinusoidal: 3840 harmonic: 5280 Sorted by residual: dihedral pdb=" N PHE E 418 " pdb=" C PHE E 418 " pdb=" CA PHE E 418 " pdb=" CB PHE E 418 " ideal model delta harmonic sigma weight residual 122.80 132.07 -9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CA PHE A 418 " pdb=" CB PHE A 418 " ideal model delta harmonic sigma weight residual 122.80 132.06 -9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" N PHE D 418 " pdb=" C PHE D 418 " pdb=" CA PHE D 418 " pdb=" CB PHE D 418 " ideal model delta harmonic sigma weight residual 122.80 132.05 -9.25 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 9117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 1813 0.096 - 0.191: 406 0.191 - 0.287: 41 0.287 - 0.383: 20 0.383 - 0.478: 10 Chirality restraints: 2290 Sorted by residual: chirality pdb=" CB VAL D 264 " pdb=" CA VAL D 264 " pdb=" CG1 VAL D 264 " pdb=" CG2 VAL D 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB VAL C 264 " pdb=" CA VAL C 264 " pdb=" CG1 VAL C 264 " pdb=" CG2 VAL C 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.48 2.00e-01 2.50e+01 5.65e+00 chirality pdb=" CB VAL E 264 " pdb=" CA VAL E 264 " pdb=" CG1 VAL E 264 " pdb=" CG2 VAL E 264 " both_signs ideal model delta sigma weight residual False -2.63 -2.15 -0.47 2.00e-01 2.50e+01 5.63e+00 ... (remaining 2287 not shown) Planarity restraints: 2540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 267 " 0.040 2.00e-02 2.50e+03 2.34e-02 1.37e+01 pdb=" CG TRP C 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP C 267 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP C 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP C 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP C 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP D 267 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP D 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP D 267 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 267 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 267 " 0.040 2.00e-02 2.50e+03 2.33e-02 1.36e+01 pdb=" CG TRP E 267 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP E 267 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP E 267 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E 267 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP E 267 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP E 267 " -0.025 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 267 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 267 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP E 267 " 0.015 2.00e-02 2.50e+03 ... (remaining 2537 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 594 2.72 - 3.26: 13771 3.26 - 3.81: 21846 3.81 - 4.35: 26995 4.35 - 4.90: 45553 Nonbonded interactions: 108759 Sorted by model distance: nonbonded pdb=" OD2 ASP D 110 " pdb=" OG SER D 112 " model vdw 2.171 2.440 nonbonded pdb=" OD2 ASP E 110 " pdb=" OG SER E 112 " model vdw 2.171 2.440 nonbonded pdb=" OD2 ASP B 110 " pdb=" OG SER B 112 " model vdw 2.172 2.440 nonbonded pdb=" OD2 ASP C 110 " pdb=" OG SER C 112 " model vdw 2.172 2.440 nonbonded pdb=" OD2 ASP A 110 " pdb=" OG SER A 112 " model vdw 2.172 2.440 ... (remaining 108754 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' and resid 32 through 442) selection = (chain 'B' and resid 32 through 442) selection = (chain 'C' and resid 32 through 442) selection = (chain 'D' and resid 32 through 442) selection = (chain 'E' and resid 32 through 442) } 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: 3.690 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: 14.060 Check model and map are aligned: 0.210 Set scattering table: 0.170 Process input model: 40.450 Find NCS groups from input model: 0.990 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 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 : 0.009 0.117 15030 Z= 0.576 Angle : 1.376 12.416 20390 Z= 0.778 Chirality : 0.085 0.478 2290 Planarity : 0.009 0.076 2535 Dihedral : 12.009 83.653 5675 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % 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 (0.19), residues: 1765 helix: 1.57 (0.19), residues: 625 sheet: 0.35 (0.27), residues: 370 loop : -2.07 (0.19), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.005 TRP C 267 HIS 0.007 0.003 HIS B 133 PHE 0.035 0.005 PHE C 72 TYR 0.050 0.005 TYR B 325 ARG 0.010 0.001 ARG D 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.846 Fit side-chains REVERT: B 257 LEU cc_start: 0.9144 (tt) cc_final: 0.8923 (tp) REVERT: B 401 LYS cc_start: 0.8469 (mptt) cc_final: 0.7980 (mttp) REVERT: E 401 LYS cc_start: 0.8352 (mptt) cc_final: 0.8080 (tptt) outliers start: 0 outliers final: 1 residues processed: 266 average time/residue: 1.5017 time to fit residues: 433.3817 Evaluate side-chains 137 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 136 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 137 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 158 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN B 85 ASN B 290 GLN C 85 ASN D 85 ASN D 290 GLN E 85 ASN E 201 GLN E 290 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15030 Z= 0.267 Angle : 0.695 7.882 20390 Z= 0.372 Chirality : 0.046 0.165 2290 Planarity : 0.005 0.050 2535 Dihedral : 6.535 72.605 2187 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.32 % Allowed : 13.73 % Favored : 83.95 % 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: 0.07 (0.19), residues: 1765 helix: 2.15 (0.20), residues: 630 sheet: 0.84 (0.26), residues: 375 loop : -2.37 (0.18), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 118 HIS 0.004 0.001 HIS A 335 PHE 0.021 0.002 PHE D 319 TYR 0.019 0.002 TYR E 433 ARG 0.004 0.001 ARG C 409 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 151 time to evaluate : 1.815 Fit side-chains REVERT: B 285 LEU cc_start: 0.9274 (tt) cc_final: 0.8979 (tp) REVERT: C 270 MET cc_start: 0.7649 (OUTLIER) cc_final: 0.7446 (mtp) outliers start: 37 outliers final: 17 residues processed: 177 average time/residue: 1.3063 time to fit residues: 254.8053 Evaluate side-chains 142 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 GLU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 270 MET Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 423 LEU Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 290 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 157 optimal weight: 0.9980 chunk 54 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 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 290 GLN C 290 GLN D 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15030 Z= 0.227 Angle : 0.623 9.917 20390 Z= 0.333 Chirality : 0.044 0.151 2290 Planarity : 0.004 0.044 2535 Dihedral : 6.218 80.993 2185 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.76 % Allowed : 14.80 % 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: 0.23 (0.19), residues: 1765 helix: 2.17 (0.20), residues: 630 sheet: 1.11 (0.26), residues: 380 loop : -2.29 (0.18), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 263 HIS 0.003 0.001 HIS C 335 PHE 0.017 0.002 PHE C 319 TYR 0.018 0.002 TYR E 433 ARG 0.003 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 123 time to evaluate : 2.118 Fit side-chains REVERT: A 287 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: B 285 LEU cc_start: 0.9244 (tt) cc_final: 0.8957 (tp) REVERT: C 410 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8995 (pt) REVERT: E 287 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8121 (ttm) outliers start: 44 outliers final: 24 residues processed: 159 average time/residue: 1.3355 time to fit residues: 234.7607 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 287 MET Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 chunk 82 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN C 290 GLN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15030 Z= 0.186 Angle : 0.585 11.854 20390 Z= 0.308 Chirality : 0.043 0.148 2290 Planarity : 0.004 0.042 2535 Dihedral : 6.226 84.144 2185 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.13 % Allowed : 15.36 % Favored : 81.50 % 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: 0.41 (0.19), residues: 1765 helix: 2.22 (0.20), residues: 630 sheet: 1.30 (0.26), residues: 380 loop : -2.15 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 PHE 0.013 0.001 PHE E 428 TYR 0.015 0.001 TYR B 433 ARG 0.002 0.000 ARG D 220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 132 time to evaluate : 1.810 Fit side-chains REVERT: B 285 LEU cc_start: 0.9257 (tt) cc_final: 0.9010 (tp) REVERT: C 287 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8815 (ttt) REVERT: C 410 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8979 (pt) outliers start: 50 outliers final: 18 residues processed: 171 average time/residue: 1.2054 time to fit residues: 228.5082 Evaluate side-chains 140 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 120 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 287 MET Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 126 ASN Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 0.5980 chunk 96 optimal weight: 9.9990 chunk 2 optimal weight: 0.0570 chunk 125 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 116 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 GLN C 290 GLN ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 15030 Z= 0.241 Angle : 0.601 11.753 20390 Z= 0.318 Chirality : 0.044 0.148 2290 Planarity : 0.004 0.038 2535 Dihedral : 6.275 86.201 2185 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.39 % Allowed : 15.67 % Favored : 79.94 % 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: 0.39 (0.20), residues: 1765 helix: 2.24 (0.20), residues: 635 sheet: 1.12 (0.26), residues: 380 loop : -2.12 (0.19), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 118 HIS 0.003 0.001 HIS C 335 PHE 0.016 0.002 PHE E 428 TYR 0.015 0.002 TYR E 433 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 119 time to evaluate : 1.792 Fit side-chains REVERT: A 287 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8103 (tmm) REVERT: B 285 LEU cc_start: 0.9224 (tt) cc_final: 0.8991 (tp) REVERT: C 410 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8923 (pt) outliers start: 70 outliers final: 43 residues processed: 169 average time/residue: 1.2105 time to fit residues: 226.1074 Evaluate side-chains 164 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 119 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 126 ASN Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 320 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 431 ILE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 126 ASN Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 32 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 32 MET Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 32 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 169 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 78 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15030 Z= 0.166 Angle : 0.559 8.376 20390 Z= 0.295 Chirality : 0.043 0.156 2290 Planarity : 0.003 0.035 2535 Dihedral : 6.083 88.825 2185 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.01 % Allowed : 17.18 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.20), residues: 1765 helix: 2.31 (0.20), residues: 635 sheet: 1.23 (0.26), residues: 375 loop : -2.02 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 310 HIS 0.003 0.001 HIS C 335 PHE 0.014 0.001 PHE E 428 TYR 0.014 0.001 TYR D 433 ARG 0.003 0.000 ARG E 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 121 time to evaluate : 1.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 285 LEU cc_start: 0.9197 (tt) cc_final: 0.8996 (tp) REVERT: C 113 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7758 (pmm) REVERT: C 410 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8897 (pt) outliers start: 48 outliers final: 19 residues processed: 155 average time/residue: 1.2464 time to fit residues: 213.4889 Evaluate side-chains 139 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 102 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15030 Z= 0.230 Angle : 0.583 8.108 20390 Z= 0.309 Chirality : 0.043 0.149 2290 Planarity : 0.003 0.032 2535 Dihedral : 6.007 89.183 2185 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.07 % Allowed : 17.43 % Favored : 79.50 % 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: 0.47 (0.20), residues: 1765 helix: 2.31 (0.20), residues: 635 sheet: 1.12 (0.26), residues: 375 loop : -2.02 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 92 HIS 0.003 0.001 HIS C 335 PHE 0.014 0.002 PHE E 428 TYR 0.014 0.002 TYR A 433 ARG 0.003 0.000 ARG A 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 121 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7356 (pmm) REVERT: A 287 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.7994 (tmm) REVERT: B 285 LEU cc_start: 0.9191 (tt) cc_final: 0.8903 (tp) REVERT: B 287 MET cc_start: 0.9050 (tpp) cc_final: 0.8704 (tpp) REVERT: C 410 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8894 (pt) REVERT: D 113 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7424 (pmm) outliers start: 49 outliers final: 32 residues processed: 158 average time/residue: 1.2789 time to fit residues: 223.3133 Evaluate side-chains 155 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 119 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 MET Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 289 THR Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 126 ASN Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 410 ILE Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 279 LEU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 50 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 107 optimal weight: 0.0070 chunk 114 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 132 optimal weight: 0.2980 chunk 153 optimal weight: 0.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15030 Z= 0.154 Angle : 0.560 8.264 20390 Z= 0.295 Chirality : 0.043 0.173 2290 Planarity : 0.003 0.032 2535 Dihedral : 5.830 89.705 2185 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.51 % Allowed : 18.18 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.20), residues: 1765 helix: 2.31 (0.20), residues: 635 sheet: 1.20 (0.26), residues: 375 loop : -1.97 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 310 HIS 0.003 0.001 HIS C 335 PHE 0.011 0.001 PHE B 319 TYR 0.015 0.001 TYR D 433 ARG 0.003 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 128 time to evaluate : 1.782 Fit side-chains revert: symmetry clash REVERT: A 113 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7333 (pmm) REVERT: A 287 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7944 (tmm) REVERT: B 287 MET cc_start: 0.9049 (tpp) cc_final: 0.8652 (tpp) REVERT: D 113 MET cc_start: 0.8237 (OUTLIER) cc_final: 0.7418 (pmm) outliers start: 40 outliers final: 21 residues processed: 158 average time/residue: 1.3544 time to fit residues: 235.3636 Evaluate side-chains 145 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 121 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 3.9990 chunk 147 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 142 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 156 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15030 Z= 0.163 Angle : 0.573 10.330 20390 Z= 0.298 Chirality : 0.043 0.168 2290 Planarity : 0.003 0.033 2535 Dihedral : 5.708 89.623 2185 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.45 % Allowed : 18.87 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.20), residues: 1765 helix: 2.22 (0.20), residues: 635 sheet: 1.25 (0.26), residues: 375 loop : -1.96 (0.19), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 310 HIS 0.003 0.001 HIS C 335 PHE 0.016 0.001 PHE E 428 TYR 0.013 0.001 TYR C 433 ARG 0.004 0.000 ARG E 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 126 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7360 (pmm) REVERT: A 190 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8672 (tm) REVERT: A 287 MET cc_start: 0.8777 (OUTLIER) cc_final: 0.7920 (tmm) REVERT: D 113 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7400 (pmm) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 1.4235 time to fit residues: 248.4072 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 187 MET Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 115 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15030 Z= 0.195 Angle : 0.591 10.016 20390 Z= 0.307 Chirality : 0.043 0.166 2290 Planarity : 0.003 0.033 2535 Dihedral : 5.660 89.526 2185 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.38 % Allowed : 19.37 % Favored : 78.24 % 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: 0.46 (0.20), residues: 1765 helix: 2.17 (0.20), residues: 635 sheet: 1.26 (0.27), residues: 370 loop : -1.97 (0.19), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 263 HIS 0.003 0.001 HIS C 335 PHE 0.012 0.001 PHE B 319 TYR 0.013 0.001 TYR A 433 ARG 0.004 0.000 ARG E 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 122 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7390 (pmm) REVERT: A 190 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8721 (tm) REVERT: A 287 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7884 (tmm) REVERT: D 113 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7358 (pmm) REVERT: D 287 MET cc_start: 0.9154 (mmm) cc_final: 0.8928 (tpp) outliers start: 38 outliers final: 23 residues processed: 152 average time/residue: 1.2914 time to fit residues: 217.1617 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 LEU Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 156 ILE Chi-restraints excluded: chain B residue 181 GLU Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain C residue 150 VAL Chi-restraints excluded: chain C residue 181 GLU Chi-restraints excluded: chain C residue 289 THR Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 181 GLU Chi-restraints excluded: chain D residue 289 THR Chi-restraints excluded: chain D residue 416 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 181 GLU Chi-restraints excluded: chain E residue 289 THR Chi-restraints excluded: chain E residue 320 SER Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 416 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.5980 chunk 42 optimal weight: 0.0170 chunk 128 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 142 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 122 optimal weight: 0.6980 overall best weight: 0.4428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 290 GLN ** B 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 290 GLN ** E 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.095666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.066856 restraints weight = 35595.548| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.49 r_work: 0.2910 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15030 Z= 0.158 Angle : 0.579 9.774 20390 Z= 0.297 Chirality : 0.043 0.168 2290 Planarity : 0.003 0.032 2535 Dihedral : 5.478 88.313 2185 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.57 % Allowed : 20.06 % Favored : 78.37 % 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: 0.55 (0.20), residues: 1765 helix: 2.16 (0.20), residues: 635 sheet: 1.13 (0.26), residues: 390 loop : -1.81 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 194 HIS 0.003 0.001 HIS C 335 PHE 0.013 0.001 PHE E 428 TYR 0.012 0.001 TYR C 433 ARG 0.007 0.000 ARG A 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4862.05 seconds wall clock time: 87 minutes 37.38 seconds (5257.38 seconds total)