Starting phenix.real_space_refine on Fri Feb 16 13:12:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vnr_32046/02_2024/7vnr_32046_trim_updated.pdb" } resolution = 2.8 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 3 8.98 5 S 84 5.16 5 C 9892 2.51 5 N 2620 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 82": "NH1" <-> "NH2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 130": "OE1" <-> "OE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A ARG 168": "NH1" <-> "NH2" Residue "A PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 551": "OE1" <-> "OE2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 82": "NH1" <-> "NH2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C GLU 130": "OE1" <-> "OE2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C ARG 168": "NH1" <-> "NH2" Residue "C PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 551": "OE1" <-> "OE2" Residue "C ARG 575": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E GLU 130": "OE1" <-> "OE2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 213": "NH1" <-> "NH2" Residue "E PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 551": "OE1" <-> "OE2" Residue "E GLU 563": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 82": "NH1" <-> "NH2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G GLU 130": "OE1" <-> "OE2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G ARG 168": "NH1" <-> "NH2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 551": "OE1" <-> "OE2" Residue "G GLU 563": "OE1" <-> "OE2" Residue "B GLU 139": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "H GLU 139": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15343 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "C" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "E" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "G" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2706 Classifications: {'peptide': 333} Link IDs: {'PTRANS': 6, 'TRANS': 326} Chain breaks: 2 Chain: "B" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "D" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "F" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1110 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 2, 'TRANS': 138} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 22 Unusual residues: {' K': 3, '7YV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'7YV': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.71, per 1000 atoms: 0.50 Number of scatterers: 15343 At special positions: 0 Unit cell: (120.54, 120.54, 120.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 3 19.00 S 84 16.00 O 2744 8.00 N 2620 7.00 C 9892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.40 Conformation dependent library (CDL) restraints added in 2.9 seconds 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 4 sheets defined 72.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'A' and resid 75 through 92 Processing helix chain 'A' and resid 100 through 118 Processing helix chain 'A' and resid 127 through 153 removed outlier: 3.528A pdb=" N CYS A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 5.116A pdb=" N ARG A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 235 through 260 Processing helix chain 'A' and resid 270 through 281 Processing helix chain 'A' and resid 294 through 333 removed outlier: 5.185A pdb=" N SER A 309 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Proline residue: A 314 - end of helix Processing helix chain 'A' and resid 340 through 355 Processing helix chain 'A' and resid 533 through 551 Processing helix chain 'A' and resid 558 through 585 removed outlier: 3.954A pdb=" N ILE A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 92 Processing helix chain 'C' and resid 100 through 118 Processing helix chain 'C' and resid 127 through 153 removed outlier: 3.528A pdb=" N CYS C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 171 removed outlier: 5.116A pdb=" N ARG C 171 " --> pdb=" O PHE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 189 Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 235 through 260 Processing helix chain 'C' and resid 270 through 281 Processing helix chain 'C' and resid 294 through 333 removed outlier: 5.186A pdb=" N SER C 309 " --> pdb=" O LEU C 305 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Proline residue: C 314 - end of helix Processing helix chain 'C' and resid 340 through 355 removed outlier: 3.699A pdb=" N ILE C 346 " --> pdb=" O ALA C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 553 removed outlier: 4.224A pdb=" N LEU C 553 " --> pdb=" O PHE C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 585 removed outlier: 3.694A pdb=" N ILE C 562 " --> pdb=" O VAL C 558 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 92 Processing helix chain 'E' and resid 100 through 118 Processing helix chain 'E' and resid 127 through 153 removed outlier: 3.529A pdb=" N CYS E 131 " --> pdb=" O LEU E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 171 removed outlier: 5.114A pdb=" N ARG E 171 " --> pdb=" O PHE E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 189 Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 235 through 260 Processing helix chain 'E' and resid 270 through 281 Processing helix chain 'E' and resid 294 through 334 removed outlier: 5.185A pdb=" N SER E 309 " --> pdb=" O LEU E 305 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE E 310 " --> pdb=" O LEU E 306 " (cutoff:3.500A) Proline residue: E 314 - end of helix Processing helix chain 'E' and resid 340 through 355 Processing helix chain 'E' and resid 533 through 553 removed outlier: 4.223A pdb=" N LEU E 553 " --> pdb=" O PHE E 549 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 585 Processing helix chain 'G' and resid 75 through 92 Processing helix chain 'G' and resid 100 through 118 Processing helix chain 'G' and resid 127 through 153 removed outlier: 3.529A pdb=" N CYS G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 163 through 171 removed outlier: 5.114A pdb=" N ARG G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 189 Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 235 through 260 Processing helix chain 'G' and resid 270 through 281 Processing helix chain 'G' and resid 294 through 335 removed outlier: 5.186A pdb=" N SER G 309 " --> pdb=" O LEU G 305 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N PHE G 310 " --> pdb=" O LEU G 306 " (cutoff:3.500A) Proline residue: G 314 - end of helix removed outlier: 3.924A pdb=" N PHE G 335 " --> pdb=" O ARG G 331 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 355 Processing helix chain 'G' and resid 533 through 553 removed outlier: 4.224A pdb=" N LEU G 553 " --> pdb=" O PHE G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 558 through 585 removed outlier: 3.516A pdb=" N ILE G 562 " --> pdb=" O VAL G 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 19 removed outlier: 3.605A pdb=" N PHE B 19 " --> pdb=" O ALA B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 38 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 74 Processing helix chain 'B' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE B 92 " --> pdb=" O ALA B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 111 Processing helix chain 'B' and resid 118 through 127 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'D' and resid 8 through 19 removed outlier: 3.604A pdb=" N PHE D 19 " --> pdb=" O ALA D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 38 Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 74 Processing helix chain 'D' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 111 Processing helix chain 'D' and resid 118 through 127 Processing helix chain 'D' and resid 138 through 145 Processing helix chain 'F' and resid 8 through 19 removed outlier: 3.605A pdb=" N PHE F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 74 Processing helix chain 'F' and resid 79 through 92 removed outlier: 4.072A pdb=" N PHE F 92 " --> pdb=" O ALA F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 111 Processing helix chain 'F' and resid 118 through 127 Processing helix chain 'F' and resid 138 through 145 Processing helix chain 'H' and resid 8 through 19 removed outlier: 3.605A pdb=" N PHE H 19 " --> pdb=" O ALA H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 38 Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 74 Processing helix chain 'H' and resid 79 through 92 removed outlier: 4.073A pdb=" N PHE H 92 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 111 Processing helix chain 'H' and resid 118 through 127 Processing helix chain 'H' and resid 138 through 145 Processing sheet with id= A, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= B, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= C, first strand: chain 'F' and resid 99 through 101 Processing sheet with id= D, first strand: chain 'H' and resid 99 through 101 997 hydrogen bonds defined for protein. 2991 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: 4.13 Time building geometry restraints manager: 6.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2488 1.30 - 1.43: 4295 1.43 - 1.56: 8725 1.56 - 1.69: 12 1.69 - 1.82: 144 Bond restraints: 15664 Sorted by residual: bond pdb=" C04 7YV A1101 " pdb=" C05 7YV A1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV C1101 " pdb=" C05 7YV C1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C04 7YV G1101 " pdb=" C05 7YV G1101 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " ideal model delta sigma weight residual 1.531 1.304 0.227 2.00e-02 2.50e+03 1.29e+02 ... (remaining 15659 not shown) Histogram of bond angle deviations from ideal: 92.63 - 101.11: 43 101.11 - 109.59: 1621 109.59 - 118.07: 10004 118.07 - 126.54: 9259 126.54 - 135.02: 217 Bond angle restraints: 21144 Sorted by residual: angle pdb=" C ARG G 554 " pdb=" N PRO G 555 " pdb=" CA PRO G 555 " ideal model delta sigma weight residual 119.82 114.66 5.16 9.80e-01 1.04e+00 2.78e+01 angle pdb=" N LYS A 559 " pdb=" CA LYS A 559 " pdb=" C LYS A 559 " ideal model delta sigma weight residual 111.82 105.71 6.11 1.16e+00 7.43e-01 2.77e+01 angle pdb=" N ARG A 554 " pdb=" CA ARG A 554 " pdb=" C ARG A 554 " ideal model delta sigma weight residual 109.81 121.26 -11.45 2.21e+00 2.05e-01 2.69e+01 angle pdb=" N ARG C 554 " pdb=" CA ARG C 554 " pdb=" C ARG C 554 " ideal model delta sigma weight residual 109.81 121.18 -11.37 2.21e+00 2.05e-01 2.65e+01 angle pdb=" C MET G 340 " pdb=" N PRO G 341 " pdb=" CA PRO G 341 " ideal model delta sigma weight residual 119.32 113.57 5.75 1.14e+00 7.69e-01 2.54e+01 ... (remaining 21139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 8243 17.87 - 35.75: 715 35.75 - 53.62: 242 53.62 - 71.50: 59 71.50 - 89.37: 17 Dihedral angle restraints: 9276 sinusoidal: 3800 harmonic: 5476 Sorted by residual: dihedral pdb=" C ARG C 554 " pdb=" N ARG C 554 " pdb=" CA ARG C 554 " pdb=" CB ARG C 554 " ideal model delta harmonic sigma weight residual -122.60 -133.95 11.35 0 2.50e+00 1.60e-01 2.06e+01 dihedral pdb=" N ARG C 554 " pdb=" C ARG C 554 " pdb=" CA ARG C 554 " pdb=" CB ARG C 554 " ideal model delta harmonic sigma weight residual 122.80 134.12 -11.32 0 2.50e+00 1.60e-01 2.05e+01 dihedral pdb=" N ARG G 554 " pdb=" C ARG G 554 " pdb=" CA ARG G 554 " pdb=" CB ARG G 554 " ideal model delta harmonic sigma weight residual 122.80 133.35 -10.55 0 2.50e+00 1.60e-01 1.78e+01 ... (remaining 9273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.151: 2305 0.151 - 0.302: 24 0.302 - 0.453: 1 0.453 - 0.605: 2 0.605 - 0.756: 8 Chirality restraints: 2340 Sorted by residual: chirality pdb=" C03 7YV C1101 " pdb=" C05 7YV C1101 " pdb=" C06 7YV C1101 " pdb=" C08 7YV C1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.76 2.00e-01 2.50e+01 1.43e+01 chirality pdb=" C03 7YV A1101 " pdb=" C05 7YV A1101 " pdb=" C06 7YV A1101 " pdb=" C08 7YV A1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C03 7YV E1101 " pdb=" C05 7YV E1101 " pdb=" C06 7YV E1101 " pdb=" C08 7YV E1101 " both_signs ideal model delta sigma weight residual False -3.26 -2.51 -0.75 2.00e-01 2.50e+01 1.42e+01 ... (remaining 2337 not shown) Planarity restraints: 2664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 237 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" CD GLU A 237 " 0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU A 237 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU A 237 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU E 237 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.14e+00 pdb=" CD GLU E 237 " -0.043 2.00e-02 2.50e+03 pdb=" OE1 GLU E 237 " 0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU E 237 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 237 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" CD GLU C 237 " 0.042 2.00e-02 2.50e+03 pdb=" OE1 GLU C 237 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU C 237 " -0.016 2.00e-02 2.50e+03 ... (remaining 2661 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.80: 4117 2.80 - 3.39: 18374 3.39 - 3.97: 30127 3.97 - 4.56: 41993 4.56 - 5.14: 57871 Nonbonded interactions: 152482 Sorted by model distance: nonbonded pdb=" OG1 THR B 28 " pdb=" OE1 GLU B 31 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR D 28 " pdb=" OE1 GLU D 31 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR F 28 " pdb=" OE1 GLU F 31 " model vdw 2.217 2.440 nonbonded pdb=" OG1 THR H 28 " pdb=" OE1 GLU H 31 " model vdw 2.217 2.440 nonbonded pdb=" O GLY E 221 " pdb=" N LYS E 225 " model vdw 2.229 2.520 ... (remaining 152477 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 74 through 588 or resid 1101)) selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.00 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: 5.470 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: 0.060 Extract box with map and model: 8.310 Check model and map are aligned: 0.290 Set scattering table: 0.180 Process input model: 41.540 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.110 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:10.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5226 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 : 0.011 0.235 15664 Z= 0.730 Angle : 1.008 11.454 21144 Z= 0.583 Chirality : 0.067 0.756 2340 Planarity : 0.005 0.058 2664 Dihedral : 16.106 89.373 5740 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.38 % Favored : 93.40 % Rotamer: Outliers : 5.60 % Allowed : 6.41 % Favored : 88.00 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.18), residues: 1864 helix: -0.18 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.95 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 86 HIS 0.005 0.001 HIS H 107 PHE 0.024 0.003 PHE C 251 TYR 0.020 0.002 TYR C 565 ARG 0.009 0.001 ARG E 351 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 455 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 TYR cc_start: 0.8525 (t80) cc_final: 0.8281 (t80) REVERT: A 112 CYS cc_start: 0.7776 (t) cc_final: 0.7520 (t) REVERT: A 218 ASP cc_start: 0.7690 (m-30) cc_final: 0.7252 (m-30) REVERT: A 225 LYS cc_start: 0.8875 (mttt) cc_final: 0.8624 (mttm) REVERT: A 557 ASP cc_start: 0.0512 (OUTLIER) cc_final: 0.0158 (p0) REVERT: C 218 ASP cc_start: 0.7678 (m-30) cc_final: 0.7291 (m-30) REVERT: C 225 LYS cc_start: 0.8831 (mttt) cc_final: 0.8585 (mttm) REVERT: E 130 GLU cc_start: 0.6835 (mt-10) cc_final: 0.6420 (tp30) REVERT: E 218 ASP cc_start: 0.7754 (m-30) cc_final: 0.7463 (m-30) REVERT: E 225 LYS cc_start: 0.8839 (mttt) cc_final: 0.8589 (mttm) REVERT: G 218 ASP cc_start: 0.7701 (m-30) cc_final: 0.7467 (m-30) REVERT: G 225 LYS cc_start: 0.8808 (mttt) cc_final: 0.8536 (mttm) outliers start: 90 outliers final: 17 residues processed: 514 average time/residue: 1.4696 time to fit residues: 818.0182 Evaluate side-chains 280 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 262 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 GLN Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain C residue 122 GLN Chi-restraints excluded: chain C residue 562 ILE Chi-restraints excluded: chain C residue 575 ARG Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain E residue 333 LYS Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 586 ILE Chi-restraints excluded: chain G residue 122 GLN Chi-restraints excluded: chain G residue 551 GLU Chi-restraints excluded: chain G residue 579 LEU Chi-restraints excluded: chain G residue 586 ILE Chi-restraints excluded: chain G residue 587 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 569 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 569 HIS C 580 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN G 332 GLN G 334 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5323 moved from start: 0.4290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15664 Z= 0.238 Angle : 0.806 12.952 21144 Z= 0.397 Chirality : 0.041 0.245 2340 Planarity : 0.006 0.121 2664 Dihedral : 6.494 58.360 2203 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 17.27 Ramachandran Plot: Outliers : 0.32 % Allowed : 4.56 % Favored : 95.12 % Rotamer: Outliers : 4.35 % Allowed : 19.65 % Favored : 76.00 % 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 (0.19), residues: 1864 helix: 1.02 (0.13), residues: 1420 sheet: None (None), residues: 0 loop : -1.55 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 350 HIS 0.005 0.001 HIS G 334 PHE 0.036 0.002 PHE D 89 TYR 0.027 0.001 TYR C 565 ARG 0.012 0.001 ARG A 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 325 time to evaluate : 1.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 218 ASP cc_start: 0.7554 (m-30) cc_final: 0.7334 (m-30) REVERT: A 565 TYR cc_start: 0.3731 (t80) cc_final: 0.3502 (t80) REVERT: C 139 MET cc_start: 0.7081 (tmm) cc_final: 0.6654 (mmm) REVERT: E 139 MET cc_start: 0.7053 (tmm) cc_final: 0.6609 (mmm) REVERT: G 139 MET cc_start: 0.6664 (tmm) cc_final: 0.6288 (mmm) outliers start: 70 outliers final: 31 residues processed: 352 average time/residue: 1.2729 time to fit residues: 494.3529 Evaluate side-chains 282 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 251 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain C residue 204 ARG Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain E residue 204 ARG Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 551 GLU Chi-restraints excluded: chain G residue 569 HIS Chi-restraints excluded: chain G residue 587 VAL Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain F residue 19 PHE Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 152 optimal weight: 4.9990 chunk 169 optimal weight: 20.0000 chunk 58 optimal weight: 0.0870 chunk 137 optimal weight: 10.0000 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 97 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15664 Z= 0.284 Angle : 0.760 16.898 21144 Z= 0.375 Chirality : 0.042 0.190 2340 Planarity : 0.005 0.064 2664 Dihedral : 4.673 44.831 2171 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 4.48 % Allowed : 21.14 % Favored : 74.38 % 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: 0.92 (0.19), residues: 1864 helix: 1.29 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -1.48 (0.30), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 350 HIS 0.001 0.000 HIS C 569 PHE 0.028 0.002 PHE E 169 TYR 0.027 0.001 TYR C 565 ARG 0.009 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 293 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ARG cc_start: 0.6690 (OUTLIER) cc_final: 0.5947 (mpt180) REVERT: C 139 MET cc_start: 0.7457 (tmm) cc_final: 0.7052 (mmm) REVERT: E 139 MET cc_start: 0.7456 (tmm) cc_final: 0.6998 (mmm) REVERT: G 139 MET cc_start: 0.7270 (tmm) cc_final: 0.6906 (mmm) outliers start: 72 outliers final: 28 residues processed: 328 average time/residue: 1.2486 time to fit residues: 451.3790 Evaluate side-chains 280 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 1.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ARG Chi-restraints excluded: chain A residue 217 MET Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 217 MET Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 332 GLN Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain E residue 551 GLU Chi-restraints excluded: chain E residue 569 HIS Chi-restraints excluded: chain G residue 217 MET Chi-restraints excluded: chain G residue 237 GLU Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain D residue 19 PHE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain F residue 32 LEU Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain H residue 19 PHE Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 126 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 2.9990 chunk 128 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 171 optimal weight: 5.9990 chunk 181 optimal weight: 9.9990 chunk 89 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN C 84 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 GLN G 84 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.5686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15664 Z= 0.265 Angle : 0.782 14.891 21144 Z= 0.378 Chirality : 0.041 0.195 2340 Planarity : 0.004 0.062 2664 Dihedral : 4.129 30.893 2163 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.94 % Favored : 94.85 % Rotamer: Outliers : 4.42 % Allowed : 22.45 % Favored : 73.13 % 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: 0.97 (0.19), residues: 1864 helix: 1.28 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.34 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 350 HIS 0.020 0.001 HIS E 334 PHE 0.039 0.002 PHE F 89 TYR 0.017 0.001 TYR E 147 ARG 0.013 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 295 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 139 MET cc_start: 0.7423 (tmm) cc_final: 0.7210 (ttm) REVERT: E 139 MET cc_start: 0.7445 (tmm) cc_final: 0.7163 (ttm) REVERT: G 139 MET cc_start: 0.7442 (tmm) cc_final: 0.7118 (mmm) REVERT: G 206 MET cc_start: 0.7203 (pp-130) cc_final: 0.6911 (mmp) REVERT: D 32 LEU cc_start: 0.3748 (OUTLIER) cc_final: 0.3313 (pp) REVERT: F 68 PHE cc_start: 0.3052 (t80) cc_final: 0.2651 (t80) outliers start: 71 outliers final: 26 residues processed: 328 average time/residue: 1.2187 time to fit residues: 441.1348 Evaluate side-chains 290 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 263 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 236 LYS Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain C residue 236 LYS Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 236 LYS Chi-restraints excluded: chain E residue 237 GLU Chi-restraints excluded: chain E residue 346 ILE Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain G residue 346 ILE Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 141 PHE Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 32 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 74 optimal weight: 40.0000 chunk 155 optimal weight: 20.0000 chunk 125 optimal weight: 0.7980 chunk 0 optimal weight: 50.0000 chunk 92 optimal weight: 0.9980 chunk 163 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5527 moved from start: 0.6247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 15664 Z= 0.381 Angle : 0.822 14.551 21144 Z= 0.403 Chirality : 0.043 0.273 2340 Planarity : 0.005 0.063 2664 Dihedral : 4.215 19.288 2160 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.63 % Favored : 94.15 % Rotamer: Outliers : 4.54 % Allowed : 24.88 % Favored : 70.58 % 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: 0.90 (0.19), residues: 1864 helix: 1.21 (0.13), residues: 1416 sheet: None (None), residues: 0 loop : -1.30 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 350 HIS 0.017 0.001 HIS E 334 PHE 0.033 0.002 PHE C 169 TYR 0.016 0.001 TYR A 565 ARG 0.015 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 293 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 93 ARG cc_start: 0.7959 (tmt90) cc_final: 0.7724 (tpt-90) REVERT: G 139 MET cc_start: 0.7443 (tmm) cc_final: 0.7206 (ttm) outliers start: 73 outliers final: 28 residues processed: 337 average time/residue: 1.2289 time to fit residues: 460.1634 Evaluate side-chains 283 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 255 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 236 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 80 ASP Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 126 ARG Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 115 LYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 44 optimal weight: 40.0000 chunk 181 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN C 210 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN G 122 GLN G 332 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5505 moved from start: 0.6655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 15664 Z= 0.292 Angle : 0.824 14.564 21144 Z= 0.404 Chirality : 0.043 0.227 2340 Planarity : 0.004 0.061 2664 Dihedral : 4.213 20.853 2160 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.26 % Favored : 94.53 % Rotamer: Outliers : 4.29 % Allowed : 26.93 % Favored : 68.78 % 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: 1.06 (0.19), residues: 1864 helix: 1.34 (0.13), residues: 1420 sheet: None (None), residues: 0 loop : -1.33 (0.31), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 350 HIS 0.018 0.001 HIS E 334 PHE 0.040 0.002 PHE B 68 TYR 0.014 0.001 TYR E 147 ARG 0.016 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 286 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 350 TRP cc_start: 0.3531 (OUTLIER) cc_final: 0.3230 (m100) REVERT: G 350 TRP cc_start: 0.3942 (OUTLIER) cc_final: 0.3667 (m100) outliers start: 69 outliers final: 27 residues processed: 331 average time/residue: 1.2483 time to fit residues: 454.7993 Evaluate side-chains 292 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 263 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 30.0000 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 113 optimal weight: 4.9990 chunk 110 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 overall best weight: 2.3362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 HIS A 564 GLN C 210 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 210 GLN G 122 GLN G 210 GLN ** F 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5528 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 15664 Z= 0.324 Angle : 0.871 16.748 21144 Z= 0.428 Chirality : 0.044 0.272 2340 Planarity : 0.004 0.059 2664 Dihedral : 4.316 22.492 2160 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.47 % Favored : 94.37 % Rotamer: Outliers : 3.92 % Allowed : 28.92 % Favored : 67.16 % 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: 0.97 (0.20), residues: 1864 helix: 1.31 (0.14), residues: 1416 sheet: None (None), residues: 0 loop : -1.44 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 350 HIS 0.017 0.001 HIS E 334 PHE 0.034 0.002 PHE C 169 TYR 0.018 0.001 TYR C 565 ARG 0.018 0.001 ARG H 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 285 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 546 LYS cc_start: 0.5470 (pptt) cc_final: 0.4762 (pptt) REVERT: C 554 ARG cc_start: 0.7632 (mpt180) cc_final: 0.7380 (mmm160) REVERT: E 350 TRP cc_start: 0.3724 (OUTLIER) cc_final: 0.3376 (m100) REVERT: E 547 ARG cc_start: 0.5566 (tpm-80) cc_final: 0.5180 (tpp80) REVERT: G 136 GLU cc_start: 0.1523 (OUTLIER) cc_final: 0.1175 (tt0) REVERT: G 350 TRP cc_start: 0.4209 (OUTLIER) cc_final: 0.3779 (m100) outliers start: 63 outliers final: 32 residues processed: 325 average time/residue: 1.1881 time to fit residues: 426.9510 Evaluate side-chains 293 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 258 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 338 ARG Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 107 HIS Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 chunk 108 optimal weight: 20.0000 chunk 54 optimal weight: 0.1980 chunk 35 optimal weight: 9.9990 chunk 115 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 142 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 334 HIS ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5478 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15664 Z= 0.246 Angle : 0.886 18.763 21144 Z= 0.435 Chirality : 0.043 0.236 2340 Planarity : 0.004 0.058 2664 Dihedral : 4.252 20.605 2160 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 3.23 % Allowed : 30.66 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1864 helix: 1.30 (0.14), residues: 1428 sheet: None (None), residues: 0 loop : -1.55 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 350 HIS 0.017 0.001 HIS E 334 PHE 0.034 0.002 PHE C 169 TYR 0.022 0.001 TYR C 565 ARG 0.012 0.001 ARG F 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 287 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ARG cc_start: 0.8052 (ttm-80) cc_final: 0.7826 (ttp-110) REVERT: E 136 GLU cc_start: 0.1614 (OUTLIER) cc_final: 0.1392 (tt0) REVERT: E 350 TRP cc_start: 0.3822 (OUTLIER) cc_final: 0.3577 (m100) REVERT: G 136 GLU cc_start: 0.1682 (OUTLIER) cc_final: 0.1329 (tt0) REVERT: G 350 TRP cc_start: 0.4079 (OUTLIER) cc_final: 0.3684 (m100) REVERT: H 71 MET cc_start: 0.5004 (pmm) cc_final: 0.4697 (pmm) REVERT: H 126 ARG cc_start: 0.5395 (OUTLIER) cc_final: 0.4222 (ppt170) outliers start: 52 outliers final: 20 residues processed: 318 average time/residue: 1.3060 time to fit residues: 455.8824 Evaluate side-chains 283 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 258 time to evaluate : 1.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain G residue 90 VAL Chi-restraints excluded: chain G residue 136 GLU Chi-restraints excluded: chain G residue 204 ARG Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 69 LEU Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 173 optimal weight: 2.9990 chunk 158 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 132 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 110 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 329 GLN C 332 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 210 GLN ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.7750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 15664 Z= 0.548 Angle : 0.995 18.788 21144 Z= 0.498 Chirality : 0.049 0.280 2340 Planarity : 0.005 0.070 2664 Dihedral : 4.757 27.634 2160 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 22.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.88 % Rotamer: Outliers : 3.79 % Allowed : 30.41 % Favored : 65.80 % 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: 1864 helix: 0.76 (0.13), residues: 1424 sheet: None (None), residues: 0 loop : -1.46 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 163 HIS 0.016 0.001 HIS E 334 PHE 0.034 0.003 PHE C 169 TYR 0.020 0.002 TYR C 565 ARG 0.024 0.001 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 271 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 331 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7893 (ttp-110) REVERT: E 136 GLU cc_start: 0.1501 (OUTLIER) cc_final: 0.1257 (tt0) REVERT: E 331 ARG cc_start: 0.5396 (tmt170) cc_final: 0.4254 (ttp80) REVERT: E 350 TRP cc_start: 0.4217 (OUTLIER) cc_final: 0.3914 (m100) REVERT: G 93 ARG cc_start: 0.7993 (tmt90) cc_final: 0.7773 (tmt170) outliers start: 61 outliers final: 27 residues processed: 310 average time/residue: 1.2057 time to fit residues: 413.0381 Evaluate side-chains 277 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 248 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain C residue 282 THR Chi-restraints excluded: chain C residue 346 ILE Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 282 THR Chi-restraints excluded: chain E residue 350 TRP Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 PHE Chi-restraints excluded: chain B residue 107 HIS Chi-restraints excluded: chain B residue 109 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 80 ASP Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain F residue 141 PHE Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 107 HIS Chi-restraints excluded: chain H residue 141 PHE Chi-restraints excluded: chain H residue 142 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 108 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 187 optimal weight: 9.9990 chunk 172 optimal weight: 5.9990 chunk 149 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 91 optimal weight: 0.0050 chunk 118 optimal weight: 0.8980 chunk 158 optimal weight: 20.0000 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 332 GLN ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5497 moved from start: 0.8004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15664 Z= 0.257 Angle : 0.973 15.771 21144 Z= 0.478 Chirality : 0.045 0.249 2340 Planarity : 0.004 0.057 2664 Dihedral : 4.534 25.653 2160 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.06 % Rotamer: Outliers : 1.93 % Allowed : 32.59 % Favored : 65.49 % 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 (0.19), residues: 1864 helix: 1.01 (0.14), residues: 1424 sheet: None (None), residues: 0 loop : -1.69 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP G 350 HIS 0.015 0.001 HIS E 334 PHE 0.033 0.002 PHE C 169 TYR 0.022 0.001 TYR C 565 ARG 0.015 0.001 ARG F 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3728 Ramachandran restraints generated. 1864 Oldfield, 0 Emsley, 1864 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7997 (tmt90) cc_final: 0.7789 (tmt90) REVERT: C 93 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7646 (ptm-80) REVERT: E 136 GLU cc_start: 0.1295 (OUTLIER) cc_final: 0.1075 (tt0) REVERT: E 331 ARG cc_start: 0.5198 (tmt170) cc_final: 0.4868 (tmt-80) REVERT: E 551 GLU cc_start: 0.6182 (mm-30) cc_final: 0.5755 (mm-30) REVERT: D 112 LEU cc_start: 0.5036 (OUTLIER) cc_final: 0.4736 (tm) REVERT: H 118 ASP cc_start: 0.3555 (t0) cc_final: 0.3318 (t0) outliers start: 31 outliers final: 14 residues processed: 297 average time/residue: 1.2182 time to fit residues: 399.3631 Evaluate side-chains 268 residues out of total 1608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 252 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 VAL Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain G residue 350 TRP Chi-restraints excluded: chain G residue 573 LEU Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain D residue 68 PHE Chi-restraints excluded: chain D residue 107 HIS Chi-restraints excluded: chain D residue 112 LEU Chi-restraints excluded: chain D residue 141 PHE Chi-restraints excluded: chain F residue 14 GLU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 55 VAL Chi-restraints excluded: chain H residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 45 optimal weight: 0.8980 chunk 137 optimal weight: 9.9990 chunk 22 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 131 optimal weight: 0.0980 chunk 8 optimal weight: 30.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.216817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.125922 restraints weight = 27203.651| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.84 r_work: 0.3215 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3206 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 20 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3206 r_free = 0.3206 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 31 | |-----------------------------------------------------------------------------| r_final: 0.3206 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.8189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 15664 Z= 0.259 Angle : 0.976 17.942 21144 Z= 0.478 Chirality : 0.045 0.266 2340 Planarity : 0.004 0.059 2664 Dihedral : 4.547 27.095 2160 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.36 % Favored : 94.47 % Rotamer: Outliers : 1.68 % Allowed : 32.96 % Favored : 65.36 % 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: 0.57 (0.20), residues: 1864 helix: 1.07 (0.14), residues: 1420 sheet: None (None), residues: 0 loop : -1.80 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 350 HIS 0.015 0.001 HIS E 334 PHE 0.033 0.002 PHE C 169 TYR 0.023 0.001 TYR C 565 ARG 0.014 0.001 ARG H 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7495.70 seconds wall clock time: 133 minutes 25.74 seconds (8005.74 seconds total)