Starting phenix.real_space_refine on Wed Feb 14 22:13:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/02_2024/7puy_13662_updated.pdb" } resolution = 3.3 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= -0.001 sd= 0.017 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 90 5.16 5 C 6576 2.51 5 N 1686 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10395 Number of models: 1 Model: "" Number of chains: 24 Chain: "a" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "b" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "c" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1535 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 4, 'TRANS': 184} Chain: "A" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "B" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "C" Number of atoms: 1745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1745 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Unusual residues: {'BDP': 1, 'XYS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "c" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.08, per 1000 atoms: 0.58 Number of scatterers: 10395 At special positions: 0 Unit cell: (86.154, 92.382, 123.522, 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 90 16.00 O 2043 8.00 N 1686 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BDP G 2 " - " XYS G 3 " " BDP K 2 " - " XYS K 3 " " BDP O 2 " - " XYS O 3 " BETA1-3 " XYS G 1 " - " BDP G 2 " " XYS K 1 " - " BDP K 2 " " XYS O 1 " - " BDP O 2 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 109 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 109 " " NAG D 1 " - " ASN A 119 " " NAG E 1 " - " ASN A 167 " " NAG F 1 " - " ASN A 79 " " NAG H 1 " - " ASN B 119 " " NAG I 1 " - " ASN B 167 " " NAG J 1 " - " ASN B 79 " " NAG L 1 " - " ASN C 119 " " NAG M 1 " - " ASN C 167 " " NAG N 1 " - " ASN C 79 " " NAG a 601 " - " ASN a 365 " " NAG a 602 " - " ASN a 373 " " NAG a 603 " - " ASN a 395 " " NAG b 601 " - " ASN b 365 " " NAG b 602 " - " ASN b 373 " " NAG b 603 " - " ASN b 395 " " NAG c 601 " - " ASN c 365 " " NAG c 602 " - " ASN c 373 " " NAG c 603 " - " ASN c 395 " Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 1.7 seconds 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2304 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 3 sheets defined 40.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'a' and resid 295 through 302 removed outlier: 4.608A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 309 through 324 Processing helix chain 'a' and resid 334 through 344 removed outlier: 5.442A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 349 through 359 Processing helix chain 'a' and resid 400 through 425 removed outlier: 3.591A pdb=" N GLU a 418 " --> pdb=" O MET a 414 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR a 419 " --> pdb=" O LEU a 415 " (cutoff:3.500A) Processing helix chain 'a' and resid 428 through 447 Processing helix chain 'b' and resid 295 through 302 removed outlier: 4.608A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) Processing helix chain 'b' and resid 309 through 324 Processing helix chain 'b' and resid 334 through 344 removed outlier: 5.444A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 349 through 359 Processing helix chain 'b' and resid 400 through 425 removed outlier: 3.591A pdb=" N GLU b 418 " --> pdb=" O MET b 414 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR b 419 " --> pdb=" O LEU b 415 " (cutoff:3.500A) Processing helix chain 'b' and resid 428 through 447 Processing helix chain 'c' and resid 295 through 302 removed outlier: 4.608A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ASN c 302 " --> pdb=" O VAL c 298 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 324 Processing helix chain 'c' and resid 334 through 344 removed outlier: 5.443A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 349 through 359 Processing helix chain 'c' and resid 400 through 425 removed outlier: 3.591A pdb=" N GLU c 418 " --> pdb=" O MET c 414 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR c 419 " --> pdb=" O LEU c 415 " (cutoff:3.500A) Processing helix chain 'c' and resid 428 through 447 Processing helix chain 'A' and resid 4 through 10 removed outlier: 3.798A pdb=" N GLN A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU A 10 " --> pdb=" O THR A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 34 Processing helix chain 'A' and resid 75 through 78 Processing helix chain 'A' and resid 120 through 125 Processing helix chain 'A' and resid 131 through 143 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.624A pdb=" N SER A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN A 247 " --> pdb=" O GLY A 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 10 removed outlier: 3.798A pdb=" N GLN B 9 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B 10 " --> pdb=" O THR B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 34 Processing helix chain 'B' and resid 75 through 78 Processing helix chain 'B' and resid 120 through 125 Processing helix chain 'B' and resid 131 through 143 Processing helix chain 'B' and resid 158 through 160 No H-bonds generated for 'chain 'B' and resid 158 through 160' Processing helix chain 'B' and resid 183 through 194 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.624A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 10 removed outlier: 3.798A pdb=" N GLN C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 10 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 34 Processing helix chain 'C' and resid 75 through 78 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 131 through 143 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.624A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR A 101 " --> pdb=" O VAL A 97 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR B 101 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 84 through 87 removed outlier: 3.622A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1098 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: 2.69 Time building geometry restraints manager: 4.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3234 1.34 - 1.46: 2640 1.46 - 1.58: 4584 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 10602 Sorted by residual: bond pdb=" C3 BDP O 2 " pdb=" O3 BDP O 2 " ideal model delta sigma weight residual 1.411 1.516 -0.105 2.00e-02 2.50e+03 2.75e+01 bond pdb=" C3 BDP K 2 " pdb=" O3 BDP K 2 " ideal model delta sigma weight residual 1.411 1.516 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" C3 BDP G 2 " pdb=" O3 BDP G 2 " ideal model delta sigma weight residual 1.411 1.515 -0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" C1 XYS G 3 " pdb=" O5 XYS G 3 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" C1 XYS O 3 " pdb=" O5 XYS O 3 " ideal model delta sigma weight residual 1.412 1.499 -0.087 2.00e-02 2.50e+03 1.89e+01 ... (remaining 10597 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.05: 160 106.05 - 113.04: 6012 113.04 - 120.03: 3581 120.03 - 127.03: 4468 127.03 - 134.02: 119 Bond angle restraints: 14340 Sorted by residual: angle pdb=" C LEU C 103 " pdb=" N GLU C 104 " pdb=" CA GLU C 104 " ideal model delta sigma weight residual 121.42 126.59 -5.17 1.43e+00 4.89e-01 1.30e+01 angle pdb=" C LEU A 103 " pdb=" N GLU A 104 " pdb=" CA GLU A 104 " ideal model delta sigma weight residual 121.42 126.57 -5.15 1.43e+00 4.89e-01 1.30e+01 angle pdb=" C LEU B 103 " pdb=" N GLU B 104 " pdb=" CA GLU B 104 " ideal model delta sigma weight residual 121.42 126.57 -5.15 1.43e+00 4.89e-01 1.30e+01 angle pdb=" CA GLU A 104 " pdb=" CB GLU A 104 " pdb=" CG GLU A 104 " ideal model delta sigma weight residual 114.10 120.25 -6.15 2.00e+00 2.50e-01 9.45e+00 angle pdb=" CA GLU C 104 " pdb=" CB GLU C 104 " pdb=" CG GLU C 104 " ideal model delta sigma weight residual 114.10 120.23 -6.13 2.00e+00 2.50e-01 9.39e+00 ... (remaining 14335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.47: 6447 26.47 - 52.93: 315 52.93 - 79.40: 27 79.40 - 105.87: 51 105.87 - 132.34: 9 Dihedral angle restraints: 6849 sinusoidal: 3282 harmonic: 3567 Sorted by residual: dihedral pdb=" CB CYS a 301 " pdb=" SG CYS a 301 " pdb=" SG CYS a 310 " pdb=" CB CYS a 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.74 -51.74 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CB CYS b 301 " pdb=" SG CYS b 301 " pdb=" SG CYS b 310 " pdb=" CB CYS b 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.71 -51.71 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CB CYS c 301 " pdb=" SG CYS c 301 " pdb=" SG CYS c 310 " pdb=" CB CYS c 310 " ideal model delta sinusoidal sigma weight residual 93.00 144.70 -51.70 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 6846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1536 0.071 - 0.141: 177 0.141 - 0.212: 12 0.212 - 0.282: 0 0.282 - 0.353: 3 Chirality restraints: 1728 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 79 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 79 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 79 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.05e+00 ... (remaining 1725 not shown) Planarity restraints: 1770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY a 429 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.78e+00 pdb=" C GLY a 429 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY a 429 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU a 430 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY c 429 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C GLY c 429 " 0.051 2.00e-02 2.50e+03 pdb=" O GLY c 429 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU c 430 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY b 429 " 0.015 2.00e-02 2.50e+03 2.92e-02 8.52e+00 pdb=" C GLY b 429 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY b 429 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU b 430 " 0.017 2.00e-02 2.50e+03 ... (remaining 1767 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 150 2.63 - 3.20: 9790 3.20 - 3.77: 16447 3.77 - 4.33: 22536 4.33 - 4.90: 36283 Nonbonded interactions: 85206 Sorted by model distance: nonbonded pdb=" O PHE C 233 " pdb=" O4 NAG c 601 " model vdw 2.067 2.440 nonbonded pdb=" OE1 GLU A 100 " pdb=" OG1 THR A 101 " model vdw 2.181 2.440 nonbonded pdb=" OE1 GLU C 100 " pdb=" OG1 THR C 101 " model vdw 2.181 2.440 nonbonded pdb=" OE1 GLU B 100 " pdb=" OG1 THR B 101 " model vdw 2.181 2.440 nonbonded pdb=" O PHE B 233 " pdb=" O4 NAG b 601 " model vdw 2.233 2.440 ... (remaining 85201 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 0.740 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: 0.000 Extract box with map and model: 4.030 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 31.160 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 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 : 0.006 0.105 10602 Z= 0.381 Angle : 0.738 6.952 14340 Z= 0.358 Chirality : 0.046 0.353 1728 Planarity : 0.005 0.039 1746 Dihedral : 17.932 132.335 4491 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.90 % Allowed : 2.72 % Favored : 95.38 % 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: -0.75 (0.22), residues: 1194 helix: 0.26 (0.23), residues: 489 sheet: -0.31 (0.43), residues: 141 loop : -1.18 (0.23), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP c 283 HIS 0.006 0.001 HIS C 93 PHE 0.018 0.001 PHE C 191 TYR 0.017 0.002 TYR C 253 ARG 0.007 0.001 ARG B 250 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 279 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 284 MET cc_start: 0.6545 (mtt) cc_final: 0.6338 (mtp) REVERT: b 323 ILE cc_start: 0.7560 (mm) cc_final: 0.7346 (mt) outliers start: 21 outliers final: 6 residues processed: 294 average time/residue: 0.2359 time to fit residues: 94.5791 Evaluate side-chains 192 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 0.0470 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.1980 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.3980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 305 HIS c 305 HIS ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10602 Z= 0.261 Angle : 0.709 7.350 14340 Z= 0.350 Chirality : 0.046 0.205 1728 Planarity : 0.004 0.054 1746 Dihedral : 13.200 98.245 2160 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.08 % Allowed : 11.41 % Favored : 86.50 % 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: -0.35 (0.23), residues: 1194 helix: 0.63 (0.23), residues: 489 sheet: -0.34 (0.45), residues: 138 loop : -0.91 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.008 0.001 HIS A 93 PHE 0.019 0.002 PHE A 191 TYR 0.017 0.002 TYR B 253 ARG 0.004 0.001 ARG C 207 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.118 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: a 410 MET cc_start: 0.6173 (mtp) cc_final: 0.5868 (mtp) REVERT: b 323 ILE cc_start: 0.7773 (mm) cc_final: 0.7551 (mt) REVERT: c 312 MET cc_start: 0.7763 (mmm) cc_final: 0.7090 (mmp) REVERT: B 191 PHE cc_start: 0.6581 (m-80) cc_final: 0.6115 (t80) outliers start: 23 outliers final: 15 residues processed: 208 average time/residue: 0.2049 time to fit residues: 61.6141 Evaluate side-chains 194 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 179 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 263 THR Chi-restraints excluded: chain b residue 263 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 280 LEU Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 359 MET Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.5980 chunk 88 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 85 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 305 HIS A 92 HIS A 131 HIS A 209 ASN B 131 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 ASN C 131 HIS C 146 ASN C 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10602 Z= 0.230 Angle : 0.657 7.406 14340 Z= 0.331 Chirality : 0.046 0.282 1728 Planarity : 0.005 0.062 1746 Dihedral : 9.385 60.656 2159 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.81 % Allowed : 12.32 % Favored : 84.87 % 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: -0.23 (0.24), residues: 1194 helix: 0.72 (0.23), residues: 495 sheet: -0.57 (0.45), residues: 144 loop : -0.78 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.006 0.001 HIS B 93 PHE 0.018 0.002 PHE A 191 TYR 0.018 0.001 TYR A 253 ARG 0.002 0.000 ARG C 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.209 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: a 410 MET cc_start: 0.6232 (mtp) cc_final: 0.5926 (mtp) REVERT: b 323 ILE cc_start: 0.7859 (mm) cc_final: 0.7644 (mt) REVERT: b 332 MET cc_start: 0.7371 (mmp) cc_final: 0.7026 (mmm) REVERT: c 312 MET cc_start: 0.7663 (mmm) cc_final: 0.7067 (mmp) REVERT: c 428 LEU cc_start: 0.6849 (mp) cc_final: 0.6623 (mp) REVERT: B 15 ILE cc_start: 0.8514 (tp) cc_final: 0.8091 (tp) REVERT: B 146 ASN cc_start: 0.7882 (m-40) cc_final: 0.7651 (m-40) outliers start: 31 outliers final: 17 residues processed: 219 average time/residue: 0.2083 time to fit residues: 65.6227 Evaluate side-chains 194 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 359 MET Chi-restraints excluded: chain b residue 431 VAL Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 0.0070 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN B 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10602 Z= 0.244 Angle : 0.668 10.569 14340 Z= 0.341 Chirality : 0.045 0.272 1728 Planarity : 0.005 0.061 1746 Dihedral : 7.929 53.374 2158 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.44 % Allowed : 14.58 % Favored : 81.97 % 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: -0.31 (0.24), residues: 1194 helix: 0.61 (0.23), residues: 495 sheet: -0.64 (0.45), residues: 144 loop : -0.75 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.008 0.001 HIS B 230 PHE 0.040 0.002 PHE B 191 TYR 0.014 0.001 TYR B 94 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 199 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7264 (t0) cc_final: 0.6999 (t0) REVERT: a 410 MET cc_start: 0.6281 (mtp) cc_final: 0.6019 (mtp) REVERT: b 323 ILE cc_start: 0.7869 (mm) cc_final: 0.7622 (mt) REVERT: b 332 MET cc_start: 0.7592 (mmp) cc_final: 0.7119 (mmt) REVERT: c 312 MET cc_start: 0.7613 (mmm) cc_final: 0.7059 (mmp) REVERT: A 134 MET cc_start: 0.8350 (tpp) cc_final: 0.8150 (tpt) REVERT: B 146 ASN cc_start: 0.7929 (m-40) cc_final: 0.7608 (m-40) outliers start: 38 outliers final: 22 residues processed: 222 average time/residue: 0.2070 time to fit residues: 65.8141 Evaluate side-chains 204 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 182 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 3.9990 chunk 1 optimal weight: 0.0170 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.7624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 146 ASN C 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 10602 Z= 0.324 Angle : 0.709 10.704 14340 Z= 0.364 Chirality : 0.045 0.207 1728 Planarity : 0.005 0.062 1746 Dihedral : 7.658 52.224 2158 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.26 % Allowed : 15.76 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.24), residues: 1194 helix: 0.65 (0.23), residues: 471 sheet: -0.51 (0.47), residues: 132 loop : -0.91 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 210 HIS 0.007 0.001 HIS B 230 PHE 0.029 0.002 PHE B 191 TYR 0.019 0.002 TYR a 278 ARG 0.005 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 198 time to evaluate : 1.274 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: a 390 ASN cc_start: 0.7193 (t0) cc_final: 0.6783 (t0) REVERT: a 410 MET cc_start: 0.6310 (mtp) cc_final: 0.5981 (mtp) REVERT: b 332 MET cc_start: 0.7606 (mmp) cc_final: 0.7020 (mmt) REVERT: b 390 ASN cc_start: 0.7431 (t0) cc_final: 0.6966 (t0) REVERT: c 312 MET cc_start: 0.7664 (mmm) cc_final: 0.7092 (mmp) REVERT: A 16 GLU cc_start: 0.5937 (pm20) cc_final: 0.5644 (pm20) REVERT: A 164 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7398 (p) REVERT: C 207 ARG cc_start: 0.4729 (mmm160) cc_final: 0.4469 (mmm160) outliers start: 47 outliers final: 30 residues processed: 229 average time/residue: 0.1961 time to fit residues: 65.7090 Evaluate side-chains 213 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 364 CYS Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 364 CYS Chi-restraints excluded: chain c residue 392 SER Chi-restraints excluded: chain c residue 428 LEU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN B 127 ASN C 127 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7023 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10602 Z= 0.199 Angle : 0.629 9.755 14340 Z= 0.324 Chirality : 0.042 0.237 1728 Planarity : 0.005 0.063 1746 Dihedral : 7.119 53.804 2158 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.81 % Allowed : 17.48 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.24 (0.24), residues: 1194 helix: 0.85 (0.23), residues: 474 sheet: -0.57 (0.45), residues: 132 loop : -0.87 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS C 230 PHE 0.039 0.002 PHE A 191 TYR 0.016 0.001 TYR a 278 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 199 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7017 (t0) cc_final: 0.6711 (t0) REVERT: a 410 MET cc_start: 0.6282 (mtp) cc_final: 0.6040 (mtp) REVERT: b 332 MET cc_start: 0.7605 (mmp) cc_final: 0.7206 (mmt) REVERT: b 390 ASN cc_start: 0.7562 (t0) cc_final: 0.7090 (t0) REVERT: c 312 MET cc_start: 0.7640 (mmm) cc_final: 0.7275 (mmm) REVERT: A 16 GLU cc_start: 0.5880 (pm20) cc_final: 0.5621 (pm20) REVERT: A 80 MET cc_start: 0.4963 (mmp) cc_final: 0.4607 (mmp) REVERT: A 164 VAL cc_start: 0.7475 (t) cc_final: 0.7259 (p) REVERT: A 191 PHE cc_start: 0.6795 (t80) cc_final: 0.6402 (t80) REVERT: B 134 MET cc_start: 0.7964 (mmm) cc_final: 0.7639 (tpt) outliers start: 31 outliers final: 19 residues processed: 218 average time/residue: 0.2094 time to fit residues: 65.9553 Evaluate side-chains 203 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 184 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 364 CYS Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain c residue 428 LEU Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 112 optimal weight: 0.4980 chunk 70 optimal weight: 0.2980 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10602 Z= 0.190 Angle : 0.624 12.209 14340 Z= 0.320 Chirality : 0.042 0.240 1728 Planarity : 0.005 0.063 1746 Dihedral : 6.725 53.561 2158 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.63 % Allowed : 18.21 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.15 (0.24), residues: 1194 helix: 1.01 (0.24), residues: 468 sheet: -0.68 (0.44), residues: 132 loop : -0.83 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS C 230 PHE 0.034 0.002 PHE A 191 TYR 0.013 0.001 TYR a 278 ARG 0.005 0.001 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 193 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7100 (t0) cc_final: 0.6792 (t0) REVERT: a 410 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.6053 (mtp) REVERT: b 332 MET cc_start: 0.7553 (mmp) cc_final: 0.7136 (mmt) REVERT: b 390 ASN cc_start: 0.7525 (t0) cc_final: 0.7067 (t0) REVERT: c 312 MET cc_start: 0.7591 (mmm) cc_final: 0.6952 (mmp) REVERT: A 164 VAL cc_start: 0.7447 (t) cc_final: 0.7223 (p) REVERT: B 134 MET cc_start: 0.7931 (mmm) cc_final: 0.7619 (tpt) REVERT: B 146 ASN cc_start: 0.8027 (m110) cc_final: 0.7763 (m110) outliers start: 29 outliers final: 21 residues processed: 211 average time/residue: 0.2136 time to fit residues: 65.3147 Evaluate side-chains 204 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 385 CYS Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 192 MET Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 76 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN C 218 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10602 Z= 0.224 Angle : 0.632 9.303 14340 Z= 0.324 Chirality : 0.043 0.239 1728 Planarity : 0.005 0.067 1746 Dihedral : 6.613 52.251 2158 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.45 % Allowed : 19.02 % Favored : 78.53 % 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: -0.20 (0.24), residues: 1194 helix: 1.01 (0.24), residues: 468 sheet: -0.34 (0.48), residues: 102 loop : -0.98 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.006 0.001 HIS C 230 PHE 0.040 0.002 PHE A 191 TYR 0.012 0.002 TYR c 278 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 181 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7124 (t0) cc_final: 0.6813 (t0) REVERT: a 410 MET cc_start: 0.6264 (mtp) cc_final: 0.6040 (mtp) REVERT: b 332 MET cc_start: 0.7624 (mmp) cc_final: 0.7181 (mmt) REVERT: b 390 ASN cc_start: 0.7556 (t0) cc_final: 0.7081 (t0) REVERT: c 312 MET cc_start: 0.7620 (mmm) cc_final: 0.7277 (mmm) REVERT: A 16 GLU cc_start: 0.5917 (pm20) cc_final: 0.5694 (pm20) REVERT: B 134 MET cc_start: 0.7995 (mmm) cc_final: 0.7682 (tpt) REVERT: B 146 ASN cc_start: 0.7969 (m110) cc_final: 0.7606 (m-40) outliers start: 27 outliers final: 18 residues processed: 200 average time/residue: 0.2003 time to fit residues: 58.0427 Evaluate side-chains 193 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 175 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN C 127 ASN C 146 ASN C 218 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10602 Z= 0.235 Angle : 0.640 8.840 14340 Z= 0.329 Chirality : 0.043 0.221 1728 Planarity : 0.005 0.065 1746 Dihedral : 6.497 51.098 2158 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 2.72 % Allowed : 18.93 % Favored : 78.35 % 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: -0.32 (0.24), residues: 1194 helix: 0.77 (0.23), residues: 483 sheet: -0.47 (0.47), residues: 102 loop : -0.95 (0.25), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.005 0.001 HIS A 230 PHE 0.036 0.002 PHE A 191 TYR 0.011 0.001 TYR a 278 ARG 0.005 0.000 ARG B 193 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7181 (t0) cc_final: 0.6864 (t0) REVERT: a 410 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.6057 (mtp) REVERT: b 332 MET cc_start: 0.7702 (mmp) cc_final: 0.7217 (mmt) REVERT: b 390 ASN cc_start: 0.7599 (t0) cc_final: 0.7168 (t0) REVERT: b 425 LYS cc_start: 0.7647 (mttp) cc_final: 0.7439 (mtpp) REVERT: c 312 MET cc_start: 0.7624 (mmm) cc_final: 0.7060 (mmp) REVERT: A 16 GLU cc_start: 0.5942 (pm20) cc_final: 0.5711 (pm20) REVERT: B 134 MET cc_start: 0.8042 (mmm) cc_final: 0.7740 (tpt) outliers start: 30 outliers final: 24 residues processed: 207 average time/residue: 0.2111 time to fit residues: 63.0277 Evaluate side-chains 204 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 179 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 358 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 358 ILE Chi-restraints excluded: chain A residue 4 ILE Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 223 GLN Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 4 ILE Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 223 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 116 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 92 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.0040 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 335 GLN ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN C 127 ASN C 146 ASN C 218 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10602 Z= 0.180 Angle : 0.628 10.532 14340 Z= 0.319 Chirality : 0.043 0.361 1728 Planarity : 0.005 0.065 1746 Dihedral : 6.165 51.508 2158 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.99 % Allowed : 20.11 % Favored : 77.90 % 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: -0.26 (0.24), residues: 1194 helix: 0.86 (0.24), residues: 486 sheet: -0.42 (0.47), residues: 102 loop : -0.97 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 210 HIS 0.005 0.001 HIS C 230 PHE 0.033 0.002 PHE A 191 TYR 0.013 0.001 TYR B 94 ARG 0.005 0.000 ARG B 193 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2388 Ramachandran restraints generated. 1194 Oldfield, 0 Emsley, 1194 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 390 ASN cc_start: 0.7113 (t0) cc_final: 0.6822 (t0) REVERT: a 410 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.6037 (mtp) REVERT: b 332 MET cc_start: 0.7600 (mmp) cc_final: 0.7191 (mmt) REVERT: b 390 ASN cc_start: 0.7436 (t0) cc_final: 0.6978 (m110) REVERT: b 425 LYS cc_start: 0.7582 (mttp) cc_final: 0.7356 (mtpp) REVERT: c 312 MET cc_start: 0.7477 (mmm) cc_final: 0.6999 (mmp) REVERT: A 16 GLU cc_start: 0.5905 (pm20) cc_final: 0.5695 (pm20) REVERT: B 134 MET cc_start: 0.7869 (mmm) cc_final: 0.7576 (tpt) outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 0.2091 time to fit residues: 60.8392 Evaluate side-chains 194 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 180 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 410 MET Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 430 LEU Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 192 MET Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 85 optimal weight: 0.0670 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 0.0060 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.171951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.149669 restraints weight = 15515.570| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.11 r_work: 0.3829 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3686 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10602 Z= 0.174 Angle : 0.635 13.193 14340 Z= 0.321 Chirality : 0.042 0.412 1728 Planarity : 0.005 0.063 1746 Dihedral : 5.919 50.259 2154 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.72 % Allowed : 20.11 % Favored : 78.17 % 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: -0.22 (0.24), residues: 1194 helix: 0.89 (0.24), residues: 486 sheet: -0.48 (0.47), residues: 102 loop : -0.92 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.006 0.001 HIS C 93 PHE 0.034 0.001 PHE A 191 TYR 0.013 0.001 TYR B 94 ARG 0.005 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.22 seconds wall clock time: 46 minutes 2.57 seconds (2762.57 seconds total)