Starting phenix.real_space_refine on Sat Dec 9 07:12:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/12_2023/7puy_13662_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/12_2023/7puy_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_13662/12_2023/7puy_13662.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/12_2023/7puy_13662.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/12_2023/7puy_13662_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7puy_13662/12_2023/7puy_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 3 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: 3 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: 3 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: 5.62, per 1000 atoms: 0.54 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: 4.72 Conformation dependent library (CDL) restraints added in 1.6 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: 1.57 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: 2.56 Time building geometry restraints manager: 4.98 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: 6384 26.47 - 52.93: 315 52.93 - 79.40: 27 79.40 - 105.87: 51 105.87 - 132.34: 9 Dihedral angle restraints: 6786 sinusoidal: 3219 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 6783 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: 0.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.910 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 29.790 Find NCS groups from input model: 0.610 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.070 ------------------------------------------------------------------------------- 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 : 18.017 132.335 4428 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 : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 6 residues processed: 294 average time/residue: 0.2481 time to fit residues: 100.3258 Evaluate side-chains 192 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 186 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0903 time to fit residues: 2.5269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 55 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- 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 131 HIS ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 HIS ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 HIS C 209 ASN ** C 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 10602 Z= 0.261 Angle : 0.712 6.952 14340 Z= 0.354 Chirality : 0.047 0.210 1728 Planarity : 0.005 0.053 1746 Dihedral : 12.459 90.786 2088 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.81 % Allowed : 11.32 % Favored : 86.87 % 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: -0.39 (0.23), residues: 1194 helix: 0.55 (0.22), residues: 489 sheet: -0.33 (0.45), residues: 138 loop : -0.90 (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 0.017 0.002 PHE A 191 TYR 0.019 0.002 TYR B 253 ARG 0.004 0.001 ARG C 256 *********************** 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 216 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 196 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 12 residues processed: 211 average time/residue: 0.2026 time to fit residues: 62.2570 Evaluate side-chains 192 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.200 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0972 time to fit residues: 3.7710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.2980 chunk 32 optimal weight: 0.7980 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: 2.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 305 HIS A 127 ASN A 209 ASN B 127 ASN B 209 ASN C 127 ASN C 146 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 10602 Z= 0.332 Angle : 0.732 8.919 14340 Z= 0.371 Chirality : 0.047 0.214 1728 Planarity : 0.005 0.057 1746 Dihedral : 9.590 59.162 2088 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.54 % Allowed : 13.13 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1194 helix: 0.39 (0.22), residues: 489 sheet: -0.25 (0.46), residues: 138 loop : -0.88 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 210 HIS 0.008 0.002 HIS B 230 PHE 0.023 0.002 PHE A 191 TYR 0.029 0.002 TYR A 253 ARG 0.004 0.001 ARG B 256 *********************** 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 229 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 12 residues processed: 218 average time/residue: 0.1988 time to fit residues: 63.1543 Evaluate side-chains 188 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0968 time to fit residues: 3.7031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 55 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10602 Z= 0.291 Angle : 0.683 7.215 14340 Z= 0.351 Chirality : 0.045 0.231 1728 Planarity : 0.005 0.061 1746 Dihedral : 8.497 52.543 2088 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.08 % Allowed : 14.76 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.23), residues: 1194 helix: 0.62 (0.22), residues: 471 sheet: -0.22 (0.45), residues: 132 loop : -0.96 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 210 HIS 0.006 0.001 HIS B 230 PHE 0.020 0.002 PHE A 191 TYR 0.019 0.002 TYR a 278 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 218 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 205 average time/residue: 0.2150 time to fit residues: 63.2821 Evaluate side-chains 185 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 176 time to evaluate : 1.221 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1169 time to fit residues: 3.5695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 0.0770 chunk 1 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 101 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN B 146 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10602 Z= 0.272 Angle : 0.663 7.170 14340 Z= 0.341 Chirality : 0.044 0.231 1728 Planarity : 0.005 0.062 1746 Dihedral : 7.726 52.706 2088 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.81 % Allowed : 17.75 % Favored : 80.43 % 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: -0.34 (0.24), residues: 1194 helix: 0.73 (0.23), residues: 471 sheet: -0.27 (0.47), residues: 132 loop : -0.97 (0.25), residues: 591 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 0.032 0.002 PHE B 191 TYR 0.016 0.002 TYR a 278 ARG 0.004 0.000 ARG a 282 *********************** 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 211 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 191 time to evaluate : 1.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 204 average time/residue: 0.2160 time to fit residues: 64.4035 Evaluate side-chains 185 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0953 time to fit residues: 2.6848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 66 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 113 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10602 Z= 0.178 Angle : 0.612 8.215 14340 Z= 0.316 Chirality : 0.043 0.255 1728 Planarity : 0.004 0.062 1746 Dihedral : 7.109 55.042 2088 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.27 % Allowed : 18.93 % Favored : 79.80 % 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: -0.17 (0.24), residues: 1194 helix: 0.99 (0.23), residues: 471 sheet: -0.40 (0.45), residues: 132 loop : -0.93 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.006 0.001 HIS B 230 PHE 0.037 0.002 PHE A 191 TYR 0.015 0.001 TYR B 94 ARG 0.004 0.000 ARG a 282 *********************** 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 210 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 196 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 203 average time/residue: 0.2206 time to fit residues: 63.8400 Evaluate side-chains 184 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.154 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0997 time to fit residues: 2.6917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 70 optimal weight: 0.3980 chunk 68 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3630 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= 0.249 Angle : 0.642 8.616 14340 Z= 0.329 Chirality : 0.043 0.243 1728 Planarity : 0.005 0.062 1746 Dihedral : 6.974 53.361 2088 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.45 % Allowed : 19.38 % Favored : 79.17 % 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: -0.21 (0.24), residues: 1194 helix: 0.97 (0.23), residues: 468 sheet: -0.46 (0.45), residues: 132 loop : -0.95 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 210 HIS 0.005 0.001 HIS C 230 PHE 0.025 0.002 PHE B 191 TYR 0.014 0.001 TYR a 278 ARG 0.006 0.000 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 204 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 197 average time/residue: 0.2111 time to fit residues: 60.2067 Evaluate side-chains 183 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 177 time to evaluate : 1.096 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1065 time to fit residues: 2.7394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.5980 chunk 76 optimal weight: 0.0050 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 ASN ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.3655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10602 Z= 0.188 Angle : 0.627 9.660 14340 Z= 0.320 Chirality : 0.042 0.249 1728 Planarity : 0.005 0.065 1746 Dihedral : 6.627 54.176 2088 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.72 % Allowed : 20.11 % Favored : 79.17 % 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: -0.17 (0.24), residues: 1194 helix: 1.05 (0.24), residues: 471 sheet: -0.58 (0.44), residues: 132 loop : -0.94 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.005 0.001 HIS B 230 PHE 0.025 0.001 PHE B 191 TYR 0.017 0.001 TYR B 94 ARG 0.006 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 198 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 190 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 191 average time/residue: 0.2173 time to fit residues: 59.6287 Evaluate side-chains 182 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 179 time to evaluate : 1.143 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1285 time to fit residues: 2.4052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 63 optimal weight: 0.0770 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN A 127 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6989 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10602 Z= 0.193 Angle : 0.629 9.849 14340 Z= 0.324 Chirality : 0.042 0.244 1728 Planarity : 0.005 0.063 1746 Dihedral : 6.376 53.062 2088 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.36 % Allowed : 20.56 % Favored : 79.08 % 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: -0.16 (0.24), residues: 1194 helix: 1.08 (0.24), residues: 471 sheet: -0.68 (0.44), residues: 132 loop : -0.93 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP c 283 HIS 0.005 0.001 HIS C 230 PHE 0.025 0.001 PHE B 191 TYR 0.015 0.001 TYR B 94 ARG 0.006 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 187 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 183 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 186 average time/residue: 0.2162 time to fit residues: 57.8399 Evaluate side-chains 175 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 92 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 390 ASN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10602 Z= 0.206 Angle : 0.627 10.012 14340 Z= 0.321 Chirality : 0.042 0.238 1728 Planarity : 0.005 0.072 1746 Dihedral : 6.212 51.956 2088 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.54 % Allowed : 20.38 % Favored : 79.08 % 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: -0.19 (0.24), residues: 1194 helix: 1.06 (0.24), residues: 471 sheet: -0.75 (0.43), residues: 132 loop : -0.94 (0.26), residues: 591 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 0.025 0.002 PHE A 191 TYR 0.019 0.001 TYR A 253 ARG 0.006 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 184 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 178 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 179 average time/residue: 0.2156 time to fit residues: 55.9629 Evaluate side-chains 180 residues out of total 1104 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 178 time to evaluate : 1.163 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1130 time to fit residues: 2.0670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 13 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 92 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 11 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 81 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 146 ASN ** 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 = 0.4219 r_free = 0.4219 target = 0.169500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.145439 restraints weight = 15896.254| |-----------------------------------------------------------------------------| r_work (start): 0.3910 rms_B_bonded: 2.30 r_work: 0.3800 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10602 Z= 0.197 Angle : 0.623 10.707 14340 Z= 0.320 Chirality : 0.042 0.234 1728 Planarity : 0.005 0.066 1746 Dihedral : 6.021 51.099 2088 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.27 % Allowed : 20.29 % Favored : 79.44 % 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: 1.07 (0.24), residues: 468 sheet: -0.74 (0.43), residues: 132 loop : -0.98 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 210 HIS 0.006 0.001 HIS A 230 PHE 0.040 0.002 PHE A 191 TYR 0.017 0.001 TYR B 94 ARG 0.006 0.000 ARG B 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.00 seconds wall clock time: 45 minutes 44.33 seconds (2744.33 seconds total)