Starting phenix.real_space_refine on Sat Mar 16 01:17:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/03_2024/7wui_32836_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3658 atoms to isotropic. 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 62 5.16 5 C 6168 2.51 5 N 1652 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 268": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "S PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 609": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9666 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 1905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1905 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "R" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1985 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 241} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "S" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1703 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 8, 'TRANS': 211} Chain breaks: 4 Chain: "L" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 87 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4PH:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 5.88, per 1000 atoms: 0.61 Number of scatterers: 9666 At special positions: 0 Unit cell: (118, 112, 97, 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 62 16.00 O 1784 8.00 N 1652 7.00 C 6168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.95 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.58 Simple disulfide: pdb=" SG CYS R 686 " - pdb=" SG CYS R 770 " distance=2.52 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.89 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.34 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 2.3 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 15 sheets defined 29.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 15 through 38 removed outlier: 3.943A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 60 removed outlier: 3.771A pdb=" N VAL A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 267 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.863A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 removed outlier: 3.872A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 9 through 20 Processing helix chain 'G' and resid 30 through 33 No H-bonds generated for 'chain 'G' and resid 30 through 33' Processing helix chain 'G' and resid 35 through 42 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'R' and resid 617 through 643 removed outlier: 3.738A pdb=" N ILE R 623 " --> pdb=" O ALA R 619 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N THR R 624 " --> pdb=" O LEU R 620 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL R 637 " --> pdb=" O ILE R 633 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR R 638 " --> pdb=" O PHE R 634 " (cutoff:3.500A) Processing helix chain 'R' and resid 646 through 650 removed outlier: 4.055A pdb=" N ARG R 650 " --> pdb=" O LYS R 647 " (cutoff:3.500A) Processing helix chain 'R' and resid 652 through 679 removed outlier: 3.836A pdb=" N ILE R 670 " --> pdb=" O LEU R 666 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA R 678 " --> pdb=" O ASP R 674 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU R 679 " --> pdb=" O SER R 675 " (cutoff:3.500A) Processing helix chain 'R' and resid 683 through 715 removed outlier: 3.781A pdb=" N ALA R 688 " --> pdb=" O GLY R 684 " (cutoff:3.500A) Processing helix chain 'R' and resid 726 through 734 removed outlier: 3.887A pdb=" N VAL R 733 " --> pdb=" O LYS R 729 " (cutoff:3.500A) Processing helix chain 'R' and resid 736 through 746 Processing helix chain 'R' and resid 750 through 752 No H-bonds generated for 'chain 'R' and resid 750 through 752' Processing helix chain 'R' and resid 775 through 781 Processing helix chain 'R' and resid 783 through 791 Processing helix chain 'R' and resid 794 through 809 removed outlier: 3.783A pdb=" N ILE R 798 " --> pdb=" O VAL R 794 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL R 799 " --> pdb=" O SER R 795 " (cutoff:3.500A) Processing helix chain 'R' and resid 824 through 833 removed outlier: 4.305A pdb=" N PHE R 832 " --> pdb=" O ALA R 828 " (cutoff:3.500A) Processing helix chain 'R' and resid 837 through 843 removed outlier: 4.123A pdb=" N ALA R 841 " --> pdb=" O TRP R 838 " (cutoff:3.500A) Processing helix chain 'R' and resid 850 through 860 removed outlier: 3.637A pdb=" N TYR R 854 " --> pdb=" O VAL R 850 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 871 Processing helix chain 'R' and resid 876 through 882 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 360 through 363 removed outlier: 5.703A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 88 through 90 removed outlier: 4.143A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 115 removed outlier: 3.669A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 145 through 151 removed outlier: 4.117A pdb=" N TYR B 145 " --> pdb=" O GLY B 162 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.805A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.493A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.606A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 52 removed outlier: 6.358A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 93 through 95 removed outlier: 5.386A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 3 through 6 Processing sheet with id= L, first strand: chain 'S' and resid 92 through 95 removed outlier: 5.661A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'S' and resid 68 through 73 Processing sheet with id= N, first strand: chain 'S' and resid 156 through 160 Processing sheet with id= O, first strand: chain 'S' and resid 174 through 179 343 hydrogen bonds defined for protein. 966 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: 2.96 Time building geometry restraints manager: 4.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1549 1.30 - 1.43: 2702 1.43 - 1.56: 5522 1.56 - 1.68: 6 1.68 - 1.81: 89 Bond restraints: 9868 Sorted by residual: bond pdb=" CG 4PH L 601 " pdb=" CD2 4PH L 601 " ideal model delta sigma weight residual 1.392 1.535 -0.143 2.00e-02 2.50e+03 5.08e+01 bond pdb=" CG 4PH L 601 " pdb=" CD1 4PH L 601 " ideal model delta sigma weight residual 1.394 1.533 -0.139 2.00e-02 2.50e+03 4.83e+01 bond pdb=" CE1 4PH L 601 " pdb=" CZ 4PH L 601 " ideal model delta sigma weight residual 1.394 1.532 -0.138 2.00e-02 2.50e+03 4.78e+01 bond pdb=" CD1 4PH L 601 " pdb=" CE1 4PH L 601 " ideal model delta sigma weight residual 1.387 1.524 -0.137 2.00e-02 2.50e+03 4.71e+01 bond pdb=" CE2 4PH L 601 " pdb=" CZ 4PH L 601 " ideal model delta sigma weight residual 1.392 1.529 -0.137 2.00e-02 2.50e+03 4.69e+01 ... (remaining 9863 not shown) Histogram of bond angle deviations from ideal: 97.99 - 105.22: 134 105.22 - 112.45: 4768 112.45 - 119.67: 3566 119.67 - 126.90: 4765 126.90 - 134.13: 116 Bond angle restraints: 13349 Sorted by residual: angle pdb=" N VAL R 783 " pdb=" CA VAL R 783 " pdb=" C VAL R 783 " ideal model delta sigma weight residual 110.53 122.95 -12.42 9.40e-01 1.13e+00 1.75e+02 angle pdb=" N GLY R 784 " pdb=" CA GLY R 784 " pdb=" C GLY R 784 " ideal model delta sigma weight residual 112.50 105.34 7.16 1.16e+00 7.43e-01 3.81e+01 angle pdb=" N LYS A 24 " pdb=" CA LYS A 24 " pdb=" C LYS A 24 " ideal model delta sigma weight residual 111.28 105.03 6.25 1.09e+00 8.42e-01 3.29e+01 angle pdb=" N CYS N 107 " pdb=" CA CYS N 107 " pdb=" C CYS N 107 " ideal model delta sigma weight residual 109.11 116.99 -7.88 1.42e+00 4.96e-01 3.08e+01 angle pdb=" N ALA N 92 " pdb=" CA ALA N 92 " pdb=" C ALA N 92 " ideal model delta sigma weight residual 109.96 118.06 -8.10 1.58e+00 4.01e-01 2.63e+01 ... (remaining 13344 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5235 17.82 - 35.64: 491 35.64 - 53.46: 71 53.46 - 71.27: 10 71.27 - 89.09: 11 Dihedral angle restraints: 5818 sinusoidal: 2278 harmonic: 3540 Sorted by residual: dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 154.76 25.24 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA LYS R 717 " pdb=" C LYS R 717 " pdb=" N VAL R 718 " pdb=" CA VAL R 718 " ideal model delta harmonic sigma weight residual 180.00 -155.60 -24.40 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ASP B 186 " pdb=" C ASP B 186 " pdb=" N VAL B 187 " pdb=" CA VAL B 187 " ideal model delta harmonic sigma weight residual -180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 ... (remaining 5815 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1205 0.080 - 0.161: 247 0.161 - 0.241: 32 0.241 - 0.322: 9 0.322 - 0.402: 1 Chirality restraints: 1494 Sorted by residual: chirality pdb=" CA VAL R 783 " pdb=" N VAL R 783 " pdb=" C VAL R 783 " pdb=" CB VAL R 783 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB VAL R 699 " pdb=" CA VAL R 699 " pdb=" CG1 VAL R 699 " pdb=" CG2 VAL R 699 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CB THR S 115 " pdb=" CA THR S 115 " pdb=" OG1 THR S 115 " pdb=" CG2 THR S 115 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.19e+00 ... (remaining 1491 not shown) Planarity restraints: 1685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB 4PH L 601 " -0.020 2.00e-02 2.50e+03 2.04e-01 8.31e+02 pdb=" CG 4PH L 601 " 0.296 2.00e-02 2.50e+03 pdb=" CD1 4PH L 601 " -0.189 2.00e-02 2.50e+03 pdb=" CD2 4PH L 601 " -0.185 2.00e-02 2.50e+03 pdb=" CE1 4PH L 601 " 0.157 2.00e-02 2.50e+03 pdb=" CE2 4PH L 601 " 0.156 2.00e-02 2.50e+03 pdb=" CZ 4PH L 601 " -0.334 2.00e-02 2.50e+03 pdb=" C33 4PH L 601 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 47 " -0.017 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C THR B 47 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 47 " -0.025 2.00e-02 2.50e+03 pdb=" N ARG B 48 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 283 " -0.016 2.00e-02 2.50e+03 3.30e-02 1.09e+01 pdb=" C ARG B 283 " 0.057 2.00e-02 2.50e+03 pdb=" O ARG B 283 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 284 " -0.019 2.00e-02 2.50e+03 ... (remaining 1682 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1319 2.76 - 3.29: 9630 3.29 - 3.83: 17825 3.83 - 4.36: 21932 4.36 - 4.90: 35399 Nonbonded interactions: 86105 Sorted by model distance: nonbonded pdb=" OH TYR R 625 " pdb=" OG SER R 675 " model vdw 2.221 2.440 nonbonded pdb=" CE MET S 93 " pdb=" OH TYR S 95 " model vdw 2.226 3.460 nonbonded pdb=" CD1 ILE R 687 " pdb=" O TYR R 753 " model vdw 2.227 3.460 nonbonded pdb=" O ARG N 98 " pdb=" OH TYR N 115 " model vdw 2.228 2.440 nonbonded pdb=" SD MET S 93 " pdb=" OH TYR S 95 " model vdw 2.240 2.800 ... (remaining 86100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.670 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 31.810 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6250 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 : 0.007 0.143 9868 Z= 0.458 Angle : 1.115 12.420 13349 Z= 0.638 Chirality : 0.068 0.402 1494 Planarity : 0.009 0.204 1685 Dihedral : 13.956 89.093 3523 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 25.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 0.29 % Allowed : 2.59 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.22), residues: 1190 helix: -1.75 (0.24), residues: 347 sheet: -2.00 (0.28), residues: 265 loop : -1.59 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP A 281 HIS 0.023 0.004 HIS B 266 PHE 0.040 0.004 PHE B 241 TYR 0.026 0.003 TYR A 358 ARG 0.017 0.001 ARG N 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 209 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 392 GLU cc_start: 0.6913 (mm-30) cc_final: 0.6649 (mm-30) REVERT: B 289 TYR cc_start: 0.6934 (m-80) cc_final: 0.6620 (m-80) REVERT: B 329 THR cc_start: 0.7459 (p) cc_final: 0.7104 (p) REVERT: R 683 ARG cc_start: 0.6995 (OUTLIER) cc_final: 0.6081 (tpt90) REVERT: S 43 LYS cc_start: 0.7389 (ttmt) cc_final: 0.6909 (tptt) outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.2169 time to fit residues: 63.7361 Evaluate side-chains 167 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 683 ARG Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN N 31 ASN R 860 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6592 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9868 Z= 0.253 Angle : 0.624 8.980 13349 Z= 0.330 Chirality : 0.044 0.172 1494 Planarity : 0.005 0.046 1685 Dihedral : 5.880 44.661 1339 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.82 % Allowed : 9.29 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.24), residues: 1190 helix: -0.60 (0.27), residues: 353 sheet: -1.80 (0.29), residues: 279 loop : -1.25 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 703 HIS 0.007 0.002 HIS B 225 PHE 0.020 0.002 PHE N 108 TYR 0.021 0.002 TYR B 264 ARG 0.006 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 199 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 ARG cc_start: 0.7668 (mtm-85) cc_final: 0.7384 (mtm-85) REVERT: B 122 SER cc_start: 0.7569 (p) cc_final: 0.7341 (t) REVERT: B 134 ARG cc_start: 0.6352 (ptp-170) cc_final: 0.5958 (ptm160) REVERT: B 297 TRP cc_start: 0.8270 (m100) cc_final: 0.7915 (m100) REVERT: R 621 THR cc_start: 0.7087 (m) cc_final: 0.6874 (m) REVERT: R 652 TYR cc_start: 0.7617 (m-10) cc_final: 0.7242 (m-10) REVERT: R 658 ILE cc_start: 0.7478 (mt) cc_final: 0.7148 (tt) REVERT: R 731 CYS cc_start: 0.5596 (t) cc_final: 0.5294 (t) REVERT: R 853 MET cc_start: 0.6803 (mmt) cc_final: 0.6371 (mmp) REVERT: S 156 SER cc_start: 0.6946 (m) cc_final: 0.6625 (p) outliers start: 19 outliers final: 13 residues processed: 211 average time/residue: 0.2033 time to fit residues: 60.9004 Evaluate side-chains 189 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 176 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.2980 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 294 GLN A 384 GLN B 125 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 668 ASN R 752 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9868 Z= 0.238 Angle : 0.575 9.974 13349 Z= 0.306 Chirality : 0.043 0.187 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.478 41.378 1335 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.97 % Allowed : 12.26 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.24), residues: 1190 helix: -0.20 (0.27), residues: 354 sheet: -1.74 (0.29), residues: 271 loop : -1.05 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 99 HIS 0.009 0.002 HIS B 225 PHE 0.018 0.002 PHE N 108 TYR 0.012 0.002 TYR A 391 ARG 0.006 0.000 ARG L 609 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 130 GLU cc_start: 0.6037 (mp0) cc_final: 0.5724 (mp0) REVERT: B 134 ARG cc_start: 0.6456 (ptp-170) cc_final: 0.6015 (ptm160) REVERT: B 297 TRP cc_start: 0.8435 (m100) cc_final: 0.8024 (m100) REVERT: N 74 ASN cc_start: 0.6476 (m-40) cc_final: 0.6258 (m-40) REVERT: R 621 THR cc_start: 0.7187 (m) cc_final: 0.6853 (m) REVERT: R 652 TYR cc_start: 0.7515 (m-10) cc_final: 0.7129 (m-10) REVERT: R 658 ILE cc_start: 0.7290 (mt) cc_final: 0.7064 (tt) REVERT: R 717 LYS cc_start: 0.7079 (tmtt) cc_final: 0.6846 (tmtt) REVERT: S 156 SER cc_start: 0.7246 (m) cc_final: 0.6931 (p) outliers start: 31 outliers final: 21 residues processed: 223 average time/residue: 0.2250 time to fit residues: 68.9801 Evaluate side-chains 220 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 232 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.1980 chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 103 optimal weight: 0.0570 chunk 31 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 362 HIS A 384 GLN B 16 ASN B 17 GLN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 167 HIS ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9868 Z= 0.220 Angle : 0.556 6.075 13349 Z= 0.296 Chirality : 0.043 0.187 1494 Planarity : 0.004 0.044 1685 Dihedral : 5.329 43.854 1335 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.07 % Allowed : 14.56 % Favored : 82.38 % 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: -1.37 (0.24), residues: 1190 helix: 0.05 (0.27), residues: 354 sheet: -1.83 (0.29), residues: 271 loop : -0.92 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.010 0.002 HIS B 183 PHE 0.016 0.002 PHE A 212 TYR 0.015 0.002 TYR A 391 ARG 0.007 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 210 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.7855 (m) cc_final: 0.7466 (p) REVERT: B 130 GLU cc_start: 0.6096 (mp0) cc_final: 0.5837 (mp0) REVERT: B 134 ARG cc_start: 0.6612 (ptp-170) cc_final: 0.6186 (ptm160) REVERT: B 290 ASP cc_start: 0.6866 (m-30) cc_final: 0.6475 (m-30) REVERT: B 297 TRP cc_start: 0.8397 (m100) cc_final: 0.8073 (m100) REVERT: N 80 TYR cc_start: 0.7218 (m-80) cc_final: 0.6498 (m-80) REVERT: R 621 THR cc_start: 0.7032 (m) cc_final: 0.6729 (m) REVERT: R 652 TYR cc_start: 0.7530 (m-10) cc_final: 0.7208 (m-10) REVERT: R 717 LYS cc_start: 0.7129 (tmtt) cc_final: 0.6832 (tmtt) REVERT: S 156 SER cc_start: 0.7127 (m) cc_final: 0.6802 (p) REVERT: S 192 MET cc_start: 0.3715 (mpp) cc_final: 0.3049 (mpp) REVERT: S 214 LEU cc_start: 0.5918 (tp) cc_final: 0.4939 (tp) outliers start: 32 outliers final: 25 residues processed: 226 average time/residue: 0.2232 time to fit residues: 70.1679 Evaluate side-chains 222 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 731 CYS Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 140 MET Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 232 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 0.2980 chunk 1 optimal weight: 0.7980 chunk 86 optimal weight: 0.0670 chunk 47 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 0 optimal weight: 0.6980 chunk 59 optimal weight: 0.2980 chunk 104 optimal weight: 0.8980 chunk 29 optimal weight: 0.0870 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9868 Z= 0.173 Angle : 0.531 7.202 13349 Z= 0.282 Chirality : 0.042 0.194 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.150 46.232 1335 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 21.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.35 % Allowed : 16.19 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.24), residues: 1190 helix: 0.31 (0.27), residues: 353 sheet: -1.69 (0.28), residues: 280 loop : -0.90 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 281 HIS 0.012 0.002 HIS A 220 PHE 0.015 0.001 PHE A 212 TYR 0.018 0.001 TYR A 391 ARG 0.007 0.000 ARG S 180 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 202 time to evaluate : 1.049 Fit side-chains REVERT: A 392 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6681 (mt-10) REVERT: B 130 GLU cc_start: 0.6165 (mp0) cc_final: 0.5963 (mp0) REVERT: B 134 ARG cc_start: 0.6629 (ptp-170) cc_final: 0.6220 (ptm160) REVERT: B 220 GLN cc_start: 0.7809 (tt0) cc_final: 0.7475 (tt0) REVERT: B 297 TRP cc_start: 0.8237 (m100) cc_final: 0.7947 (m100) REVERT: N 80 TYR cc_start: 0.7241 (m-80) cc_final: 0.6442 (m-80) REVERT: R 621 THR cc_start: 0.6837 (m) cc_final: 0.6575 (m) REVERT: R 652 TYR cc_start: 0.7578 (m-10) cc_final: 0.7185 (m-10) REVERT: R 717 LYS cc_start: 0.7032 (tmtt) cc_final: 0.6696 (tmtt) REVERT: S 100 ILE cc_start: 0.8000 (tt) cc_final: 0.7576 (tt) REVERT: S 156 SER cc_start: 0.7014 (m) cc_final: 0.6708 (p) REVERT: S 192 MET cc_start: 0.3725 (mpp) cc_final: 0.3057 (mpp) outliers start: 35 outliers final: 23 residues processed: 218 average time/residue: 0.2050 time to fit residues: 63.7350 Evaluate side-chains 208 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 185 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 635 LEU Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 731 CYS Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 68 optimal weight: 0.3980 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9868 Z= 0.233 Angle : 0.555 6.402 13349 Z= 0.295 Chirality : 0.043 0.219 1494 Planarity : 0.004 0.043 1685 Dihedral : 5.249 47.545 1335 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 22.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.35 % Allowed : 16.57 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.25), residues: 1190 helix: 0.37 (0.27), residues: 354 sheet: -1.68 (0.29), residues: 274 loop : -0.81 (0.28), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.008 0.002 HIS A 362 PHE 0.017 0.002 PHE A 212 TYR 0.018 0.002 TYR A 358 ARG 0.006 0.000 ARG S 180 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 205 time to evaluate : 1.132 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.7751 (m) cc_final: 0.7405 (p) REVERT: A 311 TYR cc_start: 0.6376 (m-10) cc_final: 0.6102 (m-10) REVERT: B 134 ARG cc_start: 0.6761 (ptp-170) cc_final: 0.6413 (ptm160) REVERT: B 284 LEU cc_start: 0.7398 (tt) cc_final: 0.7144 (tt) REVERT: B 297 TRP cc_start: 0.8332 (m100) cc_final: 0.8129 (m100) REVERT: G 50 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8237 (mp) REVERT: N 80 TYR cc_start: 0.7281 (m-80) cc_final: 0.6465 (m-80) REVERT: R 649 ARG cc_start: 0.7175 (mtp180) cc_final: 0.6888 (mpp80) REVERT: R 652 TYR cc_start: 0.7616 (m-10) cc_final: 0.7269 (m-10) REVERT: R 717 LYS cc_start: 0.7261 (tmtt) cc_final: 0.6928 (tmtt) REVERT: S 100 ILE cc_start: 0.8040 (tt) cc_final: 0.7653 (tt) REVERT: S 156 SER cc_start: 0.7330 (m) cc_final: 0.6968 (p) REVERT: S 192 MET cc_start: 0.3503 (mpp) cc_final: 0.2878 (mpp) REVERT: S 231 GLN cc_start: 0.8064 (pm20) cc_final: 0.7740 (pm20) outliers start: 35 outliers final: 23 residues processed: 226 average time/residue: 0.1921 time to fit residues: 62.4065 Evaluate side-chains 214 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 190 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 657 LEU Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 65 optimal weight: 0.0670 chunk 97 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 0.7980 chunk 72 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6760 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9868 Z= 0.226 Angle : 0.561 11.854 13349 Z= 0.294 Chirality : 0.042 0.208 1494 Planarity : 0.004 0.041 1685 Dihedral : 5.256 49.193 1335 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.78 % Allowed : 17.72 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.25), residues: 1190 helix: 0.39 (0.27), residues: 352 sheet: -1.68 (0.28), residues: 274 loop : -0.78 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.008 0.002 HIS A 362 PHE 0.015 0.002 PHE A 212 TYR 0.013 0.002 TYR B 111 ARG 0.006 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 197 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 275 SER cc_start: 0.7702 (m) cc_final: 0.7372 (p) REVERT: A 311 TYR cc_start: 0.6339 (m-10) cc_final: 0.6020 (m-10) REVERT: B 134 ARG cc_start: 0.6807 (ptp-170) cc_final: 0.6597 (ptm160) REVERT: B 183 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6401 (m170) REVERT: B 284 LEU cc_start: 0.7369 (tt) cc_final: 0.7098 (tt) REVERT: B 297 TRP cc_start: 0.8385 (m100) cc_final: 0.8136 (m100) REVERT: N 80 TYR cc_start: 0.7284 (m-80) cc_final: 0.6481 (m-80) REVERT: R 652 TYR cc_start: 0.7602 (m-10) cc_final: 0.7315 (m-10) REVERT: R 717 LYS cc_start: 0.7292 (tmtt) cc_final: 0.6920 (tmtt) REVERT: S 100 ILE cc_start: 0.8033 (tt) cc_final: 0.7626 (tt) REVERT: S 156 SER cc_start: 0.7350 (m) cc_final: 0.6953 (p) REVERT: S 192 MET cc_start: 0.3435 (mpp) cc_final: 0.2783 (mpp) outliers start: 29 outliers final: 22 residues processed: 217 average time/residue: 0.1945 time to fit residues: 61.3691 Evaluate side-chains 214 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 747 THR Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 22 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 105 optimal weight: 7.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.4002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9868 Z= 0.215 Angle : 0.552 5.997 13349 Z= 0.292 Chirality : 0.043 0.213 1494 Planarity : 0.004 0.041 1685 Dihedral : 5.307 51.206 1335 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.07 % Allowed : 17.82 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.25), residues: 1190 helix: 0.39 (0.28), residues: 352 sheet: -1.63 (0.29), residues: 274 loop : -0.76 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.007 0.002 HIS B 225 PHE 0.017 0.002 PHE A 212 TYR 0.018 0.002 TYR A 358 ARG 0.006 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 184 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 311 TYR cc_start: 0.6266 (m-10) cc_final: 0.5894 (m-10) REVERT: B 134 ARG cc_start: 0.6836 (ptp-170) cc_final: 0.6622 (ptm160) REVERT: B 183 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6386 (m170) REVERT: B 284 LEU cc_start: 0.7268 (tt) cc_final: 0.7060 (tt) REVERT: B 297 TRP cc_start: 0.8368 (m100) cc_final: 0.8121 (m100) REVERT: B 325 MET cc_start: 0.7379 (tpp) cc_final: 0.6958 (tpp) REVERT: N 80 TYR cc_start: 0.7257 (m-80) cc_final: 0.6448 (m-80) REVERT: R 652 TYR cc_start: 0.7611 (m-10) cc_final: 0.7253 (m-10) REVERT: R 717 LYS cc_start: 0.7254 (tmtt) cc_final: 0.6895 (tmtt) REVERT: S 156 SER cc_start: 0.7274 (m) cc_final: 0.6816 (p) REVERT: S 192 MET cc_start: 0.3435 (mpp) cc_final: 0.2782 (mpp) outliers start: 32 outliers final: 27 residues processed: 206 average time/residue: 0.2043 time to fit residues: 60.8373 Evaluate side-chains 203 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 175 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 362 HIS Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 747 THR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 167 HIS Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 46 optimal weight: 0.0970 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 113 optimal weight: 0.0060 chunk 69 optimal weight: 2.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9868 Z= 0.241 Angle : 0.564 5.786 13349 Z= 0.299 Chirality : 0.044 0.248 1494 Planarity : 0.004 0.040 1685 Dihedral : 5.379 52.427 1335 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 24.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.45 % Allowed : 18.39 % Favored : 78.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.25), residues: 1190 helix: 0.35 (0.27), residues: 352 sheet: -1.55 (0.29), residues: 270 loop : -0.72 (0.28), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 99 HIS 0.008 0.002 HIS A 362 PHE 0.018 0.002 PHE A 212 TYR 0.018 0.002 TYR B 111 ARG 0.007 0.000 ARG A 280 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 181 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 220 HIS cc_start: 0.7358 (t-90) cc_final: 0.7015 (t-170) REVERT: A 311 TYR cc_start: 0.6263 (m-10) cc_final: 0.5900 (m-10) REVERT: B 134 ARG cc_start: 0.6948 (ptp-170) cc_final: 0.6741 (ptm160) REVERT: B 183 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6510 (m170) REVERT: B 297 TRP cc_start: 0.8417 (m100) cc_final: 0.8200 (m100) REVERT: N 80 TYR cc_start: 0.7314 (m-80) cc_final: 0.6495 (m-80) REVERT: R 652 TYR cc_start: 0.7530 (m-10) cc_final: 0.7241 (m-10) REVERT: R 717 LYS cc_start: 0.7326 (tmtt) cc_final: 0.6840 (tmtt) REVERT: S 156 SER cc_start: 0.7337 (m) cc_final: 0.6885 (p) REVERT: S 192 MET cc_start: 0.3510 (mpp) cc_final: 0.2832 (mpp) outliers start: 36 outliers final: 26 residues processed: 205 average time/residue: 0.2110 time to fit residues: 60.6349 Evaluate side-chains 205 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 747 THR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 73 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9868 Z= 0.222 Angle : 0.571 8.108 13349 Z= 0.300 Chirality : 0.043 0.235 1494 Planarity : 0.004 0.047 1685 Dihedral : 5.399 53.932 1335 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 23.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.68 % Allowed : 19.25 % Favored : 78.07 % 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: -0.96 (0.25), residues: 1190 helix: 0.35 (0.27), residues: 351 sheet: -1.51 (0.29), residues: 267 loop : -0.69 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.026 0.002 HIS A 362 PHE 0.025 0.002 PHE R 832 TYR 0.016 0.002 TYR A 391 ARG 0.008 0.001 ARG B 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 181 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 280 ARG cc_start: 0.7060 (ttt-90) cc_final: 0.6838 (tpt90) REVERT: A 311 TYR cc_start: 0.6306 (m-10) cc_final: 0.5861 (m-10) REVERT: B 183 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6378 (m170) REVERT: B 290 ASP cc_start: 0.6587 (m-30) cc_final: 0.6380 (m-30) REVERT: B 297 TRP cc_start: 0.8314 (m100) cc_final: 0.8093 (m100) REVERT: B 325 MET cc_start: 0.7211 (tpp) cc_final: 0.6803 (tpp) REVERT: N 80 TYR cc_start: 0.7307 (m-80) cc_final: 0.6565 (m-80) REVERT: R 652 TYR cc_start: 0.7581 (m-10) cc_final: 0.7302 (m-10) REVERT: R 717 LYS cc_start: 0.7279 (tmtt) cc_final: 0.6980 (tmtt) REVERT: S 156 SER cc_start: 0.7344 (m) cc_final: 0.6887 (p) REVERT: S 192 MET cc_start: 0.3454 (mpp) cc_final: 0.2781 (mpp) outliers start: 28 outliers final: 25 residues processed: 198 average time/residue: 0.2152 time to fit residues: 60.3244 Evaluate side-chains 206 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 SER Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain R residue 654 SER Chi-restraints excluded: chain R residue 747 THR Chi-restraints excluded: chain R residue 776 VAL Chi-restraints excluded: chain R residue 780 ILE Chi-restraints excluded: chain R residue 783 VAL Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 158 SER Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain S residue 232 HIS Chi-restraints excluded: chain S residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 5.9990 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 12 optimal weight: 0.0470 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 266 HIS ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.196514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.170476 restraints weight = 10040.696| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 1.57 r_work: 0.3775 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9868 Z= 0.232 Angle : 0.569 7.480 13349 Z= 0.300 Chirality : 0.043 0.227 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.376 55.066 1335 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 23.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.78 % Allowed : 19.25 % Favored : 77.97 % 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: -0.99 (0.25), residues: 1190 helix: 0.31 (0.27), residues: 351 sheet: -1.52 (0.29), residues: 266 loop : -0.70 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.012 0.002 HIS A 220 PHE 0.023 0.002 PHE R 832 TYR 0.016 0.002 TYR B 111 ARG 0.008 0.001 ARG B 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2561.03 seconds wall clock time: 47 minutes 6.01 seconds (2826.01 seconds total)