Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 17:42:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/10_2023/7wui_32836_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/10_2023/7wui_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_32836/10_2023/7wui_32836.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/10_2023/7wui_32836.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/10_2023/7wui_32836_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wui_32836/10_2023/7wui_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 5.35, per 1000 atoms: 0.55 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: 3.88 Conformation dependent library (CDL) restraints added in 1.3 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: 1.41 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: 2.68 Time building geometry restraints manager: 4.23 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: 1.250 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: 4.250 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 28.170 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.010 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.023 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 211 average time/residue: 0.2208 time to fit residues: 65.5989 Evaluate side-chains 167 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 166 time to evaluate : 1.010 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0868 time to fit residues: 1.5874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 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: 0.8180 ------------------------------------------------------------------------------- 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 R 860 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: 0.6613 moved from start: 0.2368 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= 0.261 Angle : 0.626 10.284 13349 Z= 0.330 Chirality : 0.044 0.161 1494 Planarity : 0.005 0.046 1685 Dihedral : 5.632 43.053 1334 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.01 % Allowed : 9.48 % Favored : 88.51 % 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: -1.84 (0.24), residues: 1190 helix: -0.55 (0.27), residues: 353 sheet: -1.78 (0.29), residues: 279 loop : -1.22 (0.27), residues: 558 *********************** 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 220 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 199 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 15 residues processed: 213 average time/residue: 0.2121 time to fit residues: 64.5992 Evaluate side-chains 190 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 1.182 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1321 time to fit residues: 4.8276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 0.0980 chunk 33 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 117 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 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 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 384 GLN B 125 ASN ** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN R 668 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: 0.6706 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9868 Z= 0.236 Angle : 0.579 11.334 13349 Z= 0.308 Chirality : 0.042 0.179 1494 Planarity : 0.004 0.045 1685 Dihedral : 5.357 40.790 1334 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.01 % Allowed : 12.36 % Favored : 85.63 % 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: -0.22 (0.27), residues: 354 sheet: -1.74 (0.28), residues: 282 loop : -1.01 (0.27), residues: 554 *********************** 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 237 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.040 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 224 average time/residue: 0.2397 time to fit residues: 74.4885 Evaluate side-chains 206 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 196 time to evaluate : 1.566 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1467 time to fit residues: 3.9893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 0.2980 chunk 82 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 109 optimal weight: 0.0770 chunk 115 optimal weight: 0.0770 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 31 optimal weight: 0.0030 overall best weight: 0.2706 ------------------------------------------------------------------------------- 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** A 362 HIS A 384 GLN B 16 ASN B 17 GLN B 125 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.6611 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9868 Z= 0.170 Angle : 0.533 5.819 13349 Z= 0.287 Chirality : 0.041 0.160 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.107 42.279 1334 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.63 % Allowed : 16.48 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.24), residues: 1190 helix: 0.05 (0.27), residues: 353 sheet: -1.57 (0.29), residues: 279 loop : -0.97 (0.27), residues: 558 *********************** 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 215 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 205 average time/residue: 0.2207 time to fit residues: 63.8262 Evaluate side-chains 187 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 181 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0959 time to fit residues: 2.5953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 86 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 104 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6754 moved from start: 0.3602 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= 0.243 Angle : 0.568 9.114 13349 Z= 0.300 Chirality : 0.043 0.208 1494 Planarity : 0.004 0.045 1685 Dihedral : 5.205 44.184 1334 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.39 % Allowed : 16.38 % Favored : 81.23 % 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: -1.26 (0.24), residues: 1190 helix: 0.23 (0.27), residues: 352 sheet: -1.67 (0.28), residues: 291 loop : -0.93 (0.28), residues: 547 *********************** 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 227 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 202 time to evaluate : 1.092 Fit side-chains outliers start: 25 outliers final: 14 residues processed: 214 average time/residue: 0.2314 time to fit residues: 70.5216 Evaluate side-chains 205 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1150 time to fit residues: 4.5191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 0.0770 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 60 optimal weight: 0.0870 overall best weight: 0.4716 ------------------------------------------------------------------------------- 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** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN ** 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: 0.6706 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9868 Z= 0.198 Angle : 0.552 9.551 13349 Z= 0.292 Chirality : 0.042 0.202 1494 Planarity : 0.004 0.042 1685 Dihedral : 5.149 47.641 1334 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 22.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.44 % Allowed : 17.82 % Favored : 80.75 % 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: -1.16 (0.24), residues: 1190 helix: 0.34 (0.27), residues: 349 sheet: -1.63 (0.29), residues: 271 loop : -0.92 (0.27), residues: 570 *********************** 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 211 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 196 time to evaluate : 0.984 Fit side-chains outliers start: 15 outliers final: 6 residues processed: 205 average time/residue: 0.2092 time to fit residues: 61.2571 Evaluate side-chains 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 180 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1048 time to fit residues: 2.7222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.0030 chunk 13 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 overall best weight: 0.4948 ------------------------------------------------------------------------------- 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 ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.3810 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= 0.200 Angle : 0.540 6.907 13349 Z= 0.286 Chirality : 0.042 0.240 1494 Planarity : 0.004 0.041 1685 Dihedral : 5.114 49.505 1334 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 21.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.53 % Allowed : 18.39 % 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: -1.10 (0.24), residues: 1190 helix: 0.41 (0.27), residues: 349 sheet: -1.61 (0.29), residues: 272 loop : -0.89 (0.27), residues: 569 *********************** 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 204 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 188 time to evaluate : 1.028 Fit side-chains outliers start: 16 outliers final: 12 residues processed: 198 average time/residue: 0.2217 time to fit residues: 62.2162 Evaluate side-chains 192 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.094 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1015 time to fit residues: 3.7774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 46 optimal weight: 0.0770 chunk 69 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 57 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 90 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN B 125 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6724 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9868 Z= 0.209 Angle : 0.548 7.204 13349 Z= 0.290 Chirality : 0.043 0.258 1494 Planarity : 0.004 0.041 1685 Dihedral : 5.136 51.214 1334 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 22.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.67 % Allowed : 19.54 % Favored : 79.79 % 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: -1.08 (0.25), residues: 1190 helix: 0.34 (0.27), residues: 356 sheet: -1.55 (0.29), residues: 272 loop : -0.85 (0.28), residues: 562 *********************** 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 200 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 193 time to evaluate : 1.006 Fit side-chains outliers start: 7 outliers final: 2 residues processed: 196 average time/residue: 0.2443 time to fit residues: 66.6633 Evaluate side-chains 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 184 time to evaluate : 1.106 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1149 time to fit residues: 2.0379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6770 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9868 Z= 0.235 Angle : 0.571 7.686 13349 Z= 0.302 Chirality : 0.043 0.271 1494 Planarity : 0.004 0.040 1685 Dihedral : 5.240 54.681 1334 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 23.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.96 % Allowed : 20.02 % Favored : 79.02 % 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: -1.08 (0.25), residues: 1190 helix: 0.32 (0.27), residues: 355 sheet: -1.54 (0.29), residues: 276 loop : -0.83 (0.28), residues: 559 *********************** 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 201 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 1.064 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 195 average time/residue: 0.2107 time to fit residues: 59.2342 Evaluate side-chains 193 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 187 time to evaluate : 1.048 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0985 time to fit residues: 2.5124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN B 125 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.6845 moved from start: 0.4391 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= 0.286 Angle : 0.613 7.818 13349 Z= 0.321 Chirality : 0.045 0.295 1494 Planarity : 0.004 0.045 1685 Dihedral : 5.415 55.628 1334 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.48 % Allowed : 20.11 % Favored : 79.41 % 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: -1.15 (0.24), residues: 1190 helix: 0.13 (0.27), residues: 355 sheet: -1.53 (0.29), residues: 272 loop : -0.82 (0.28), residues: 563 ********************** 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 201 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 196 time to evaluate : 1.122 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 198 average time/residue: 0.1965 time to fit residues: 56.5296 Evaluate side-chains 191 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 187 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1004 time to fit residues: 2.1835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 0.0770 chunk 26 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 39 optimal weight: 0.9990 chunk 97 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 68 optimal weight: 5.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.199436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.172630 restraints weight = 10205.054| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 1.69 r_work: 0.3824 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3680 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.4278 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= 0.199 Angle : 0.581 8.380 13349 Z= 0.302 Chirality : 0.043 0.228 1494 Planarity : 0.004 0.041 1685 Dihedral : 5.292 58.838 1334 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 23.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.57 % Allowed : 20.50 % Favored : 78.93 % 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: -1.08 (0.25), residues: 1190 helix: 0.32 (0.27), residues: 351 sheet: -1.60 (0.29), residues: 273 loop : -0.80 (0.28), residues: 566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.28 seconds wall clock time: 47 minutes 27.47 seconds (2847.47 seconds total)