Starting phenix.real_space_refine on Mon Mar 11 13:54:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uzb_26885/03_2024/7uzb_26885.pdb" } resolution = 4.1 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 5342 2.51 5 N 1393 2.21 5 O 1625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8392 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5026 Classifications: {'peptide': 643} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 35, 'TRANS': 607} Chain breaks: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "H" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1662 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 14, 'TRANS': 205} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1648 Classifications: {'peptide': 214} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 202} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.09, per 1000 atoms: 0.61 Number of scatterers: 8392 At special positions: 0 Unit cell: (99.066, 112.101, 128.612, 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 32 16.00 O 1625 8.00 N 1393 7.00 C 5342 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 104 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 104 " distance=2.03 Simple disulfide: pdb=" SG CYS L 154 " - pdb=" SG CYS L 214 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 61 " Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.8 seconds 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2002 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 21 sheets defined 9.6% alpha, 37.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 245 through 250 removed outlier: 3.532A pdb=" N THR A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.901A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.377A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.823A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 498 through 502 removed outlier: 4.153A pdb=" N GLY A 502 " --> pdb=" O PRO A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 630 removed outlier: 3.948A pdb=" N ALA A 626 " --> pdb=" O VAL A 622 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 74 removed outlier: 4.328A pdb=" N ASP H 74 " --> pdb=" O GLY H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 202 through 207 removed outlier: 3.858A pdb=" N THR H 206 " --> pdb=" O SER H 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 removed outlier: 3.718A pdb=" N PHE L 99 " --> pdb=" O PRO L 96 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 148 Processing helix chain 'L' and resid 203 through 209 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.777A pdb=" N GLY A 89 " --> pdb=" O LEU A 270 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 50 through 55 removed outlier: 7.432A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.651A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N MET A 153 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.769A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.443A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 326 through 328 removed outlier: 3.646A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.843A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP A 436 " --> pdb=" O ARG A 509 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 553 through 554 removed outlier: 4.515A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.809A pdb=" N GLN H 3 " --> pdb=" O SER H 26 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.288A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N MET H 39 " --> pdb=" O ARG H 55 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG H 55 " --> pdb=" O MET H 39 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP H 41 " --> pdb=" O ILE H 53 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 13 removed outlier: 6.288A pdb=" N GLU H 11 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N TYR H 117 " --> pdb=" O ARG H 106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.904A pdb=" N ASP H 159 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.904A pdb=" N ASP H 159 " --> pdb=" O TYR H 191 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 166 through 169 removed outlier: 4.495A pdb=" N TYR H 209 " --> pdb=" O VAL H 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.819A pdb=" N LEU L 11 " --> pdb=" O GLU L 125 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LYS L 127 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ALA L 13 " --> pdb=" O LYS L 127 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY L 100 " --> pdb=" O LEU L 124 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU L 39 " --> pdb=" O ARG L 56 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN L 43 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU L 52 " --> pdb=" O GLN L 43 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 134 through 138 removed outlier: 3.761A pdb=" N VAL L 153 " --> pdb=" O PHE L 138 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N TYR L 193 " --> pdb=" O ASN L 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 174 through 175 removed outlier: 4.630A pdb=" N TRP L 168 " --> pdb=" O GLN L 175 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 753 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: 2.76 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2676 1.34 - 1.46: 2181 1.46 - 1.58: 3717 1.58 - 1.70: 0 1.70 - 1.82: 36 Bond restraints: 8610 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.05e+00 bond pdb=" C5 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.413 1.441 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.72e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.432 -0.026 2.00e-02 2.50e+03 1.63e+00 ... (remaining 8605 not shown) Histogram of bond angle deviations from ideal: 99.91 - 106.73: 272 106.73 - 113.56: 4689 113.56 - 120.39: 2988 120.39 - 127.21: 3686 127.21 - 134.04: 97 Bond angle restraints: 11732 Sorted by residual: angle pdb=" N SER A 637 " pdb=" CA SER A 637 " pdb=" C SER A 637 " ideal model delta sigma weight residual 112.86 107.39 5.47 1.22e+00 6.72e-01 2.01e+01 angle pdb=" C PRO A 631 " pdb=" N THR A 632 " pdb=" CA THR A 632 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" C THR A 638 " pdb=" CA THR A 638 " pdb=" CB THR A 638 " ideal model delta sigma weight residual 110.42 116.18 -5.76 1.99e+00 2.53e-01 8.38e+00 angle pdb=" N GLU H 163 " pdb=" CA GLU H 163 " pdb=" C GLU H 163 " ideal model delta sigma weight residual 109.81 115.12 -5.31 2.21e+00 2.05e-01 5.77e+00 angle pdb=" C LEU A 546 " pdb=" N THR A 547 " pdb=" CA THR A 547 " ideal model delta sigma weight residual 122.40 125.87 -3.47 1.45e+00 4.76e-01 5.72e+00 ... (remaining 11727 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 4889 23.07 - 46.13: 216 46.13 - 69.20: 19 69.20 - 92.26: 5 92.26 - 115.33: 17 Dihedral angle restraints: 5146 sinusoidal: 2015 harmonic: 3131 Sorted by residual: dihedral pdb=" CA TYR A 636 " pdb=" C TYR A 636 " pdb=" N SER A 637 " pdb=" CA SER A 637 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA TYR H 57 " pdb=" C TYR H 57 " pdb=" N PRO H 58 " pdb=" CA PRO H 58 " ideal model delta harmonic sigma weight residual 180.00 -157.37 -22.63 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CB CYS L 154 " pdb=" SG CYS L 154 " pdb=" SG CYS L 214 " pdb=" CB CYS L 214 " ideal model delta sinusoidal sigma weight residual 93.00 128.46 -35.46 1 1.00e+01 1.00e-02 1.78e+01 ... (remaining 5143 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1078 0.050 - 0.100: 169 0.100 - 0.149: 65 0.149 - 0.199: 0 0.199 - 0.249: 1 Chirality restraints: 1313 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CA PRO H 58 " pdb=" N PRO H 58 " pdb=" C PRO H 58 " pdb=" CB PRO H 58 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 1310 not shown) Planarity restraints: 1514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 620 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.20e+00 pdb=" N PRO A 621 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 328 " -0.145 9.50e-02 1.11e+02 6.49e-02 2.60e+00 pdb=" NE ARG A 328 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 328 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 328 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 328 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR L 114 " -0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO L 115 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO L 115 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO L 115 " -0.018 5.00e-02 4.00e+02 ... (remaining 1511 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 107 2.61 - 3.18: 7505 3.18 - 3.75: 13434 3.75 - 4.33: 18618 4.33 - 4.90: 29299 Nonbonded interactions: 68963 Sorted by model distance: nonbonded pdb=" OG1 THR A 393 " pdb=" OH TYR H 110 " model vdw 2.037 2.440 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.144 2.440 nonbonded pdb=" NH2 ARG A 328 " pdb=" O SER A 530 " model vdw 2.147 2.520 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.153 2.440 nonbonded pdb=" OD1 ASN A 122 " pdb=" OG1 THR A 124 " model vdw 2.187 2.440 ... (remaining 68958 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 group one per residue 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: 3.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 10.170 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.510 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:3.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 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 : 0.003 0.049 8610 Z= 0.194 Angle : 0.599 6.850 11732 Z= 0.332 Chirality : 0.042 0.249 1313 Planarity : 0.004 0.065 1510 Dihedral : 14.481 115.325 3105 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.43 (0.25), residues: 1067 helix: -0.62 (0.63), residues: 63 sheet: 1.07 (0.27), residues: 365 loop : -0.04 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 104 HIS 0.003 0.001 HIS L 106 PHE 0.018 0.002 PHE A 541 TYR 0.022 0.001 TYR H 57 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.014 Fit side-chains revert: symmetry clash REVERT: H 39 MET cc_start: 0.7895 (ttp) cc_final: 0.7315 (tmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1863 time to fit residues: 11.6666 Evaluate side-chains 30 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 30 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN H 219 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8610 Z= 0.320 Angle : 0.648 9.533 11732 Z= 0.336 Chirality : 0.045 0.299 1313 Planarity : 0.005 0.087 1510 Dihedral : 10.840 101.204 1248 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.11 % Allowed : 4.02 % Favored : 95.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.18 (0.25), residues: 1067 helix: -0.93 (0.58), residues: 73 sheet: 0.86 (0.27), residues: 372 loop : -0.16 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 52 HIS 0.004 0.002 HIS L 107 PHE 0.018 0.002 PHE A 238 TYR 0.016 0.002 TYR L 55 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: H 39 MET cc_start: 0.7541 (ttp) cc_final: 0.7195 (tmm) REVERT: H 51 GLU cc_start: 0.8987 (tp30) cc_final: 0.8703 (tp30) REVERT: L 24 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8626 (mtm110) outliers start: 1 outliers final: 0 residues processed: 36 average time/residue: 0.1864 time to fit residues: 10.8075 Evaluate side-chains 28 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 78 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8610 Z= 0.172 Angle : 0.540 6.199 11732 Z= 0.283 Chirality : 0.043 0.192 1313 Planarity : 0.004 0.047 1510 Dihedral : 7.623 83.643 1248 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.26), residues: 1067 helix: -0.85 (0.58), residues: 78 sheet: 0.90 (0.27), residues: 368 loop : -0.12 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.010 0.001 HIS A 207 PHE 0.011 0.002 PHE A 318 TYR 0.017 0.001 TYR H 57 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 41 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9016 (m-10) cc_final: 0.8787 (m-10) outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.1822 time to fit residues: 12.1339 Evaluate side-chains 29 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 5.9990 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8610 Z= 0.324 Angle : 0.617 7.439 11732 Z= 0.322 Chirality : 0.043 0.217 1313 Planarity : 0.004 0.055 1510 Dihedral : 7.662 82.935 1248 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.03 (0.26), residues: 1067 helix: -0.80 (0.60), residues: 76 sheet: 0.67 (0.27), residues: 368 loop : -0.29 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 64 HIS 0.009 0.002 HIS L 106 PHE 0.020 0.002 PHE A 238 TYR 0.013 0.002 TYR A 200 ARG 0.006 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 38 time to evaluate : 1.019 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1842 time to fit residues: 11.2253 Evaluate side-chains 26 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 86 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 42 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 0.4980 chunk 92 optimal weight: 7.9990 chunk 26 optimal weight: 1.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 540 ASN ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8610 Z= 0.248 Angle : 0.577 6.509 11732 Z= 0.303 Chirality : 0.044 0.209 1313 Planarity : 0.004 0.098 1510 Dihedral : 7.544 81.098 1248 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.10 (0.26), residues: 1067 helix: -0.76 (0.61), residues: 76 sheet: 0.57 (0.27), residues: 368 loop : -0.32 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 52 HIS 0.006 0.001 HIS L 106 PHE 0.020 0.002 PHE A 318 TYR 0.013 0.001 TYR L 55 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7681 (ppp) cc_final: 0.7453 (ppp) REVERT: A 157 PHE cc_start: 0.9199 (m-10) cc_final: 0.8937 (m-10) REVERT: A 160 TYR cc_start: 0.9112 (p90) cc_final: 0.8909 (p90) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1835 time to fit residues: 11.4560 Evaluate side-chains 28 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 34 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 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 625 HIS ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8610 Z= 0.143 Angle : 0.533 6.472 11732 Z= 0.275 Chirality : 0.043 0.187 1313 Planarity : 0.004 0.060 1510 Dihedral : 7.167 77.782 1248 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.26), residues: 1067 helix: -0.68 (0.60), residues: 76 sheet: 0.72 (0.27), residues: 369 loop : -0.25 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.007 0.001 HIS A 625 PHE 0.015 0.001 PHE A 318 TYR 0.015 0.001 TYR L 55 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7621 (ppp) cc_final: 0.7326 (ppp) REVERT: A 157 PHE cc_start: 0.9191 (m-10) cc_final: 0.8956 (m-10) REVERT: A 458 LYS cc_start: 0.9378 (mtpt) cc_final: 0.9038 (mmtt) REVERT: H 51 GLU cc_start: 0.8967 (tp30) cc_final: 0.8749 (tp30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1915 time to fit residues: 12.2024 Evaluate side-chains 29 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 29 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 11 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8610 Z= 0.187 Angle : 0.533 6.581 11732 Z= 0.276 Chirality : 0.042 0.190 1313 Planarity : 0.004 0.055 1510 Dihedral : 7.102 75.277 1248 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.04 (0.26), residues: 1067 helix: -0.64 (0.61), residues: 76 sheet: 0.69 (0.27), residues: 370 loop : -0.24 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 104 HIS 0.004 0.001 HIS L 106 PHE 0.015 0.001 PHE A 318 TYR 0.012 0.001 TYR L 55 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9248 (m-10) cc_final: 0.9026 (m-10) REVERT: A 238 PHE cc_start: 0.8286 (t80) cc_final: 0.7938 (t80) REVERT: A 458 LYS cc_start: 0.9389 (mtpt) cc_final: 0.9053 (mmtt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1850 time to fit residues: 12.3814 Evaluate side-chains 28 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8610 Z= 0.169 Angle : 0.530 6.752 11732 Z= 0.273 Chirality : 0.042 0.182 1313 Planarity : 0.004 0.049 1510 Dihedral : 6.911 71.799 1248 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.06 (0.26), residues: 1067 helix: -0.60 (0.61), residues: 76 sheet: 0.70 (0.27), residues: 370 loop : -0.23 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 52 HIS 0.004 0.001 HIS L 107 PHE 0.016 0.001 PHE A 318 TYR 0.013 0.001 TYR L 55 ARG 0.009 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9261 (m-10) cc_final: 0.9049 (m-10) REVERT: A 458 LYS cc_start: 0.9398 (mtpt) cc_final: 0.9077 (mmtt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1973 time to fit residues: 12.5456 Evaluate side-chains 27 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 96 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.0070 chunk 95 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8610 Z= 0.135 Angle : 0.522 6.916 11732 Z= 0.267 Chirality : 0.043 0.164 1313 Planarity : 0.004 0.044 1510 Dihedral : 6.615 66.741 1248 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.10 (0.26), residues: 1067 helix: -0.65 (0.60), residues: 76 sheet: 0.77 (0.27), residues: 370 loop : -0.22 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 168 HIS 0.002 0.001 HIS L 106 PHE 0.015 0.001 PHE A 318 TYR 0.015 0.001 TYR A 144 ARG 0.003 0.000 ARG A 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.9396 (mtpt) cc_final: 0.9095 (mmtt) REVERT: H 51 GLU cc_start: 0.8981 (tp30) cc_final: 0.8611 (tp30) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.2068 time to fit residues: 14.2938 Evaluate side-chains 28 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 62 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 90 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8610 Z= 0.139 Angle : 0.537 8.523 11732 Z= 0.270 Chirality : 0.043 0.172 1313 Planarity : 0.004 0.046 1510 Dihedral : 6.394 61.410 1248 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.15 (0.26), residues: 1067 helix: -0.62 (0.61), residues: 76 sheet: 0.82 (0.27), residues: 370 loop : -0.21 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 633 HIS 0.002 0.001 HIS L 106 PHE 0.015 0.001 PHE A 318 TYR 0.012 0.001 TYR L 55 ARG 0.010 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2134 Ramachandran restraints generated. 1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 458 LYS cc_start: 0.9343 (mtpt) cc_final: 0.9083 (mmtt) REVERT: H 51 GLU cc_start: 0.8988 (tp30) cc_final: 0.8573 (tp30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1908 time to fit residues: 13.2284 Evaluate side-chains 32 residues out of total 941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 26 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** L 105 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 = 0.3360 r_free = 0.3360 target = 0.048000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.037788 restraints weight = 63036.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039188 restraints weight = 36100.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.040185 restraints weight = 24750.450| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8610 Z= 0.141 Angle : 0.519 6.786 11732 Z= 0.264 Chirality : 0.043 0.152 1313 Planarity : 0.003 0.043 1510 Dihedral : 6.202 59.463 1248 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.13 (0.26), residues: 1067 helix: -0.59 (0.61), residues: 76 sheet: 0.81 (0.27), residues: 370 loop : -0.22 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 633 HIS 0.002 0.001 HIS L 106 PHE 0.014 0.001 PHE A 318 TYR 0.012 0.001 TYR L 55 ARG 0.005 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1723.27 seconds wall clock time: 32 minutes 30.33 seconds (1950.33 seconds total)