Starting phenix.real_space_refine on Sat Jul 26 12:49:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_26885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_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/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_26885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_26885.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_26885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzb_26885/07_2025/7uzb_26885.cif" } 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. Time to flip 17 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.84, per 1000 atoms: 0.70 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 - 3.00 Amino acid : True - 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: 2.84 Conformation dependent library (CDL) restraints added in 1.3 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: 1.49 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: 3.25 Time building geometry restraints manager: 3.18 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: 0.00 - 1.37: 11293 1.37 - 2.74: 359 2.74 - 4.11: 62 4.11 - 5.48: 14 5.48 - 6.85: 4 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 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.144 3.040 nonbonded pdb=" NH2 ARG A 328 " pdb=" O SER A 530 " model vdw 2.147 3.120 nonbonded pdb=" OG1 THR A 645 " pdb=" O GLY A 648 " model vdw 2.153 3.040 nonbonded pdb=" OD1 ASN A 122 " pdb=" OG1 THR A 124 " model vdw 2.187 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== 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: 3.530 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.940 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.860 ------------------------------------------------------------------------------- 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 8627 Z= 0.152 Angle : 0.600 6.850 11770 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 4) link_NAG-ASN : angle 1.02794 ( 12) hydrogen bonds : bond 0.27901 ( 270) hydrogen bonds : angle 10.57782 ( 753) SS BOND : bond 0.00171 ( 13) SS BOND : angle 0.76895 ( 26) covalent geometry : bond 0.00299 ( 8610) covalent geometry : angle 0.59867 (11732) *********************** 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 to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.983 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: 0.1835 time to fit residues: 11.5008 Evaluate side-chains 30 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.984 ------------------------------------------------------------------------------- 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: 0.0980 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.047192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036769 restraints weight = 61343.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038162 restraints weight = 34948.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039154 restraints weight = 23934.292| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8627 Z= 0.137 Angle : 0.583 9.619 11770 Z= 0.303 Chirality : 0.045 0.275 1313 Planarity : 0.005 0.090 1510 Dihedral : 10.574 101.719 1248 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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 (0.26), residues: 1067 helix: -0.69 (0.60), residues: 73 sheet: 1.11 (0.27), residues: 384 loop : -0.08 (0.25), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS L 106 PHE 0.014 0.001 PHE A 238 TYR 0.018 0.001 TYR H 57 ARG 0.005 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00271 ( 4) link_NAG-ASN : angle 1.15810 ( 12) hydrogen bonds : bond 0.04755 ( 270) hydrogen bonds : angle 7.61216 ( 753) SS BOND : bond 0.00236 ( 13) SS BOND : angle 0.77454 ( 26) covalent geometry : bond 0.00286 ( 8610) covalent geometry : angle 0.58212 (11732) *********************** 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 40 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8877 (mtm110) cc_final: 0.8601 (mtm110) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1804 time to fit residues: 11.6338 Evaluate side-chains 28 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 7 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 8.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 144 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.045433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.035222 restraints weight = 64304.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.036557 restraints weight = 36808.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.037526 restraints weight = 25204.082| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8627 Z= 0.236 Angle : 0.637 8.346 11770 Z= 0.332 Chirality : 0.044 0.209 1313 Planarity : 0.004 0.074 1510 Dihedral : 7.760 83.404 1248 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 0.11 (0.26), residues: 1067 helix: -0.86 (0.62), residues: 73 sheet: 0.79 (0.27), residues: 373 loop : -0.20 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 41 HIS 0.009 0.002 HIS L 106 PHE 0.021 0.002 PHE A 238 TYR 0.016 0.002 TYR H 114 ARG 0.005 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 4) link_NAG-ASN : angle 1.84685 ( 12) hydrogen bonds : bond 0.04587 ( 270) hydrogen bonds : angle 7.15526 ( 753) SS BOND : bond 0.00369 ( 13) SS BOND : angle 1.05400 ( 26) covalent geometry : bond 0.00495 ( 8610) covalent geometry : angle 0.63381 (11732) *********************** 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 39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: H 51 GLU cc_start: 0.9060 (tp30) cc_final: 0.8701 (tp30) REVERT: H 97 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9079 (tm-30) REVERT: L 4 MET cc_start: 0.8520 (mmp) cc_final: 0.8306 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1844 time to fit residues: 11.5032 Evaluate side-chains 28 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 75 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** 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 = 0.3251 r_free = 0.3251 target = 0.044326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.034362 restraints weight = 64989.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.035648 restraints weight = 37510.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036553 restraints weight = 25752.849| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8627 Z= 0.278 Angle : 0.679 8.455 11770 Z= 0.354 Chirality : 0.045 0.235 1313 Planarity : 0.005 0.078 1510 Dihedral : 7.941 84.332 1248 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.29 (0.25), residues: 1067 helix: -1.09 (0.61), residues: 72 sheet: 0.38 (0.27), residues: 369 loop : -0.38 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 64 HIS 0.010 0.002 HIS A 207 PHE 0.019 0.002 PHE L 87 TYR 0.015 0.002 TYR A 674 ARG 0.006 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00181 ( 4) link_NAG-ASN : angle 1.85017 ( 12) hydrogen bonds : bond 0.04446 ( 270) hydrogen bonds : angle 6.94930 ( 753) SS BOND : bond 0.00329 ( 13) SS BOND : angle 0.97231 ( 26) covalent geometry : bond 0.00586 ( 8610) covalent geometry : angle 0.67580 (11732) *********************** 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 36 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8982 (p90) cc_final: 0.8778 (p90) REVERT: L 138 PHE cc_start: 0.8743 (m-80) cc_final: 0.8533 (m-80) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.2156 time to fit residues: 11.8995 Evaluate side-chains 24 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 79 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.045837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.035717 restraints weight = 63115.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.037061 restraints weight = 36278.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.038026 restraints weight = 24847.038| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8627 Z= 0.137 Angle : 0.573 6.778 11770 Z= 0.298 Chirality : 0.044 0.207 1313 Planarity : 0.005 0.135 1510 Dihedral : 7.497 80.799 1248 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -0.91 (0.63), residues: 72 sheet: 0.45 (0.27), residues: 375 loop : -0.26 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 52 HIS 0.004 0.001 HIS L 106 PHE 0.024 0.002 PHE A 318 TYR 0.015 0.001 TYR L 55 ARG 0.010 0.000 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00172 ( 4) link_NAG-ASN : angle 1.71300 ( 12) hydrogen bonds : bond 0.03685 ( 270) hydrogen bonds : angle 6.65611 ( 753) SS BOND : bond 0.00338 ( 13) SS BOND : angle 1.14866 ( 26) covalent geometry : bond 0.00295 ( 8610) covalent geometry : angle 0.56884 (11732) *********************** 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 41 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.8990 (m-10) cc_final: 0.8744 (m-10) REVERT: A 160 TYR cc_start: 0.8918 (p90) cc_final: 0.8713 (p90) REVERT: L 138 PHE cc_start: 0.8569 (m-80) cc_final: 0.8291 (m-80) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1768 time to fit residues: 11.6495 Evaluate side-chains 28 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 15 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 55 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.044506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.034502 restraints weight = 65320.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.035759 restraints weight = 37959.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.036647 restraints weight = 26335.046| |-----------------------------------------------------------------------------| r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8627 Z= 0.243 Angle : 0.640 7.480 11770 Z= 0.335 Chirality : 0.044 0.225 1313 Planarity : 0.005 0.110 1510 Dihedral : 7.744 80.689 1248 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: -0.33 (0.25), residues: 1067 helix: -0.88 (0.65), residues: 70 sheet: 0.27 (0.27), residues: 368 loop : -0.39 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 64 HIS 0.005 0.002 HIS A 245 PHE 0.018 0.002 PHE L 87 TYR 0.013 0.002 TYR A 365 ARG 0.007 0.001 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00225 ( 4) link_NAG-ASN : angle 1.78488 ( 12) hydrogen bonds : bond 0.04142 ( 270) hydrogen bonds : angle 6.68698 ( 753) SS BOND : bond 0.00337 ( 13) SS BOND : angle 1.28720 ( 26) covalent geometry : bond 0.00514 ( 8610) covalent geometry : angle 0.63541 (11732) *********************** 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 38 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7853 (ppp) cc_final: 0.7614 (ppp) REVERT: A 160 TYR cc_start: 0.9027 (p90) cc_final: 0.8808 (p90) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1759 time to fit residues: 10.7840 Evaluate side-chains 24 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 58 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.045107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.035123 restraints weight = 63751.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.036442 restraints weight = 36309.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.037380 restraints weight = 24773.232| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8627 Z= 0.200 Angle : 0.607 6.895 11770 Z= 0.318 Chirality : 0.044 0.217 1313 Planarity : 0.005 0.112 1510 Dihedral : 7.607 78.580 1248 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: -0.34 (0.25), residues: 1067 helix: -0.80 (0.65), residues: 70 sheet: 0.22 (0.27), residues: 368 loop : -0.37 (0.25), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 52 HIS 0.007 0.001 HIS L 106 PHE 0.016 0.002 PHE A 238 TYR 0.014 0.002 TYR L 55 ARG 0.010 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 1.72286 ( 12) hydrogen bonds : bond 0.03955 ( 270) hydrogen bonds : angle 6.60808 ( 753) SS BOND : bond 0.00276 ( 13) SS BOND : angle 1.04231 ( 26) covalent geometry : bond 0.00425 ( 8610) covalent geometry : angle 0.60378 (11732) *********************** 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 40 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7871 (ppp) cc_final: 0.7569 (ppp) REVERT: A 157 PHE cc_start: 0.9202 (m-10) cc_final: 0.8999 (m-10) REVERT: H 39 MET cc_start: 0.6613 (tmm) cc_final: 0.6405 (tmm) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1776 time to fit residues: 11.3829 Evaluate side-chains 26 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 48 optimal weight: 0.6980 chunk 87 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 0.0050 chunk 27 optimal weight: 0.3980 chunk 101 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 60 optimal weight: 0.0570 overall best weight: 0.3712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.047462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.037286 restraints weight = 64215.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038695 restraints weight = 36562.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.039698 restraints weight = 24940.115| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8627 Z= 0.100 Angle : 0.560 7.147 11770 Z= 0.288 Chirality : 0.044 0.175 1313 Planarity : 0.004 0.084 1510 Dihedral : 7.042 72.909 1248 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.09 (0.26), residues: 1067 helix: -0.67 (0.64), residues: 70 sheet: 0.50 (0.27), residues: 372 loop : -0.27 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 52 HIS 0.002 0.001 HIS H 215 PHE 0.016 0.001 PHE A 592 TYR 0.016 0.001 TYR L 55 ARG 0.008 0.001 ARG A 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00174 ( 4) link_NAG-ASN : angle 1.78065 ( 12) hydrogen bonds : bond 0.03294 ( 270) hydrogen bonds : angle 6.25551 ( 753) SS BOND : bond 0.00204 ( 13) SS BOND : angle 0.90993 ( 26) covalent geometry : bond 0.00217 ( 8610) covalent geometry : angle 0.55658 (11732) *********************** 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 44 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9201 (m-10) cc_final: 0.8989 (m-10) REVERT: A 160 TYR cc_start: 0.9055 (p90) cc_final: 0.8849 (p90) REVERT: A 458 LYS cc_start: 0.9406 (mtpt) cc_final: 0.9028 (mmtt) REVERT: L 138 PHE cc_start: 0.8324 (m-80) cc_final: 0.8069 (m-80) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1922 time to fit residues: 13.2050 Evaluate side-chains 33 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 5.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.046091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.035882 restraints weight = 63621.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.037255 restraints weight = 36394.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.038234 restraints weight = 24796.565| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8627 Z= 0.165 Angle : 0.583 6.634 11770 Z= 0.301 Chirality : 0.044 0.194 1313 Planarity : 0.004 0.084 1510 Dihedral : 7.150 71.211 1248 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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 (0.25), residues: 1067 helix: -0.62 (0.65), residues: 70 sheet: 0.49 (0.27), residues: 369 loop : -0.28 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 633 HIS 0.006 0.001 HIS L 106 PHE 0.017 0.002 PHE A 318 TYR 0.014 0.001 TYR L 55 ARG 0.013 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00140 ( 4) link_NAG-ASN : angle 1.80774 ( 12) hydrogen bonds : bond 0.03591 ( 270) hydrogen bonds : angle 6.33160 ( 753) SS BOND : bond 0.00315 ( 13) SS BOND : angle 0.98068 ( 26) covalent geometry : bond 0.00353 ( 8610) covalent geometry : angle 0.57933 (11732) *********************** 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 39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.9057 (p90) cc_final: 0.8691 (p90) REVERT: A 458 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9042 (mmtt) REVERT: L 138 PHE cc_start: 0.8489 (m-80) cc_final: 0.8179 (m-80) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2034 time to fit residues: 12.0927 Evaluate side-chains 27 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 53 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 94 optimal weight: 0.0040 chunk 97 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 85 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.047339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.037175 restraints weight = 63322.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.038589 restraints weight = 36109.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.039568 restraints weight = 24635.621| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8627 Z= 0.105 Angle : 0.571 8.338 11770 Z= 0.289 Chirality : 0.044 0.172 1313 Planarity : 0.004 0.081 1510 Dihedral : 6.815 66.902 1248 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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: 0.04 (0.26), residues: 1067 helix: -0.58 (0.64), residues: 70 sheet: 0.65 (0.27), residues: 370 loop : -0.22 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 633 HIS 0.002 0.001 HIS L 106 PHE 0.029 0.001 PHE H 115 TYR 0.016 0.001 TYR L 55 ARG 0.005 0.000 ARG A 328 Details of bonding type rmsd link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 3.51936 ( 12) hydrogen bonds : bond 0.03283 ( 270) hydrogen bonds : angle 6.21589 ( 753) SS BOND : bond 0.00231 ( 13) SS BOND : angle 0.91699 ( 26) covalent geometry : bond 0.00232 ( 8610) covalent geometry : angle 0.55880 (11732) ********************** 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 43 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9150 (m-10) cc_final: 0.8928 (m-10) REVERT: A 160 TYR cc_start: 0.9034 (p90) cc_final: 0.8645 (p90) REVERT: A 458 LYS cc_start: 0.9401 (mtpt) cc_final: 0.9040 (mmtt) REVERT: L 138 PHE cc_start: 0.8307 (m-80) cc_final: 0.8044 (m-80) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.1977 time to fit residues: 13.2970 Evaluate side-chains 31 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 93 optimal weight: 0.9990 chunk 73 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** ** H 215 HIS ** 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 = 0.3346 r_free = 0.3346 target = 0.047453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.037224 restraints weight = 64268.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.038652 restraints weight = 36553.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.039658 restraints weight = 24884.507| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8627 Z= 0.111 Angle : 0.563 7.441 11770 Z= 0.285 Chirality : 0.043 0.161 1313 Planarity : 0.004 0.078 1510 Dihedral : 6.679 62.439 1248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: 0.07 (0.26), residues: 1067 helix: -0.54 (0.65), residues: 70 sheet: 0.70 (0.27), residues: 370 loop : -0.24 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 168 HIS 0.003 0.001 HIS L 106 PHE 0.022 0.001 PHE H 115 TYR 0.016 0.001 TYR H 160 ARG 0.010 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00112 ( 4) link_NAG-ASN : angle 2.92029 ( 12) hydrogen bonds : bond 0.03245 ( 270) hydrogen bonds : angle 6.14114 ( 753) SS BOND : bond 0.00249 ( 13) SS BOND : angle 0.83716 ( 26) covalent geometry : bond 0.00248 ( 8610) covalent geometry : angle 0.55462 (11732) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2726.14 seconds wall clock time: 48 minutes 34.18 seconds (2914.18 seconds total)