Starting phenix.real_space_refine on Thu Feb 13 02:21:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uzb_26885/02_2025/7uzb_26885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uzb_26885/02_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_26885/02_2025/7uzb_26885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uzb_26885/02_2025/7uzb_26885.map" model { file = "/net/cci-nas-00/data/ceres_data/7uzb_26885/02_2025/7uzb_26885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uzb_26885/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.13, per 1000 atoms: 0.73 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: 2.18 Conformation dependent library (CDL) restraints added in 1.0 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: 1.19 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: 3.18 Time building geometry restraints manager: 2.54 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: 4.220 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: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.150 Find NCS groups from input model: 0.130 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.860 ------------------------------------------------------------------------------- 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 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 to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.986 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: 0.1926 time to fit residues: 12.0783 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 : 0.992 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.036769 restraints weight = 61343.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038165 restraints weight = 34948.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039152 restraints weight = 23903.060| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 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 8610 Z= 0.186 Angle : 0.582 9.619 11732 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 *********************** 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 : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 24 ARG cc_start: 0.8884 (mtm110) cc_final: 0.8607 (mtm110) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1827 time to fit residues: 11.5391 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 : 0.943 ------------------------------------------------------------------------------- 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: 3.9990 chunk 61 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 86 optimal weight: 4.9990 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 = 0.3288 r_free = 0.3288 target = 0.045368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.035192 restraints weight = 64345.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.036518 restraints weight = 36809.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.037468 restraints weight = 25175.369| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1622 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= 0.322 Angle : 0.639 8.838 11732 Z= 0.333 Chirality : 0.044 0.214 1313 Planarity : 0.004 0.073 1510 Dihedral : 7.753 83.091 1248 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % 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: -0.88 (0.62), residues: 73 sheet: 0.77 (0.27), residues: 373 loop : -0.21 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP L 41 HIS 0.008 0.002 HIS L 106 PHE 0.020 0.002 PHE A 238 TYR 0.015 0.002 TYR H 114 ARG 0.005 0.001 ARG A 328 *********************** 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 : 0.987 Fit side-chains revert: symmetry clash REVERT: A 160 TYR cc_start: 0.8825 (p90) cc_final: 0.8534 (p90) REVERT: H 51 GLU cc_start: 0.9071 (tp30) cc_final: 0.8710 (tp30) REVERT: H 97 GLU cc_start: 0.9302 (tm-30) cc_final: 0.9084 (tm-30) REVERT: L 4 MET cc_start: 0.8504 (mmp) cc_final: 0.8300 (mmm) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1882 time to fit residues: 11.7138 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 : 0.918 ------------------------------------------------------------------------------- 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: 0.6980 chunk 97 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 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 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 = 0.3293 r_free = 0.3293 target = 0.045601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.035415 restraints weight = 64262.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.036730 restraints weight = 36903.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.037676 restraints weight = 25361.847| |-----------------------------------------------------------------------------| r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1929 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= 0.275 Angle : 0.600 7.454 11732 Z= 0.313 Chirality : 0.044 0.218 1313 Planarity : 0.004 0.072 1510 Dihedral : 7.608 82.610 1248 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % 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: -0.86 (0.63), residues: 72 sheet: 0.56 (0.27), residues: 372 loop : -0.30 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 52 HIS 0.007 0.001 HIS L 106 PHE 0.015 0.002 PHE L 87 TYR 0.015 0.002 TYR L 55 ARG 0.009 0.001 ARG A 190 *********************** 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 40 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.2014 time to fit residues: 12.2256 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 : 0.901 ------------------------------------------------------------------------------- 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: 0.2980 chunk 84 optimal weight: 8.9990 chunk 103 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.046800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036463 restraints weight = 62768.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037906 restraints weight = 35151.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.038940 restraints weight = 23671.182| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8610 Z= 0.169 Angle : 0.550 6.340 11732 Z= 0.286 Chirality : 0.044 0.197 1313 Planarity : 0.005 0.136 1510 Dihedral : 7.315 79.682 1248 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % 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: 0.00 (0.26), residues: 1067 helix: -0.78 (0.63), residues: 72 sheet: 0.61 (0.27), residues: 377 loop : -0.23 (0.25), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 52 HIS 0.003 0.001 HIS L 106 PHE 0.027 0.002 PHE A 318 TYR 0.015 0.001 TYR H 57 ARG 0.002 0.000 ARG A 237 *********************** 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 44 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.114 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.7782 (ppp) cc_final: 0.7562 (ppp) REVERT: A 157 PHE cc_start: 0.9025 (m-10) cc_final: 0.8755 (m-10) REVERT: A 458 LYS cc_start: 0.9382 (mtpt) cc_final: 0.9001 (mmtt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1964 time to fit residues: 13.2543 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 : 0.999 ------------------------------------------------------------------------------- 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: 10.0000 chunk 38 optimal weight: 8.9990 chunk 55 optimal weight: 0.1980 chunk 58 optimal weight: 0.0470 chunk 47 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 88 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 overall best weight: 1.8282 ------------------------------------------------------------------------------- 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 = 0.3304 r_free = 0.3304 target = 0.045873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.035729 restraints weight = 63008.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.037091 restraints weight = 35977.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.038050 restraints weight = 24536.500| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8610 Z= 0.231 Angle : 0.568 6.879 11732 Z= 0.297 Chirality : 0.043 0.202 1313 Planarity : 0.005 0.104 1510 Dihedral : 7.316 78.170 1248 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % 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: -0.03 (0.26), residues: 1067 helix: -0.77 (0.63), residues: 72 sheet: 0.62 (0.27), residues: 370 loop : -0.26 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 52 HIS 0.003 0.001 HIS L 106 PHE 0.016 0.002 PHE A 318 TYR 0.012 0.001 TYR A 365 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 38 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.7846 (ppp) cc_final: 0.7503 (ppp) outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.1876 time to fit residues: 11.4710 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 : 1.013 ------------------------------------------------------------------------------- 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: 3.9990 chunk 78 optimal weight: 1.9990 chunk 102 optimal weight: 0.0980 chunk 38 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 4.9990 chunk 91 optimal weight: 0.0870 chunk 48 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** 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 = 0.3360 r_free = 0.3360 target = 0.047835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.037609 restraints weight = 63930.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.039052 restraints weight = 36486.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.040077 restraints weight = 24668.046| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8610 Z= 0.139 Angle : 0.542 6.761 11732 Z= 0.279 Chirality : 0.044 0.177 1313 Planarity : 0.004 0.094 1510 Dihedral : 6.947 74.201 1248 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.63 (0.64), residues: 70 sheet: 0.68 (0.27), residues: 377 loop : -0.21 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 633 HIS 0.002 0.001 HIS L 106 PHE 0.017 0.001 PHE A 318 TYR 0.020 0.001 TYR H 160 ARG 0.005 0.000 ARG A 403 *********************** 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 46 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 PHE cc_start: 0.9172 (m-10) cc_final: 0.8949 (m-10) REVERT: A 458 LYS cc_start: 0.9388 (mtpt) cc_final: 0.9018 (mmtt) REVERT: H 51 GLU cc_start: 0.9063 (tp30) cc_final: 0.8749 (tp30) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1894 time to fit residues: 13.2736 Evaluate side-chains 32 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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: 5.9990 chunk 87 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 102 optimal weight: 0.0060 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 27 optimal weight: 0.0010 chunk 101 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.047624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.037208 restraints weight = 63040.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.038678 restraints weight = 35382.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.039703 restraints weight = 23840.898| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2495 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= 0.142 Angle : 0.539 7.548 11732 Z= 0.276 Chirality : 0.043 0.172 1313 Planarity : 0.004 0.077 1510 Dihedral : 6.756 70.771 1248 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 0.14 (0.26), residues: 1067 helix: -0.52 (0.65), residues: 70 sheet: 0.82 (0.27), residues: 372 loop : -0.23 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 633 HIS 0.002 0.001 HIS L 106 PHE 0.015 0.001 PHE A 318 TYR 0.016 0.001 TYR L 193 ARG 0.010 0.001 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 to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8392 (t80) cc_final: 0.8011 (t80) REVERT: A 458 LYS cc_start: 0.9389 (mtpt) cc_final: 0.9019 (mmtt) REVERT: H 51 GLU cc_start: 0.9038 (tp30) cc_final: 0.8715 (tp30) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2209 time to fit residues: 13.7666 Evaluate side-chains 34 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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: 4.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 0.0070 chunk 100 optimal weight: 6.9990 chunk 58 optimal weight: 0.3980 chunk 95 optimal weight: 0.8980 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.048324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.038028 restraints weight = 63960.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.039473 restraints weight = 36284.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.040503 restraints weight = 24644.755| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2649 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 : 0.523 6.916 11732 Z= 0.267 Chirality : 0.043 0.160 1313 Planarity : 0.003 0.040 1510 Dihedral : 6.502 65.737 1248 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % 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: 0.21 (0.26), residues: 1067 helix: -0.47 (0.66), residues: 70 sheet: 0.87 (0.27), residues: 372 loop : -0.20 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 41 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 0.005 0.000 ARG A 328 *********************** 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 45 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.9392 (mtpt) cc_final: 0.9023 (mmtt) REVERT: H 51 GLU cc_start: 0.9052 (tp30) cc_final: 0.8742 (tp30) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1933 time to fit residues: 13.5163 Evaluate side-chains 32 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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: 4.9990 chunk 60 optimal weight: 2.9990 chunk 94 optimal weight: 0.0770 chunk 97 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 71 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.6146 ------------------------------------------------------------------------------- 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 = 0.3291 r_free = 0.3291 target = 0.045495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.035405 restraints weight = 64151.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.036765 restraints weight = 36777.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.037702 restraints weight = 25119.234| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 8610 Z= 0.307 Angle : 0.602 6.943 11732 Z= 0.314 Chirality : 0.043 0.193 1313 Planarity : 0.004 0.037 1510 Dihedral : 6.889 65.348 1248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.61 (0.65), residues: 70 sheet: 0.70 (0.27), residues: 369 loop : -0.27 (0.25), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 633 HIS 0.008 0.002 HIS L 106 PHE 0.019 0.002 PHE A 238 TYR 0.011 0.002 TYR H 114 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 39 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.9036 (p90) cc_final: 0.8675 (p90) REVERT: H 51 GLU cc_start: 0.8994 (tp30) cc_final: 0.8705 (tp30) outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.1808 time to fit residues: 11.3476 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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** 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 = 0.3321 r_free = 0.3321 target = 0.046679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.036556 restraints weight = 65052.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.037960 restraints weight = 36850.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038969 restraints weight = 25017.580| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8610 Z= 0.197 Angle : 0.552 7.052 11732 Z= 0.285 Chirality : 0.043 0.170 1313 Planarity : 0.004 0.041 1510 Dihedral : 6.707 60.789 1248 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % 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: 0.06 (0.26), residues: 1067 helix: -0.61 (0.64), residues: 70 sheet: 0.69 (0.27), residues: 370 loop : -0.24 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 633 HIS 0.005 0.001 HIS L 106 PHE 0.021 0.002 PHE H 115 TYR 0.016 0.001 TYR H 160 ARG 0.002 0.000 ARG A 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2617.74 seconds wall clock time: 48 minutes 11.71 seconds (2891.71 seconds total)