Starting phenix.real_space_refine on Fri Feb 14 15:04:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.map" model { file = "/net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pmx_13543/02_2025/7pmx_13543.cif" } resolution = 3.5 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= 1.000 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: 5 Type Number sf(0) Gaussians S 32 5.16 5 C 3384 2.51 5 N 830 2.21 5 O 918 1.98 5 H 5253 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 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: 10417 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 10384 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 30, 'TRANS': 626} Chain breaks: 3 Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Classifications: {'peptide': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'TRANS': 1} Time building chain proxies: 5.67, per 1000 atoms: 0.54 Number of scatterers: 10417 At special positions: 0 Unit cell: (85.09, 89.11, 121.94, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 O 918 8.00 N 830 7.00 C 3384 6.00 H 5253 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 722.3 milliseconds 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 61.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 12 through 45 removed outlier: 4.214A pdb=" N PHE A 18 " --> pdb=" O LEU A 14 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 35 " --> pdb=" O TYR A 31 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU A 39 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE A 41 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR A 42 " --> pdb=" O ILE A 38 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 56 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 66 through 75 removed outlier: 3.532A pdb=" N GLY A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 108 removed outlier: 3.737A pdb=" N LYS A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 83 " --> pdb=" O GLY A 79 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 85 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 149 removed outlier: 3.942A pdb=" N LEU A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER A 125 " --> pdb=" O HIS A 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 139 " --> pdb=" O GLY A 135 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) Proline residue: A 141 - end of helix removed outlier: 3.537A pdb=" N SER A 144 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 185 removed outlier: 3.560A pdb=" N SER A 164 " --> pdb=" O ASN A 160 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 171 " --> pdb=" O TYR A 167 " (cutoff:3.500A) Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 197 through 219 Proline residue: A 205 - end of helix removed outlier: 3.529A pdb=" N VAL A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.505A pdb=" N LYS A 245 " --> pdb=" O GLY A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 Processing helix chain 'A' and resid 270 through 286 removed outlier: 3.876A pdb=" N LEU A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'A' and resid 292 through 298 removed outlier: 3.565A pdb=" N ASP A 298 " --> pdb=" O TRP A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 311 removed outlier: 4.157A pdb=" N SER A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N TRP A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N THR A 305 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 307 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR A 309 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 325 removed outlier: 3.720A pdb=" N MET A 325 " --> pdb=" O PRO A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 343 removed outlier: 4.238A pdb=" N ALA A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) Proline residue: A 338 - end of helix Processing helix chain 'A' and resid 343 through 351 Processing helix chain 'A' and resid 356 through 384 removed outlier: 3.697A pdb=" N VAL A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL A 374 " --> pdb=" O MET A 370 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A 375 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 435 No H-bonds generated for 'chain 'A' and resid 433 through 435' Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 580 through 583 removed outlier: 3.671A pdb=" N LEU A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 583' Processing helix chain 'A' and resid 584 through 610 removed outlier: 3.580A pdb=" N LEU A 591 " --> pdb=" O GLN A 587 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 597 " --> pdb=" O CYS A 593 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR A 601 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 637 removed outlier: 3.639A pdb=" N LEU A 618 " --> pdb=" O MET A 614 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 625 " --> pdb=" O GLY A 621 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 626 " --> pdb=" O TRP A 622 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE A 631 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE A 632 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 633 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 651 removed outlier: 3.556A pdb=" N ALA A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR A 649 " --> pdb=" O GLN A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 Processing helix chain 'A' and resid 669 through 674 removed outlier: 5.739A pdb=" N TYR A 672 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 674 " --> pdb=" O THR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 680 removed outlier: 4.322A pdb=" N ALA A 680 " --> pdb=" O ALA A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing sheet with id=AA1, first strand: chain 'A' and resid 422 through 423 Processing sheet with id=AA2, first strand: chain 'A' and resid 422 through 423 removed outlier: 6.723A pdb=" N HIS A 469 " --> pdb=" O TRP A 465 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 414 through 418 Processing sheet with id=AA4, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.653A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 514 through 515 removed outlier: 3.653A pdb=" N ASN A 514 " --> pdb=" O ASN A 492 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY A 487 " --> pdb=" O TYR A 554 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR A 556 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG A 489 " --> pdb=" O TYR A 556 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 558 " --> pdb=" O ARG A 489 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 491 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N ARG A 560 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA A 553 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 505 through 510 removed outlier: 5.889A pdb=" N ILE A 498 " --> pdb=" O ASN A 509 " (cutoff:3.500A) 279 hydrogen bonds defined for protein. 795 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: 4.25 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5243 1.03 - 1.23: 10 1.23 - 1.42: 2199 1.42 - 1.61: 3033 1.61 - 1.81: 54 Bond restraints: 10539 Sorted by residual: bond pdb=" C GLN A 609 " pdb=" N ALA A 610 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.47e-02 4.63e+03 9.42e+00 bond pdb=" CA VAL A 204 " pdb=" CB VAL A 204 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.10e+00 bond pdb=" C ILE A 320 " pdb=" N GLN A 321 " ideal model delta sigma weight residual 1.329 1.360 -0.031 3.03e-02 1.09e+03 1.06e+00 bond pdb=" CA PRO A 536 " pdb=" C PRO A 536 " ideal model delta sigma weight residual 1.514 1.519 -0.005 5.50e-03 3.31e+04 6.72e-01 bond pdb=" CA ILE A 585 " pdb=" CB ILE A 585 " ideal model delta sigma weight residual 1.539 1.535 0.004 5.40e-03 3.43e+04 6.67e-01 ... (remaining 10534 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.06: 19071 7.06 - 14.12: 0 14.12 - 21.18: 0 21.18 - 28.24: 0 28.24 - 35.30: 3 Bond angle restraints: 19074 Sorted by residual: angle pdb=" C GLN A 609 " pdb=" CA GLN A 609 " pdb=" HA GLN A 609 " ideal model delta sigma weight residual 109.00 73.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" N GLN A 609 " pdb=" CA GLN A 609 " pdb=" HA GLN A 609 " ideal model delta sigma weight residual 110.00 75.41 34.59 3.00e+00 1.11e-01 1.33e+02 angle pdb=" CB GLN A 609 " pdb=" CA GLN A 609 " pdb=" HA GLN A 609 " ideal model delta sigma weight residual 109.00 76.17 32.83 3.00e+00 1.11e-01 1.20e+02 angle pdb=" N GLN A 609 " pdb=" CA GLN A 609 " pdb=" C GLN A 609 " ideal model delta sigma weight residual 113.18 116.37 -3.19 1.21e+00 6.83e-01 6.94e+00 angle pdb=" N VAL A 334 " pdb=" CA VAL A 334 " pdb=" C VAL A 334 " ideal model delta sigma weight residual 113.07 109.63 3.44 1.37e+00 5.33e-01 6.30e+00 ... (remaining 19069 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.85: 4628 16.85 - 33.70: 240 33.70 - 50.56: 63 50.56 - 67.41: 46 67.41 - 84.26: 9 Dihedral angle restraints: 4986 sinusoidal: 2660 harmonic: 2326 Sorted by residual: dihedral pdb=" C GLN A 609 " pdb=" N GLN A 609 " pdb=" CA GLN A 609 " pdb=" CB GLN A 609 " ideal model delta harmonic sigma weight residual -122.60 -131.27 8.67 0 2.50e+00 1.60e-01 1.20e+01 dihedral pdb=" CA LYS A 257 " pdb=" C LYS A 257 " pdb=" N ARG A 258 " pdb=" CA ARG A 258 " ideal model delta harmonic sigma weight residual 180.00 162.87 17.13 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" N GLN A 609 " pdb=" C GLN A 609 " pdb=" CA GLN A 609 " pdb=" CB GLN A 609 " ideal model delta harmonic sigma weight residual 122.80 131.07 -8.27 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 4983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 775 0.076 - 0.153: 53 0.153 - 0.229: 0 0.229 - 0.305: 0 0.305 - 0.381: 1 Chirality restraints: 829 Sorted by residual: chirality pdb=" CA GLN A 609 " pdb=" N GLN A 609 " pdb=" C GLN A 609 " pdb=" CB GLN A 609 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PRO A 291 " pdb=" N PRO A 291 " pdb=" C PRO A 291 " pdb=" CB PRO A 291 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.81e-01 chirality pdb=" CA ILE A 438 " pdb=" N ILE A 438 " pdb=" C ILE A 438 " pdb=" CB ILE A 438 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.72e-01 ... (remaining 826 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 345 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.82e+00 pdb=" N PRO A 346 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 346 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 346 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 288 " 0.022 5.00e-02 4.00e+02 3.32e-02 1.77e+00 pdb=" N PRO A 289 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 540 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 541 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 541 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 541 " 0.017 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 637 2.21 - 2.81: 21876 2.81 - 3.40: 27998 3.40 - 4.00: 35922 4.00 - 4.60: 55672 Nonbonded interactions: 142105 Sorted by model distance: nonbonded pdb=" OE1 GLU A 271 " pdb=" H GLU A 271 " model vdw 1.609 2.450 nonbonded pdb=" O GLY A 419 " pdb=" HG SER A 422 " model vdw 1.615 2.450 nonbonded pdb=" OD1 ASN A 486 " pdb=" HG SER A 552 " model vdw 1.649 2.450 nonbonded pdb=" O PHE A 652 " pdb=" H LEU A 656 " model vdw 1.652 2.450 nonbonded pdb=" O GLU A 156 " pdb="HD22 ASN A 160 " model vdw 1.653 2.450 ... (remaining 142100 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: 1.820 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: 0.180 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.540 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 0.045 5286 Z= 0.208 Angle : 0.536 5.749 7178 Z= 0.313 Chirality : 0.040 0.381 829 Planarity : 0.003 0.042 898 Dihedral : 10.516 84.261 1885 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.13 % Allowed : 4.08 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.33), residues: 649 helix: 0.56 (0.30), residues: 318 sheet: 2.02 (0.61), residues: 64 loop : -0.07 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.001 0.000 HIS A 260 PHE 0.009 0.001 PHE A 598 TYR 0.007 0.001 TYR A 12 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 LEU cc_start: 0.9155 (tt) cc_final: 0.8798 (tt) REVERT: A 255 PHE cc_start: 0.5399 (t80) cc_final: 0.5187 (t80) REVERT: A 296 LEU cc_start: 0.8938 (mm) cc_final: 0.8726 (mm) REVERT: A 397 ILE cc_start: 0.9220 (mt) cc_final: 0.8167 (mp) REVERT: A 407 MET cc_start: 0.7532 (mmt) cc_final: 0.7246 (mmm) REVERT: A 609 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8206 (mp10) outliers start: 12 outliers final: 4 residues processed: 104 average time/residue: 0.3774 time to fit residues: 50.8501 Evaluate side-chains 70 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 GLN A 393 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.120848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.086640 restraints weight = 36482.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.090680 restraints weight = 16285.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.093190 restraints weight = 10837.286| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5286 Z= 0.234 Angle : 0.639 6.729 7178 Z= 0.350 Chirality : 0.044 0.409 829 Planarity : 0.005 0.046 898 Dihedral : 6.149 55.744 711 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 8.87 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.34), residues: 649 helix: 0.71 (0.28), residues: 341 sheet: 1.41 (0.56), residues: 85 loop : -0.09 (0.44), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.004 0.001 HIS A 121 PHE 0.016 0.001 PHE A 166 TYR 0.014 0.001 TYR A 12 ARG 0.002 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7609 (mmt) cc_final: 0.7307 (mmm) REVERT: A 646 TRP cc_start: 0.5723 (m100) cc_final: 0.4897 (t60) outliers start: 9 outliers final: 9 residues processed: 81 average time/residue: 0.2925 time to fit residues: 33.0143 Evaluate side-chains 77 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 577 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 29 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 34 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.121974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088511 restraints weight = 35566.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.092570 restraints weight = 15456.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.095059 restraints weight = 10064.108| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5286 Z= 0.188 Angle : 0.560 5.863 7178 Z= 0.302 Chirality : 0.043 0.397 829 Planarity : 0.004 0.048 898 Dihedral : 5.883 53.984 708 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.60 % Allowed : 9.40 % Favored : 89.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.34), residues: 649 helix: 0.93 (0.29), residues: 344 sheet: 1.12 (0.63), residues: 69 loop : -0.35 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 260 PHE 0.017 0.001 PHE A 166 TYR 0.007 0.001 TYR A 507 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7935 (tp30) cc_final: 0.7682 (tp30) REVERT: A 407 MET cc_start: 0.7576 (mmt) cc_final: 0.7280 (mmm) REVERT: A 609 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7975 (mp10) outliers start: 9 outliers final: 6 residues processed: 76 average time/residue: 0.3000 time to fit residues: 31.8746 Evaluate side-chains 71 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 4 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN ** A 584 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 = 0.3984 r_free = 0.3984 target = 0.119673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.085725 restraints weight = 35746.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.089497 restraints weight = 16220.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.091830 restraints weight = 10847.104| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5286 Z= 0.361 Angle : 0.605 6.098 7178 Z= 0.334 Chirality : 0.044 0.396 829 Planarity : 0.004 0.047 898 Dihedral : 6.105 51.419 708 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.77 % Allowed : 11.17 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.34), residues: 649 helix: 0.75 (0.29), residues: 342 sheet: 0.53 (0.55), residues: 85 loop : -0.55 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 646 HIS 0.002 0.001 HIS A 469 PHE 0.020 0.002 PHE A 605 TYR 0.011 0.001 TYR A 588 ARG 0.003 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7685 (mmt) cc_final: 0.7086 (mmm) REVERT: A 609 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8217 (mp10) REVERT: A 646 TRP cc_start: 0.5818 (m100) cc_final: 0.5242 (t-100) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.2930 time to fit residues: 29.3201 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 609 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.121213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.087670 restraints weight = 35599.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.091653 restraints weight = 15651.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.094092 restraints weight = 10312.576| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5286 Z= 0.190 Angle : 0.554 7.110 7178 Z= 0.297 Chirality : 0.042 0.406 829 Planarity : 0.004 0.047 898 Dihedral : 5.932 50.377 708 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.13 % Allowed : 11.35 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.34), residues: 649 helix: 0.97 (0.29), residues: 343 sheet: 0.58 (0.56), residues: 85 loop : -0.51 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 260 PHE 0.017 0.001 PHE A 166 TYR 0.007 0.001 TYR A 12 ARG 0.001 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 407 MET cc_start: 0.7651 (mmt) cc_final: 0.7054 (mmm) REVERT: A 577 ASN cc_start: 0.8571 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: A 609 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8139 (mp10) REVERT: A 646 TRP cc_start: 0.5718 (m100) cc_final: 0.5264 (t-100) outliers start: 12 outliers final: 8 residues processed: 72 average time/residue: 0.2832 time to fit residues: 28.9279 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.121533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089981 restraints weight = 35494.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.091886 restraints weight = 15673.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092828 restraints weight = 11246.591| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5286 Z= 0.186 Angle : 0.540 7.385 7178 Z= 0.289 Chirality : 0.042 0.400 829 Planarity : 0.004 0.047 898 Dihedral : 5.833 50.286 708 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.13 % Allowed : 11.52 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.34), residues: 649 helix: 1.12 (0.29), residues: 343 sheet: 0.59 (0.56), residues: 85 loop : -0.50 (0.44), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 260 PHE 0.015 0.001 PHE A 166 TYR 0.007 0.001 TYR A 12 ARG 0.001 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 577 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8240 (m-40) REVERT: A 609 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.7928 (mp10) REVERT: A 646 TRP cc_start: 0.5755 (m100) cc_final: 0.5320 (t-100) outliers start: 12 outliers final: 9 residues processed: 73 average time/residue: 0.2878 time to fit residues: 29.5965 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 1 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.123062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.089908 restraints weight = 35567.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094021 restraints weight = 15353.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.096573 restraints weight = 10028.626| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5286 Z= 0.146 Angle : 0.522 6.375 7178 Z= 0.275 Chirality : 0.042 0.396 829 Planarity : 0.004 0.047 898 Dihedral : 5.672 50.921 708 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.95 % Allowed : 10.99 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.35), residues: 649 helix: 1.40 (0.29), residues: 337 sheet: 0.62 (0.55), residues: 85 loop : -0.31 (0.45), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.002 0.000 HIS A 260 PHE 0.015 0.001 PHE A 166 TYR 0.012 0.001 TYR A 40 ARG 0.002 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7978 (tp30) cc_final: 0.7772 (tp30) REVERT: A 41 PHE cc_start: 0.7627 (m-80) cc_final: 0.7270 (m-80) REVERT: A 577 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8255 (m-40) REVERT: A 609 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7902 (mp10) outliers start: 11 outliers final: 8 residues processed: 69 average time/residue: 0.2895 time to fit residues: 28.2946 Evaluate side-chains 69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 307 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 584 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 = 0.4010 r_free = 0.4010 target = 0.121118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.087306 restraints weight = 36705.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.091250 restraints weight = 16404.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.093665 restraints weight = 10991.128| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5286 Z= 0.274 Angle : 0.559 5.949 7178 Z= 0.302 Chirality : 0.043 0.390 829 Planarity : 0.004 0.046 898 Dihedral : 5.845 53.209 708 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.95 % Allowed : 11.17 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.34), residues: 649 helix: 1.24 (0.29), residues: 338 sheet: 0.57 (0.56), residues: 85 loop : -0.51 (0.43), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.001 0.001 HIS A 250 PHE 0.017 0.001 PHE A 166 TYR 0.008 0.001 TYR A 588 ARG 0.002 0.000 ARG A 159 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7665 (m-80) cc_final: 0.7331 (m-80) REVERT: A 577 ASN cc_start: 0.8587 (OUTLIER) cc_final: 0.8271 (m-40) REVERT: A 609 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8087 (mp10) REVERT: A 646 TRP cc_start: 0.5795 (m100) cc_final: 0.5433 (t-100) outliers start: 11 outliers final: 8 residues processed: 71 average time/residue: 0.2835 time to fit residues: 28.4172 Evaluate side-chains 72 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.121793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.090215 restraints weight = 35863.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092586 restraints weight = 15532.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.093241 restraints weight = 11089.361| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5286 Z= 0.175 Angle : 0.537 5.894 7178 Z= 0.285 Chirality : 0.042 0.400 829 Planarity : 0.004 0.045 898 Dihedral : 5.767 53.798 708 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.77 % Allowed : 11.17 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.35), residues: 649 helix: 1.20 (0.29), residues: 350 sheet: 0.61 (0.56), residues: 85 loop : -0.43 (0.46), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 264 HIS 0.002 0.001 HIS A 260 PHE 0.016 0.001 PHE A 166 TYR 0.010 0.001 TYR A 56 ARG 0.001 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7660 (m-80) cc_final: 0.7258 (m-80) REVERT: A 577 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.8217 (m-40) REVERT: A 609 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7942 (mp10) REVERT: A 646 TRP cc_start: 0.5732 (m100) cc_final: 0.5368 (t-100) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.2869 time to fit residues: 27.6058 Evaluate side-chains 69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.122166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.090213 restraints weight = 36410.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.092205 restraints weight = 16369.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092930 restraints weight = 11892.134| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5286 Z= 0.192 Angle : 0.541 6.331 7178 Z= 0.288 Chirality : 0.042 0.393 829 Planarity : 0.004 0.046 898 Dihedral : 5.427 55.057 705 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.77 % Allowed : 11.17 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.34), residues: 649 helix: 1.29 (0.29), residues: 344 sheet: 0.58 (0.56), residues: 85 loop : -0.44 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 646 HIS 0.001 0.000 HIS A 260 PHE 0.016 0.001 PHE A 166 TYR 0.008 0.001 TYR A 56 ARG 0.001 0.000 ARG A 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1298 Ramachandran restraints generated. 649 Oldfield, 0 Emsley, 649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.7675 (m-80) cc_final: 0.7262 (m-80) REVERT: A 577 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: A 609 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7917 (mp10) REVERT: A 646 TRP cc_start: 0.5752 (m100) cc_final: 0.5396 (t-100) outliers start: 10 outliers final: 8 residues processed: 68 average time/residue: 0.3012 time to fit residues: 28.9019 Evaluate side-chains 69 residues out of total 564 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 355 PHE Chi-restraints excluded: chain A residue 372 PHE Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 577 ASN Chi-restraints excluded: chain A residue 603 LEU Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 616 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.123305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.092506 restraints weight = 36267.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.093917 restraints weight = 15380.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094400 restraints weight = 11711.226| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5286 Z= 0.150 Angle : 0.519 5.776 7178 Z= 0.272 Chirality : 0.042 0.397 829 Planarity : 0.004 0.047 898 Dihedral : 5.311 56.265 705 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.95 % Allowed : 10.82 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.35), residues: 649 helix: 1.46 (0.29), residues: 344 sheet: 0.62 (0.56), residues: 85 loop : -0.38 (0.45), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 264 HIS 0.002 0.001 HIS A 260 PHE 0.015 0.001 PHE A 166 TYR 0.008 0.001 TYR A 56 ARG 0.001 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3616.46 seconds wall clock time: 64 minutes 49.82 seconds (3889.82 seconds total)