Starting phenix.real_space_refine on Tue Jan 14 12:10:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.map" model { file = "/net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erd_19912/01_2025/9erd_19912.cif" } resolution = 3.72 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= -0.002 sd= 0.075 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3 5.49 5 Mg 2 5.21 5 S 43 5.16 5 C 4174 2.51 5 N 1141 2.21 5 O 1205 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 6569 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 813, 6535 Classifications: {'peptide': 813} Link IDs: {'PCIS': 3, 'PTRANS': 37, 'TRANS': 772} Chain breaks: 5 Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' MG': 2, ' ZN': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1928 SG CYS A 287 29.694 31.565 57.065 1.00118.64 S ATOM 2205 SG CYS A 321 30.103 32.101 53.326 1.00101.29 S ATOM 2211 SG CYS A 322 29.412 35.064 55.601 1.00100.97 S Time building chain proxies: 4.28, per 1000 atoms: 0.65 Number of scatterers: 6569 At special positions: 0 Unit cell: (65.835, 97.185, 127.49, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 43 16.00 P 3 15.00 Mg 2 11.99 O 1205 8.00 N 1141 7.00 C 4174 6.00 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: 1.96 Conformation dependent library (CDL) restraints added in 977.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1004 " pdb="ZN ZN A1004 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 322 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1004 " - pdb=" SG CYS A 287 " Number of angles added : 3 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1536 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 9 sheets defined 39.7% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 35 through 56 removed outlier: 4.720A pdb=" N GLN A 41 " --> pdb=" O ILE A 37 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 86 removed outlier: 3.909A pdb=" N ARG A 82 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 4.169A pdb=" N PHE A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 93' Processing helix chain 'A' and resid 144 through 155 Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 229 through 241 removed outlier: 4.212A pdb=" N GLU A 233 " --> pdb=" O ARG A 229 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N TYR A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Proline residue: A 236 - end of helix removed outlier: 3.948A pdb=" N THR A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 265 Processing helix chain 'A' and resid 266 through 281 removed outlier: 4.204A pdb=" N ARG A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 389 through 399 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.863A pdb=" N LYS A 429 " --> pdb=" O GLU A 425 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.514A pdb=" N ASN A 450 " --> pdb=" O VAL A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.549A pdb=" N TYR A 486 " --> pdb=" O GLU A 482 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 removed outlier: 3.912A pdb=" N SER A 540 " --> pdb=" O ALA A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 559 removed outlier: 3.818A pdb=" N VAL A 557 " --> pdb=" O SER A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 570 removed outlier: 4.272A pdb=" N GLN A 568 " --> pdb=" O LEU A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 587 removed outlier: 3.968A pdb=" N ARG A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 621 removed outlier: 3.596A pdb=" N GLU A 614 " --> pdb=" O MET A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 642 removed outlier: 3.800A pdb=" N ASP A 642 " --> pdb=" O ASN A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 680 through 689 Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 746 Processing helix chain 'A' and resid 784 through 801 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 830 removed outlier: 3.773A pdb=" N TYR A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 858 Processing helix chain 'A' and resid 880 through 887 removed outlier: 3.807A pdb=" N CYS A 884 " --> pdb=" O ASN A 880 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.830A pdb=" N VAL A 9 " --> pdb=" O ASN A 20 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 removed outlier: 3.504A pdb=" N ARG A 134 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 141 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.642A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N THR A 296 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE A 315 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LYS A 298 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS A 313 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL A 300 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N TYR A 311 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 302 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 369 removed outlier: 6.532A pdb=" N VAL A 381 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N TYR A 382 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 405 through 408 removed outlier: 7.530A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU A 476 " --> pdb=" O LEU A 515 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 596 through 599 removed outlier: 4.041A pdb=" N GLU A 725 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU A 727 " --> pdb=" O HIS A 598 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 627 through 630 Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 6.480A pdb=" N THR A 776 " --> pdb=" O LEU A 893 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ILE A 895 " --> pdb=" O THR A 776 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG A 778 " --> pdb=" O ILE A 895 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL A 850 " --> pdb=" O VAL A 809 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 852 " --> pdb=" O VAL A 811 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 681 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1071 1.29 - 1.42: 1686 1.42 - 1.55: 3876 1.55 - 1.68: 6 1.68 - 1.81: 61 Bond restraints: 6700 Sorted by residual: bond pdb=" C TYR A 535 " pdb=" O TYR A 535 " ideal model delta sigma weight residual 1.238 1.161 0.077 1.28e-02 6.10e+03 3.61e+01 bond pdb=" C TYR A 535 " pdb=" N PRO A 536 " ideal model delta sigma weight residual 1.332 1.271 0.060 1.26e-02 6.30e+03 2.30e+01 bond pdb=" CA TYR A 535 " pdb=" C TYR A 535 " ideal model delta sigma weight residual 1.524 1.466 0.058 1.26e-02 6.30e+03 2.12e+01 bond pdb=" CA ARG A 674 " pdb=" C ARG A 674 " ideal model delta sigma weight residual 1.521 1.569 -0.048 1.24e-02 6.50e+03 1.51e+01 bond pdb=" CA TYR A 535 " pdb=" CB TYR A 535 " ideal model delta sigma weight residual 1.530 1.484 0.045 1.58e-02 4.01e+03 8.28e+00 ... (remaining 6695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 8628 1.46 - 2.92: 335 2.92 - 4.38: 66 4.38 - 5.85: 9 5.85 - 7.31: 7 Bond angle restraints: 9045 Sorted by residual: angle pdb=" N LEU A 393 " pdb=" CA LEU A 393 " pdb=" C LEU A 393 " ideal model delta sigma weight residual 111.28 117.76 -6.48 1.09e+00 8.42e-01 3.53e+01 angle pdb=" N GLN A 395 " pdb=" CA GLN A 395 " pdb=" C GLN A 395 " ideal model delta sigma weight residual 111.36 104.89 6.47 1.09e+00 8.42e-01 3.52e+01 angle pdb=" N GLN A 395 " pdb=" CA GLN A 395 " pdb=" CB GLN A 395 " ideal model delta sigma weight residual 110.16 117.47 -7.31 1.48e+00 4.57e-01 2.44e+01 angle pdb=" N HIS A 869 " pdb=" CA HIS A 869 " pdb=" C HIS A 869 " ideal model delta sigma weight residual 112.23 118.94 -6.71 2.20e+00 2.07e-01 9.31e+00 angle pdb=" CA GLU A 209 " pdb=" C GLU A 209 " pdb=" N SER A 210 " ideal model delta sigma weight residual 115.51 119.18 -3.67 1.27e+00 6.20e-01 8.36e+00 ... (remaining 9040 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3639 17.03 - 34.06: 331 34.06 - 51.10: 124 51.10 - 68.13: 19 68.13 - 85.16: 10 Dihedral angle restraints: 4123 sinusoidal: 1749 harmonic: 2374 Sorted by residual: dihedral pdb=" CA ALA A 876 " pdb=" C ALA A 876 " pdb=" N ILE A 877 " pdb=" CA ILE A 877 " ideal model delta harmonic sigma weight residual 180.00 160.20 19.80 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA TYR A 704 " pdb=" C TYR A 704 " pdb=" N PHE A 705 " pdb=" CA PHE A 705 " ideal model delta harmonic sigma weight residual 180.00 161.23 18.77 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA VAL A 836 " pdb=" C VAL A 836 " pdb=" N GLN A 837 " pdb=" CA GLN A 837 " ideal model delta harmonic sigma weight residual 180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 4120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 830 0.051 - 0.101: 128 0.101 - 0.152: 38 0.152 - 0.203: 1 0.203 - 0.253: 2 Chirality restraints: 999 Sorted by residual: chirality pdb=" CA LEU A 393 " pdb=" N LEU A 393 " pdb=" C LEU A 393 " pdb=" CB LEU A 393 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA TYR A 535 " pdb=" N TYR A 535 " pdb=" C TYR A 535 " pdb=" CB TYR A 535 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA HIS A 869 " pdb=" N HIS A 869 " pdb=" C HIS A 869 " pdb=" CB HIS A 869 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.34e-01 ... (remaining 996 not shown) Planarity restraints: 1155 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 539 " 0.001 2.00e-02 2.50e+03 1.08e-02 2.32e+00 pdb=" CG TYR A 539 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 539 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A 539 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A 539 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR A 539 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 539 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 539 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 535 " 0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO A 536 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO A 536 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 536 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 609 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.67e+00 pdb=" C ALA A 609 " -0.022 2.00e-02 2.50e+03 pdb=" O ALA A 609 " 0.008 2.00e-02 2.50e+03 pdb=" N MET A 610 " 0.008 2.00e-02 2.50e+03 ... (remaining 1152 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 15 2.38 - 3.01: 3977 3.01 - 3.64: 9443 3.64 - 4.27: 14019 4.27 - 4.90: 24075 Nonbonded interactions: 51529 Sorted by model distance: nonbonded pdb="MG MG A1001 " pdb=" O2B ATP A1002 " model vdw 1.752 2.170 nonbonded pdb="MG MG A1001 " pdb=" O1G ATP A1002 " model vdw 1.795 2.170 nonbonded pdb="MG MG A1001 " pdb=" O3B ATP A1002 " model vdw 2.036 2.170 nonbonded pdb="MG MG A1001 " pdb=" PG ATP A1002 " model vdw 2.151 2.530 nonbonded pdb=" OE1 GLU A 209 " pdb="MG MG A1003 " model vdw 2.167 2.170 ... (remaining 51524 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.410 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 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 : 0.005 0.077 6700 Z= 0.298 Angle : 0.707 7.306 9045 Z= 0.404 Chirality : 0.043 0.253 999 Planarity : 0.004 0.037 1155 Dihedral : 15.665 85.159 2587 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 0.28 % Allowed : 12.79 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.42 (0.28), residues: 801 helix: -0.61 (0.29), residues: 264 sheet: -0.68 (0.46), residues: 146 loop : -1.19 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 699 HIS 0.004 0.001 HIS A 664 PHE 0.010 0.002 PHE A 106 TYR 0.021 0.002 TYR A 539 ARG 0.004 0.000 ARG A 674 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8329 (p90) cc_final: 0.8074 (p90) REVERT: A 272 ARG cc_start: 0.8590 (ptp90) cc_final: 0.8131 (ptt-90) REVERT: A 273 LYS cc_start: 0.8215 (mmpt) cc_final: 0.7615 (mmpt) REVERT: A 824 TYR cc_start: 0.8382 (t80) cc_final: 0.8179 (t80) outliers start: 2 outliers final: 1 residues processed: 96 average time/residue: 0.2421 time to fit residues: 30.0469 Evaluate side-chains 82 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 880 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.162505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.129204 restraints weight = 9748.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131068 restraints weight = 7087.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.133054 restraints weight = 5060.713| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 6700 Z= 0.332 Angle : 0.712 11.357 9045 Z= 0.360 Chirality : 0.045 0.141 999 Planarity : 0.004 0.041 1155 Dihedral : 7.970 82.985 931 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.03 % Allowed : 13.34 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.00 (0.29), residues: 801 helix: -0.02 (0.32), residues: 268 sheet: -0.67 (0.44), residues: 149 loop : -1.04 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 699 HIS 0.006 0.001 HIS A 892 PHE 0.014 0.002 PHE A 103 TYR 0.016 0.002 TYR A 629 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 91 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8274 (p90) cc_final: 0.7991 (p90) REVERT: A 272 ARG cc_start: 0.8713 (ptp90) cc_final: 0.8285 (ptp-170) REVERT: A 314 MET cc_start: 0.7409 (mpp) cc_final: 0.7033 (ptp) REVERT: A 497 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8507 (mmtm) REVERT: A 498 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8012 (mt) REVERT: A 562 ARG cc_start: 0.8086 (tmm-80) cc_final: 0.7717 (tmm-80) REVERT: A 789 MET cc_start: 0.5142 (tpp) cc_final: 0.4934 (mmm) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.2270 time to fit residues: 31.3001 Evaluate side-chains 94 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 881 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 63 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 15 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.161326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127630 restraints weight = 10001.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129750 restraints weight = 7554.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131099 restraints weight = 5242.823| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6700 Z= 0.382 Angle : 0.723 11.106 9045 Z= 0.362 Chirality : 0.045 0.141 999 Planarity : 0.005 0.040 1155 Dihedral : 7.732 84.061 929 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.85 % Allowed : 14.31 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -1.11 (0.29), residues: 801 helix: -0.09 (0.31), residues: 274 sheet: -0.74 (0.42), residues: 153 loop : -1.14 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 413 HIS 0.007 0.002 HIS A 664 PHE 0.014 0.002 PHE A 398 TYR 0.018 0.002 TYR A 629 ARG 0.005 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 88 time to evaluate : 0.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9419 (pttp) cc_final: 0.9161 (pttp) REVERT: A 68 GLU cc_start: 0.7665 (mp0) cc_final: 0.7400 (mp0) REVERT: A 198 TYR cc_start: 0.8281 (p90) cc_final: 0.8043 (p90) REVERT: A 272 ARG cc_start: 0.8737 (ptp90) cc_final: 0.7946 (ptt-90) REVERT: A 273 LYS cc_start: 0.8138 (mmpt) cc_final: 0.7821 (mmpt) REVERT: A 314 MET cc_start: 0.7416 (mpp) cc_final: 0.6974 (ptp) REVERT: A 472 LEU cc_start: 0.7522 (OUTLIER) cc_final: 0.7103 (tm) REVERT: A 497 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8541 (mmtm) REVERT: A 498 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.8028 (mt) REVERT: A 562 ARG cc_start: 0.8122 (tmm-80) cc_final: 0.7692 (tmm-80) REVERT: A 655 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6672 (tt) REVERT: A 789 MET cc_start: 0.5231 (tpp) cc_final: 0.4989 (mmm) outliers start: 28 outliers final: 20 residues processed: 104 average time/residue: 0.2450 time to fit residues: 32.7827 Evaluate side-chains 106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 0.0770 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 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 = 0.4016 r_free = 0.4016 target = 0.162896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.129575 restraints weight = 9925.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.131886 restraints weight = 7115.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.133373 restraints weight = 4897.740| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6700 Z= 0.268 Angle : 0.656 14.474 9045 Z= 0.328 Chirality : 0.043 0.136 999 Planarity : 0.004 0.034 1155 Dihedral : 7.169 82.940 929 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 4.54 % Allowed : 15.54 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.85 (0.30), residues: 801 helix: 0.24 (0.32), residues: 273 sheet: -0.53 (0.43), residues: 146 loop : -1.11 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.006 0.001 HIS A 598 PHE 0.012 0.002 PHE A 103 TYR 0.016 0.002 TYR A 824 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9457 (pttp) cc_final: 0.9239 (pttp) REVERT: A 68 GLU cc_start: 0.7658 (mp0) cc_final: 0.7401 (mp0) REVERT: A 198 TYR cc_start: 0.8356 (p90) cc_final: 0.8119 (p90) REVERT: A 272 ARG cc_start: 0.8751 (ptp90) cc_final: 0.8002 (ptt-90) REVERT: A 273 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7809 (mmpt) REVERT: A 405 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7934 (tp) REVERT: A 472 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7016 (tm) REVERT: A 497 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8067 (mptt) REVERT: A 498 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7997 (mt) REVERT: A 534 ASP cc_start: 0.7896 (p0) cc_final: 0.7620 (p0) REVERT: A 789 MET cc_start: 0.5201 (tpp) cc_final: 0.4994 (mmm) outliers start: 33 outliers final: 25 residues processed: 108 average time/residue: 0.2152 time to fit residues: 30.3447 Evaluate side-chains 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 589 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 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 = 0.4036 r_free = 0.4036 target = 0.164452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.133223 restraints weight = 9809.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.133412 restraints weight = 7462.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.135622 restraints weight = 5855.660| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6700 Z= 0.236 Angle : 0.638 12.709 9045 Z= 0.315 Chirality : 0.043 0.140 999 Planarity : 0.004 0.031 1155 Dihedral : 6.817 81.848 929 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.36 % Allowed : 15.82 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.62 (0.30), residues: 801 helix: 0.41 (0.32), residues: 273 sheet: -0.32 (0.44), residues: 142 loop : -0.99 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 892 PHE 0.010 0.001 PHE A 103 TYR 0.033 0.002 TYR A 539 ARG 0.006 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 88 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8296 (p90) cc_final: 0.8054 (p90) REVERT: A 273 LYS cc_start: 0.8214 (mmpt) cc_final: 0.7818 (mmpt) REVERT: A 351 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7488 (tpp) REVERT: A 405 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8103 (tp) REVERT: A 472 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7056 (tm) REVERT: A 498 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7946 (mt) REVERT: A 789 MET cc_start: 0.5460 (OUTLIER) cc_final: 0.5222 (mmm) outliers start: 39 outliers final: 25 residues processed: 109 average time/residue: 0.2121 time to fit residues: 30.7132 Evaluate side-chains 112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 82 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 881 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 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 = 0.4057 r_free = 0.4057 target = 0.166177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135013 restraints weight = 9700.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.134976 restraints weight = 7423.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137492 restraints weight = 5944.407| |-----------------------------------------------------------------------------| r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6700 Z= 0.207 Angle : 0.623 11.740 9045 Z= 0.307 Chirality : 0.042 0.133 999 Planarity : 0.004 0.035 1155 Dihedral : 6.497 82.769 929 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 4.54 % Allowed : 17.61 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.30), residues: 801 helix: 0.58 (0.32), residues: 275 sheet: -0.12 (0.48), residues: 123 loop : -0.76 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 PHE 0.011 0.001 PHE A 705 TYR 0.024 0.001 TYR A 539 ARG 0.008 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 88 time to evaluate : 0.714 Fit side-chains REVERT: A 198 TYR cc_start: 0.8220 (p90) cc_final: 0.8005 (p90) REVERT: A 273 LYS cc_start: 0.8257 (mmpt) cc_final: 0.7867 (mmmt) REVERT: A 472 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7036 (tm) REVERT: A 498 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7835 (mt) REVERT: A 789 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.5260 (mmm) REVERT: A 797 ARG cc_start: 0.7815 (ttp-170) cc_final: 0.7205 (ttp-170) outliers start: 33 outliers final: 21 residues processed: 107 average time/residue: 0.1966 time to fit residues: 27.9244 Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 chunk 20 optimal weight: 0.0980 chunk 67 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 6 optimal weight: 0.0670 chunk 42 optimal weight: 0.5980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN ** A 721 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 = 0.4084 r_free = 0.4084 target = 0.168492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137192 restraints weight = 9616.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139249 restraints weight = 6908.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140908 restraints weight = 5280.914| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6700 Z= 0.170 Angle : 0.625 11.479 9045 Z= 0.304 Chirality : 0.042 0.134 999 Planarity : 0.004 0.039 1155 Dihedral : 6.215 81.448 929 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.99 % Allowed : 18.84 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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 (0.30), residues: 801 helix: 0.76 (0.32), residues: 276 sheet: -0.21 (0.45), residues: 137 loop : -0.60 (0.33), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.020 0.001 PHE A 238 TYR 0.017 0.001 TYR A 539 ARG 0.010 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8117 (p90) cc_final: 0.7868 (p90) REVERT: A 273 LYS cc_start: 0.8211 (mmpt) cc_final: 0.7792 (mmpt) REVERT: A 472 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7046 (tm) REVERT: A 704 TYR cc_start: 0.8275 (t80) cc_final: 0.7933 (t80) outliers start: 29 outliers final: 19 residues processed: 107 average time/residue: 0.1941 time to fit residues: 27.6919 Evaluate side-chains 102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 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 = 0.4006 r_free = 0.4006 target = 0.161718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.131047 restraints weight = 10040.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130698 restraints weight = 7269.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132425 restraints weight = 7187.838| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 6700 Z= 0.395 Angle : 0.741 11.398 9045 Z= 0.365 Chirality : 0.046 0.141 999 Planarity : 0.005 0.046 1155 Dihedral : 6.945 86.415 929 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.87 % Favored : 93.01 % Rotamer: Outliers : 4.54 % Allowed : 18.57 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.66 (0.30), residues: 801 helix: 0.32 (0.31), residues: 275 sheet: -0.49 (0.45), residues: 146 loop : -0.91 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 110 HIS 0.007 0.002 HIS A 892 PHE 0.017 0.002 PHE A 398 TYR 0.020 0.002 TYR A 629 ARG 0.010 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.835 Fit side-chains REVERT: A 63 MET cc_start: 0.8208 (mtm) cc_final: 0.7933 (mpp) REVERT: A 198 TYR cc_start: 0.8116 (p90) cc_final: 0.7834 (p90) REVERT: A 273 LYS cc_start: 0.8151 (mmpt) cc_final: 0.7829 (mmpt) REVERT: A 472 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7010 (tm) REVERT: A 498 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7884 (mt) REVERT: A 797 ARG cc_start: 0.7918 (ttp-170) cc_final: 0.7302 (ttp-170) outliers start: 33 outliers final: 26 residues processed: 102 average time/residue: 0.2053 time to fit residues: 28.3616 Evaluate side-chains 107 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 79 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 564 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 chunk 39 optimal weight: 0.3980 chunk 64 optimal weight: 0.0570 chunk 55 optimal weight: 0.7980 chunk 6 optimal weight: 9.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 721 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 = 0.4083 r_free = 0.4083 target = 0.168219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.136884 restraints weight = 9600.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.138503 restraints weight = 6908.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140333 restraints weight = 5380.002| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6700 Z= 0.172 Angle : 0.656 11.720 9045 Z= 0.317 Chirality : 0.042 0.132 999 Planarity : 0.004 0.042 1155 Dihedral : 6.207 80.321 929 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.12 % Favored : 96.75 % Rotamer: Outliers : 3.16 % Allowed : 20.22 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.16 (0.30), residues: 801 helix: 0.71 (0.32), residues: 276 sheet: -0.13 (0.44), residues: 142 loop : -0.63 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.012 0.001 PHE A 705 TYR 0.015 0.001 TYR A 539 ARG 0.007 0.000 ARG A 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.700 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8125 (p90) cc_final: 0.7863 (p90) REVERT: A 273 LYS cc_start: 0.8272 (mmpt) cc_final: 0.7873 (mmpt) REVERT: A 472 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7077 (tm) outliers start: 23 outliers final: 18 residues processed: 101 average time/residue: 0.2025 time to fit residues: 27.3559 Evaluate side-chains 101 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 842 CYS Chi-restraints excluded: chain A residue 858 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.9990 chunk 63 optimal weight: 0.0070 chunk 68 optimal weight: 2.9990 chunk 38 optimal weight: 0.0670 chunk 44 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 74 optimal weight: 0.2980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.167364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136601 restraints weight = 9817.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138496 restraints weight = 6453.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.139948 restraints weight = 5244.191| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6700 Z= 0.183 Angle : 0.662 11.536 9045 Z= 0.320 Chirality : 0.042 0.131 999 Planarity : 0.004 0.039 1155 Dihedral : 6.092 82.896 929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.20 % Allowed : 21.46 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.08 (0.31), residues: 801 helix: 0.79 (0.32), residues: 276 sheet: -0.05 (0.45), residues: 142 loop : -0.60 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 413 HIS 0.005 0.001 HIS A 598 PHE 0.009 0.001 PHE A 705 TYR 0.038 0.002 TYR A 539 ARG 0.006 0.000 ARG A 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1602 Ramachandran restraints generated. 801 Oldfield, 0 Emsley, 801 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8126 (p90) cc_final: 0.7883 (p90) REVERT: A 273 LYS cc_start: 0.8304 (mmpt) cc_final: 0.7881 (mmpt) REVERT: A 472 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7022 (tm) REVERT: A 507 LYS cc_start: 0.6950 (ttmt) cc_final: 0.6695 (pttp) REVERT: A 704 TYR cc_start: 0.8357 (t80) cc_final: 0.7589 (t80) outliers start: 16 outliers final: 12 residues processed: 98 average time/residue: 0.2283 time to fit residues: 29.5785 Evaluate side-chains 98 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 60 optimal weight: 0.5980 chunk 71 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 598 HIS A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134587 restraints weight = 9904.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135557 restraints weight = 6974.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136893 restraints weight = 5977.379| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 6700 Z= 0.251 Angle : 0.686 11.199 9045 Z= 0.332 Chirality : 0.043 0.142 999 Planarity : 0.004 0.054 1155 Dihedral : 6.327 88.255 929 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.89 % Allowed : 20.91 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % 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: -0.20 (0.30), residues: 801 helix: 0.69 (0.32), residues: 276 sheet: -0.13 (0.45), residues: 142 loop : -0.67 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.005 0.001 HIS A 598 PHE 0.011 0.002 PHE A 398 TYR 0.041 0.002 TYR A 539 ARG 0.016 0.001 ARG A 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2068.95 seconds wall clock time: 38 minutes 34.27 seconds (2314.27 seconds total)