Starting phenix.real_space_refine on Tue Mar 11 20:05:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erd_19912/03_2025/9erd_19912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erd_19912/03_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_19912/03_2025/9erd_19912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erd_19912/03_2025/9erd_19912.map" model { file = "/net/cci-nas-00/data/ceres_data/9erd_19912/03_2025/9erd_19912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erd_19912/03_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 4.15, per 1000 atoms: 0.63 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: 1.55 Conformation dependent library (CDL) restraints added in 864.8 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: 0.78 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: 2.08 Time building geometry restraints manager: 1.87 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: 0.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.040 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.300 ------------------------------------------------------------------------------- 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 : 0.788 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: 0.2396 time to fit residues: 29.9059 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 : 0.773 ------------------------------------------------------------------------------- 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 = 9748.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.131148 restraints weight = 7087.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.133121 restraints weight = 5038.525| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 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 : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8273 (p90) cc_final: 0.7990 (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: 0.7034 (ptp) REVERT: A 497 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8506 (mmtm) REVERT: A 498 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8009 (mt) REVERT: A 562 ARG cc_start: 0.8084 (tmm-80) cc_final: 0.7715 (tmm-80) REVERT: A 789 MET cc_start: 0.5144 (tpp) cc_final: 0.4938 (mmm) outliers start: 22 outliers final: 12 residues processed: 106 average time/residue: 0.2140 time to fit residues: 29.5954 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 : 0.705 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7980 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3996 r_free = 0.3996 target = 0.161171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128964 restraints weight = 9982.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129827 restraints weight = 7327.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.131218 restraints weight = 5927.761| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 6700 Z= 0.384 Angle : 0.725 11.188 9045 Z= 0.364 Chirality : 0.046 0.140 999 Planarity : 0.005 0.040 1155 Dihedral : 7.745 84.112 929 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.85 % Allowed : 14.44 % Favored : 81.71 % 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: -1.13 (0.29), residues: 801 helix: -0.11 (0.31), residues: 274 sheet: -0.75 (0.42), residues: 153 loop : -1.15 (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 103 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 : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9358 (pttp) cc_final: 0.9136 (pttp) REVERT: A 68 GLU cc_start: 0.7639 (mp0) cc_final: 0.7389 (mp0) REVERT: A 272 ARG cc_start: 0.8618 (ptp90) cc_final: 0.7887 (ptp-170) REVERT: A 273 LYS cc_start: 0.8084 (mmpt) cc_final: 0.7791 (mmpt) REVERT: A 314 MET cc_start: 0.7404 (mpp) cc_final: 0.7115 (ptp) REVERT: A 472 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7120 (tm) REVERT: A 497 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8545 (mmtm) REVERT: A 498 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 562 ARG cc_start: 0.8114 (tmm-80) cc_final: 0.7687 (tmm-80) REVERT: A 655 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6686 (tt) REVERT: A 789 MET cc_start: 0.5507 (tpp) cc_final: 0.5242 (mmm) outliers start: 28 outliers final: 20 residues processed: 104 average time/residue: 0.2155 time to fit residues: 29.3101 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 : 0.757 ------------------------------------------------------------------------------- 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: 2.9990 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 47 optimal weight: 0.0670 chunk 66 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 overall best weight: 0.4836 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.167118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136348 restraints weight = 9664.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136604 restraints weight = 7342.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.138921 restraints weight = 5766.081| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 6700 Z= 0.173 Angle : 0.611 15.032 9045 Z= 0.306 Chirality : 0.042 0.130 999 Planarity : 0.004 0.030 1155 Dihedral : 6.681 82.298 929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.03 % Allowed : 16.23 % Favored : 80.74 % 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: -0.48 (0.30), residues: 801 helix: 0.49 (0.32), residues: 274 sheet: -0.35 (0.44), residues: 142 loop : -0.84 (0.32), residues: 385 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 0.011 0.001 PHE A 857 TYR 0.016 0.001 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 117 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 ARG cc_start: 0.8559 (ptp90) cc_final: 0.8170 (ptp-170) REVERT: A 351 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7476 (tpp) REVERT: A 405 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8032 (tp) REVERT: A 472 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7079 (tm) REVERT: A 534 ASP cc_start: 0.7726 (p0) cc_final: 0.7449 (p0) REVERT: A 789 MET cc_start: 0.5512 (tpp) cc_final: 0.5310 (mmm) outliers start: 22 outliers final: 11 residues processed: 106 average time/residue: 0.2223 time to fit residues: 30.4073 Evaluate side-chains 100 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE 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 405 LEU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 881 VAL 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: 0.6980 chunk 29 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 35 optimal weight: 0.2980 chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 2 optimal weight: 7.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 633 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.136374 restraints weight = 9756.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136375 restraints weight = 7413.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138852 restraints weight = 5956.192| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 6700 Z= 0.184 Angle : 0.612 12.667 9045 Z= 0.303 Chirality : 0.042 0.133 999 Planarity : 0.004 0.032 1155 Dihedral : 6.419 79.051 929 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 4.13 % Allowed : 17.47 % Favored : 78.40 % 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: -0.32 (0.30), residues: 801 helix: 0.67 (0.32), residues: 275 sheet: -0.28 (0.42), residues: 150 loop : -0.78 (0.33), residues: 376 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 0.010 0.001 PHE A 705 TYR 0.034 0.001 TYR A 539 ARG 0.007 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 117 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.694 Fit side-chains REVERT: A 273 LYS cc_start: 0.8197 (mmpt) cc_final: 0.7795 (mmpt) REVERT: A 351 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7559 (tpp) REVERT: A 472 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7061 (tm) REVERT: A 534 ASP cc_start: 0.7685 (p0) cc_final: 0.7446 (p0) REVERT: A 789 MET cc_start: 0.5525 (tpp) cc_final: 0.5294 (mmm) REVERT: A 797 ARG cc_start: 0.7785 (ttp-170) cc_final: 0.7186 (ttp-170) outliers start: 30 outliers final: 20 residues processed: 104 average time/residue: 0.2045 time to fit residues: 28.1348 Evaluate side-chains 101 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 351 MET Chi-restraints excluded: chain A residue 359 LEU 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 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: 0.2980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 0.0000 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.165293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.134298 restraints weight = 9850.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.135016 restraints weight = 7531.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.136996 restraints weight = 6078.627| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 6700 Z= 0.247 Angle : 0.639 11.823 9045 Z= 0.315 Chirality : 0.043 0.141 999 Planarity : 0.004 0.037 1155 Dihedral : 6.496 83.314 929 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.68 % Allowed : 17.47 % 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: -0.29 (0.30), residues: 801 helix: 0.66 (0.32), residues: 275 sheet: -0.32 (0.43), residues: 145 loop : -0.70 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.004 0.001 HIS A 664 PHE 0.011 0.001 PHE A 398 TYR 0.026 0.002 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 112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.754 Fit side-chains REVERT: A 273 LYS cc_start: 0.8205 (mmpt) cc_final: 0.7811 (mmpt) REVERT: A 472 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7053 (tm) REVERT: A 498 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7848 (mt) REVERT: A 789 MET cc_start: 0.5568 (OUTLIER) cc_final: 0.5303 (mmm) REVERT: A 797 ARG cc_start: 0.7840 (ttp-170) cc_final: 0.7232 (ttp-170) outliers start: 34 outliers final: 24 residues processed: 101 average time/residue: 0.1938 time to fit residues: 26.3857 Evaluate side-chains 102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 75 time to evaluate : 0.704 ------------------------------------------------------------------------------- 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 294 THR 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 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 789 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 20 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 6 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 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 = 0.4084 r_free = 0.4084 target = 0.168681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137852 restraints weight = 9614.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.137679 restraints weight = 7294.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.139995 restraints weight = 5953.911| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 6700 Z= 0.173 Angle : 0.615 11.662 9045 Z= 0.301 Chirality : 0.042 0.141 999 Planarity : 0.004 0.037 1155 Dihedral : 6.158 80.651 929 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 3.44 % Allowed : 18.98 % Favored : 77.58 % 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: -0.10 (0.30), residues: 801 helix: 0.80 (0.32), residues: 276 sheet: -0.17 (0.43), residues: 145 loop : -0.59 (0.33), residues: 380 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 0.015 0.001 PHE A 238 TYR 0.018 0.001 TYR A 539 ARG 0.009 0.000 ARG A 229 *********************** 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 118 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 93 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8232 (mmpt) cc_final: 0.7775 (mmpt) REVERT: A 472 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7051 (tm) REVERT: A 789 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.5261 (mmm) outliers start: 25 outliers final: 20 residues processed: 109 average time/residue: 0.2032 time to fit residues: 29.6498 Evaluate side-chains 102 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU 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 427 ILE 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 715 LEU Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 789 MET Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 46 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 6 optimal weight: 0.0170 chunk 17 optimal weight: 5.9990 chunk 80 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.0470 chunk 67 optimal weight: 0.8980 overall best weight: 0.4116 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.169379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138226 restraints weight = 9597.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138191 restraints weight = 7195.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140770 restraints weight = 5816.982| |-----------------------------------------------------------------------------| r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6700 Z= 0.173 Angle : 0.623 11.518 9045 Z= 0.305 Chirality : 0.042 0.178 999 Planarity : 0.004 0.037 1155 Dihedral : 5.987 81.672 929 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.61 % Allowed : 20.08 % Favored : 77.30 % 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: -0.04 (0.30), residues: 801 helix: 0.89 (0.31), residues: 276 sheet: -0.15 (0.43), residues: 152 loop : -0.59 (0.34), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.011 0.001 PHE A 238 TYR 0.017 0.001 TYR A 704 ARG 0.006 0.000 ARG A 135 *********************** 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 105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8266 (mmpt) cc_final: 0.7803 (mmpt) REVERT: A 472 LEU cc_start: 0.7396 (OUTLIER) cc_final: 0.7047 (tm) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.2132 time to fit residues: 27.3709 Evaluate side-chains 95 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 126 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU 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 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 850 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: 5.9990 chunk 1 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 64 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.167888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.136681 restraints weight = 9665.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136888 restraints weight = 7360.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.139196 restraints weight = 5888.731| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 6700 Z= 0.221 Angle : 0.651 11.213 9045 Z= 0.318 Chirality : 0.042 0.175 999 Planarity : 0.004 0.036 1155 Dihedral : 6.122 85.409 929 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.75 % Allowed : 20.08 % 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: -0.08 (0.30), residues: 801 helix: 0.79 (0.31), residues: 278 sheet: -0.01 (0.42), residues: 155 loop : -0.64 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 413 HIS 0.004 0.001 HIS A 664 PHE 0.011 0.001 PHE A 238 TYR 0.042 0.002 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 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8237 (mmpt) cc_final: 0.7781 (mmpt) REVERT: A 472 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7075 (tm) outliers start: 20 outliers final: 18 residues processed: 99 average time/residue: 0.2152 time to fit residues: 28.1031 Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 215 PHE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU 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 441 PHE Chi-restraints excluded: chain A residue 472 LEU 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 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 74 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.169188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.137934 restraints weight = 9687.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138333 restraints weight = 7213.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.140669 restraints weight = 5860.710| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2936 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= 0.185 Angle : 0.623 11.256 9045 Z= 0.305 Chirality : 0.042 0.162 999 Planarity : 0.004 0.038 1155 Dihedral : 5.922 83.024 929 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.89 % Allowed : 20.08 % Favored : 77.03 % 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: 0.05 (0.30), residues: 801 helix: 0.95 (0.32), residues: 276 sheet: 0.06 (0.43), residues: 155 loop : -0.61 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.013 0.001 PHE A 705 TYR 0.017 0.001 TYR A 824 ARG 0.007 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 112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 91 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8236 (mmpt) cc_final: 0.7778 (mmpt) REVERT: A 472 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7036 (tm) REVERT: A 498 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7707 (mt) outliers start: 21 outliers final: 17 residues processed: 104 average time/residue: 0.2010 time to fit residues: 27.7218 Evaluate side-chains 106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 87 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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 308 LEU 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 498 LEU Chi-restraints excluded: chain A residue 507 LYS 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 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER 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: 1.9990 chunk 7 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.4980 chunk 27 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.4091 r_free = 0.4091 target = 0.169023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.135704 restraints weight = 9721.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137609 restraints weight = 7040.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139084 restraints weight = 4976.292| |-----------------------------------------------------------------------------| r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 6700 Z= 0.180 Angle : 0.631 11.186 9045 Z= 0.309 Chirality : 0.042 0.167 999 Planarity : 0.004 0.038 1155 Dihedral : 5.881 83.691 929 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.89 % Allowed : 21.18 % Favored : 75.93 % 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: 0.07 (0.30), residues: 801 helix: 0.99 (0.32), residues: 277 sheet: 0.13 (0.43), residues: 155 loop : -0.65 (0.34), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.013 0.001 PHE A 238 TYR 0.014 0.001 TYR A 582 ARG 0.008 0.000 ARG A 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2083.96 seconds wall clock time: 36 minutes 53.27 seconds (2213.27 seconds total)