Starting phenix.real_space_refine on Thu Jun 5 18:49:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erd_19912/06_2025/9erd_19912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erd_19912/06_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_19912/06_2025/9erd_19912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erd_19912/06_2025/9erd_19912.map" model { file = "/net/cci-nas-00/data/ceres_data/9erd_19912/06_2025/9erd_19912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erd_19912/06_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-5710/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: 4.34, per 1000 atoms: 0.66 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: 1.67 Conformation dependent library (CDL) restraints added in 927.2 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: 0.84 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: 1.96 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: 1.100 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.740 Find NCS groups from input model: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.270 ------------------------------------------------------------------------------- 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 6704 Z= 0.244 Angle : 0.707 7.306 9048 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 Details of bonding type rmsd hydrogen bonds : bond 0.21446 ( 241) hydrogen bonds : angle 7.80236 ( 681) metal coordination : bond 0.00615 ( 4) metal coordination : angle 1.87135 ( 3) covalent geometry : bond 0.00466 ( 6700) covalent geometry : angle 0.70661 ( 9045) *********************** 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 : 0.710 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: 0.2306 time to fit residues: 28.6129 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 : 0.695 ------------------------------------------------------------------------------- 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: 0.8980 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4022 r_free = 0.4022 target = 0.163432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.130110 restraints weight = 9705.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132084 restraints weight = 6977.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.134457 restraints weight = 4989.363| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6704 Z= 0.190 Angle : 0.698 11.671 9048 Z= 0.352 Chirality : 0.045 0.145 999 Planarity : 0.004 0.039 1155 Dihedral : 7.822 83.173 931 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.03 % Allowed : 13.20 % Favored : 83.77 % 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: -0.90 (0.30), residues: 801 helix: 0.07 (0.32), residues: 268 sheet: -0.62 (0.44), residues: 149 loop : -0.99 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 699 HIS 0.005 0.001 HIS A 892 PHE 0.014 0.002 PHE A 103 TYR 0.015 0.002 TYR A 629 ARG 0.003 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 241) hydrogen bonds : angle 5.65461 ( 681) metal coordination : bond 0.00433 ( 4) metal coordination : angle 1.60496 ( 3) covalent geometry : bond 0.00452 ( 6700) covalent geometry : angle 0.69712 ( 9045) *********************** 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 112 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8291 (p90) cc_final: 0.8006 (p90) REVERT: A 272 ARG cc_start: 0.8710 (ptp90) cc_final: 0.8267 (ptp-170) REVERT: A 314 MET cc_start: 0.7411 (mpp) cc_final: 0.7025 (ptp) REVERT: A 497 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8521 (mmtm) REVERT: A 562 ARG cc_start: 0.8066 (tmm-80) cc_final: 0.7668 (tmm-80) outliers start: 22 outliers final: 12 residues processed: 104 average time/residue: 0.2174 time to fit residues: 29.5050 Evaluate side-chains 93 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.706 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 13 optimal weight: 3.9990 chunk 50 optimal weight: 0.0030 chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.166816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.132945 restraints weight = 9740.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135336 restraints weight = 6800.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.136505 restraints weight = 4904.001| |-----------------------------------------------------------------------------| r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6704 Z= 0.124 Angle : 0.603 9.639 9048 Z= 0.304 Chirality : 0.042 0.130 999 Planarity : 0.004 0.031 1155 Dihedral : 6.777 81.828 929 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.61 % Allowed : 14.03 % Favored : 83.36 % 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: -0.46 (0.30), residues: 801 helix: 0.48 (0.32), residues: 269 sheet: -0.42 (0.42), residues: 149 loop : -0.74 (0.33), residues: 383 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 0.010 0.001 PHE A 103 TYR 0.014 0.001 TYR A 824 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 241) hydrogen bonds : angle 5.19337 ( 681) metal coordination : bond 0.00346 ( 4) metal coordination : angle 0.78654 ( 3) covalent geometry : bond 0.00287 ( 6700) covalent geometry : angle 0.60314 ( 9045) *********************** 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 118 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 99 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9436 (pttp) cc_final: 0.9230 (pttp) REVERT: A 198 TYR cc_start: 0.8291 (p90) cc_final: 0.8042 (p90) REVERT: A 272 ARG cc_start: 0.8722 (ptp90) cc_final: 0.8176 (ptt-90) REVERT: A 314 MET cc_start: 0.7328 (mpp) cc_final: 0.6919 (ptp) REVERT: A 351 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7557 (tpp) REVERT: A 405 LEU cc_start: 0.8344 (tp) cc_final: 0.8079 (tp) REVERT: A 472 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7089 (tm) REVERT: A 497 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8453 (mmtm) REVERT: A 534 ASP cc_start: 0.7820 (p0) cc_final: 0.7512 (p0) REVERT: A 824 TYR cc_start: 0.8494 (t80) cc_final: 0.8242 (t80) outliers start: 19 outliers final: 11 residues processed: 109 average time/residue: 0.2579 time to fit residues: 36.6991 Evaluate side-chains 101 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 299 ILE 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 472 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 721 GLN Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 881 VAL 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: 2.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 47 optimal weight: 0.1980 chunk 66 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 A 721 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.166754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.133824 restraints weight = 9758.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.134846 restraints weight = 7127.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.136478 restraints weight = 5275.833| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6704 Z= 0.132 Angle : 0.600 9.080 9048 Z= 0.301 Chirality : 0.042 0.131 999 Planarity : 0.004 0.031 1155 Dihedral : 6.553 79.066 929 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.85 % Allowed : 13.89 % Favored : 82.26 % 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: -0.24 (0.30), residues: 801 helix: 0.64 (0.32), residues: 271 sheet: -0.21 (0.43), residues: 147 loop : -0.63 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 PHE 0.011 0.001 PHE A 103 TYR 0.030 0.002 TYR A 539 ARG 0.006 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 241) hydrogen bonds : angle 5.07002 ( 681) metal coordination : bond 0.00600 ( 4) metal coordination : angle 1.62592 ( 3) covalent geometry : bond 0.00304 ( 6700) covalent geometry : angle 0.59896 ( 9045) *********************** 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 119 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 91 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9443 (pttp) cc_final: 0.9228 (pttp) REVERT: A 198 TYR cc_start: 0.8306 (p90) cc_final: 0.8062 (p90) REVERT: A 272 ARG cc_start: 0.8716 (ptp90) cc_final: 0.8167 (ptt-90) REVERT: A 314 MET cc_start: 0.7399 (mpp) cc_final: 0.6955 (ptp) REVERT: A 351 MET cc_start: 0.7829 (OUTLIER) cc_final: 0.7558 (tpp) REVERT: A 405 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8078 (tp) REVERT: A 472 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7045 (tm) REVERT: A 498 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7851 (mt) REVERT: A 534 ASP cc_start: 0.7755 (p0) cc_final: 0.7493 (p0) REVERT: A 824 TYR cc_start: 0.8525 (t80) cc_final: 0.8258 (t80) REVERT: A 851 LEU cc_start: 0.7542 (tt) cc_final: 0.7329 (tt) outliers start: 28 outliers final: 19 residues processed: 107 average time/residue: 0.2260 time to fit residues: 31.6884 Evaluate side-chains 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.766 ------------------------------------------------------------------------------- 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 412 LEU 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 721 GLN 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: 10.0000 chunk 46 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.162114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.129355 restraints weight = 10026.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130143 restraints weight = 7711.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132260 restraints weight = 5769.807| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 6704 Z= 0.246 Angle : 0.713 15.983 9048 Z= 0.351 Chirality : 0.045 0.135 999 Planarity : 0.005 0.034 1155 Dihedral : 7.165 85.340 929 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.95 % Allowed : 14.99 % Favored : 80.06 % 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: -0.70 (0.30), residues: 801 helix: 0.30 (0.31), residues: 275 sheet: -0.55 (0.43), residues: 153 loop : -0.91 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 110 HIS 0.007 0.002 HIS A 664 PHE 0.016 0.002 PHE A 398 TYR 0.023 0.002 TYR A 539 ARG 0.007 0.001 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.04364 ( 241) hydrogen bonds : angle 5.32255 ( 681) metal coordination : bond 0.00526 ( 4) metal coordination : angle 1.88153 ( 3) covalent geometry : bond 0.00589 ( 6700) covalent geometry : angle 0.71214 ( 9045) *********************** 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 116 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 80 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9448 (pttp) cc_final: 0.9217 (pttp) REVERT: A 198 TYR cc_start: 0.8270 (p90) cc_final: 0.8029 (p90) REVERT: A 273 LYS cc_start: 0.8176 (mmpt) cc_final: 0.7825 (mmpt) REVERT: A 472 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.6972 (tm) REVERT: A 498 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7925 (mt) REVERT: A 655 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6674 (tt) REVERT: A 824 TYR cc_start: 0.8563 (t80) cc_final: 0.8266 (t80) REVERT: A 851 LEU cc_start: 0.7602 (tt) cc_final: 0.7398 (tt) outliers start: 36 outliers final: 25 residues processed: 100 average time/residue: 0.2605 time to fit residues: 34.8977 Evaluate side-chains 104 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 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 333 ILE Chi-restraints excluded: chain A residue 351 MET 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 606 THR Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 698 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.166066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132481 restraints weight = 9725.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.133765 restraints weight = 7137.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135991 restraints weight = 5317.707| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6704 Z= 0.129 Angle : 0.612 13.139 9048 Z= 0.301 Chirality : 0.042 0.145 999 Planarity : 0.004 0.038 1155 Dihedral : 6.569 80.892 929 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.13 % Allowed : 16.92 % Favored : 78.95 % 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: -0.38 (0.30), residues: 801 helix: 0.58 (0.31), residues: 276 sheet: -0.29 (0.43), residues: 150 loop : -0.78 (0.33), residues: 375 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 0.009 0.001 PHE A 492 TYR 0.015 0.001 TYR A 539 ARG 0.007 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03710 ( 241) hydrogen bonds : angle 5.05254 ( 681) metal coordination : bond 0.00386 ( 4) metal coordination : angle 1.28751 ( 3) covalent geometry : bond 0.00299 ( 6700) covalent geometry : angle 0.61128 ( 9045) *********************** 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 115 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9469 (pttp) cc_final: 0.9251 (pttp) REVERT: A 198 TYR cc_start: 0.8401 (p90) cc_final: 0.8132 (p90) REVERT: A 472 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7049 (tm) REVERT: A 498 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (mt) REVERT: A 797 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7268 (ttp-170) REVERT: A 824 TYR cc_start: 0.8573 (t80) cc_final: 0.8297 (t80) outliers start: 30 outliers final: 22 residues processed: 103 average time/residue: 0.1960 time to fit residues: 27.0460 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 : 0.752 ------------------------------------------------------------------------------- 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 297 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 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 606 THR Chi-restraints excluded: chain A residue 721 GLN 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=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: 8.9990 chunk 67 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 16 optimal weight: 0.1980 chunk 6 optimal weight: 0.0270 chunk 42 optimal weight: 0.5980 overall best weight: 0.5038 ------------------------------------------------------------------------------- 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 = 0.4074 r_free = 0.4074 target = 0.167826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133873 restraints weight = 9673.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135572 restraints weight = 6963.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.137156 restraints weight = 5005.856| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6704 Z= 0.115 Angle : 0.617 12.620 9048 Z= 0.301 Chirality : 0.042 0.131 999 Planarity : 0.004 0.041 1155 Dihedral : 6.307 79.058 929 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.30 % Allowed : 17.47 % Favored : 79.23 % 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: -0.24 (0.30), residues: 801 helix: 0.67 (0.31), residues: 276 sheet: -0.14 (0.45), residues: 143 loop : -0.71 (0.33), residues: 382 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 106 TYR 0.025 0.001 TYR A 539 ARG 0.009 0.000 ARG A 229 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 241) hydrogen bonds : angle 4.94893 ( 681) metal coordination : bond 0.00383 ( 4) metal coordination : angle 1.19482 ( 3) covalent geometry : bond 0.00264 ( 6700) covalent geometry : angle 0.61692 ( 9045) *********************** 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 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.767 Fit side-chains REVERT: A 32 LYS cc_start: 0.9473 (pttp) cc_final: 0.9269 (pttp) REVERT: A 198 TYR cc_start: 0.8422 (p90) cc_final: 0.8164 (p90) REVERT: A 273 LYS cc_start: 0.8272 (mmpt) cc_final: 0.7781 (mmpt) REVERT: A 472 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7039 (tm) REVERT: A 704 TYR cc_start: 0.8400 (t80) cc_final: 0.8005 (t80) REVERT: A 797 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7308 (ttp-170) REVERT: A 824 TYR cc_start: 0.8564 (t80) cc_final: 0.8300 (t80) outliers start: 24 outliers final: 17 residues processed: 103 average time/residue: 0.2034 time to fit residues: 27.8857 Evaluate side-chains 98 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.788 ------------------------------------------------------------------------------- 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 297 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 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 606 THR Chi-restraints excluded: chain A residue 718 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: 0.8980 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 32 optimal weight: 0.0870 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.4061 r_free = 0.4061 target = 0.166267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133508 restraints weight = 9750.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.135241 restraints weight = 7437.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.136787 restraints weight = 5332.584| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 6704 Z= 0.148 Angle : 0.651 12.132 9048 Z= 0.320 Chirality : 0.043 0.138 999 Planarity : 0.004 0.037 1155 Dihedral : 6.353 82.782 929 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.99 % Allowed : 18.02 % Favored : 77.99 % 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: -0.23 (0.30), residues: 801 helix: 0.65 (0.31), residues: 277 sheet: -0.13 (0.45), residues: 143 loop : -0.69 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS A 664 PHE 0.017 0.002 PHE A 238 TYR 0.018 0.001 TYR A 582 ARG 0.010 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03685 ( 241) hydrogen bonds : angle 5.07545 ( 681) metal coordination : bond 0.00271 ( 4) metal coordination : angle 1.33359 ( 3) covalent geometry : bond 0.00353 ( 6700) covalent geometry : angle 0.65056 ( 9045) *********************** 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 113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 135 ARG cc_start: 0.7284 (mtt90) cc_final: 0.7060 (ttt90) REVERT: A 198 TYR cc_start: 0.8260 (p90) cc_final: 0.8016 (p90) REVERT: A 273 LYS cc_start: 0.8267 (mmpt) cc_final: 0.7817 (mmpt) REVERT: A 472 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7027 (tm) REVERT: A 498 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7800 (mt) REVERT: A 507 LYS cc_start: 0.7095 (tttt) cc_final: 0.6735 (pttt) REVERT: A 824 TYR cc_start: 0.8500 (t80) cc_final: 0.8214 (t80) outliers start: 29 outliers final: 24 residues processed: 101 average time/residue: 0.2156 time to fit residues: 29.1252 Evaluate side-chains 105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL 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 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 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 718 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 7.9990 overall best weight: 0.9344 ------------------------------------------------------------------------------- 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 = 0.4058 r_free = 0.4058 target = 0.166053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.132201 restraints weight = 9813.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.134346 restraints weight = 7039.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.136236 restraints weight = 5080.606| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 6704 Z= 0.147 Angle : 0.663 11.792 9048 Z= 0.322 Chirality : 0.043 0.146 999 Planarity : 0.004 0.039 1155 Dihedral : 6.376 83.750 929 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.85 % Allowed : 18.02 % Favored : 78.13 % 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: 0.59 (0.31), residues: 277 sheet: -0.15 (0.45), residues: 143 loop : -0.72 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS A 664 PHE 0.014 0.001 PHE A 238 TYR 0.021 0.001 TYR A 582 ARG 0.007 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03668 ( 241) hydrogen bonds : angle 5.07858 ( 681) metal coordination : bond 0.00298 ( 4) metal coordination : angle 1.37449 ( 3) covalent geometry : bond 0.00349 ( 6700) covalent geometry : angle 0.66218 ( 9045) *********************** 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 113 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8454 (p90) cc_final: 0.8159 (p90) REVERT: A 273 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7823 (mmpt) REVERT: A 472 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7036 (tm) REVERT: A 498 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7826 (mt) REVERT: A 704 TYR cc_start: 0.8398 (t80) cc_final: 0.8016 (t80) REVERT: A 824 TYR cc_start: 0.8565 (t80) cc_final: 0.8285 (t80) outliers start: 28 outliers final: 24 residues processed: 102 average time/residue: 0.2084 time to fit residues: 27.9661 Evaluate side-chains 107 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 81 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 718 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 69 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.166348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133668 restraints weight = 9770.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134806 restraints weight = 7071.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.136660 restraints weight = 5074.625| |-----------------------------------------------------------------------------| r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 6704 Z= 0.136 Angle : 0.670 11.764 9048 Z= 0.324 Chirality : 0.042 0.155 999 Planarity : 0.004 0.039 1155 Dihedral : 6.281 83.386 929 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.58 % Allowed : 18.71 % Favored : 77.72 % 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: -0.25 (0.30), residues: 801 helix: 0.64 (0.32), residues: 277 sheet: -0.20 (0.45), residues: 145 loop : -0.69 (0.33), residues: 379 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 0.012 0.001 PHE A 238 TYR 0.019 0.001 TYR A 582 ARG 0.008 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 241) hydrogen bonds : angle 5.09919 ( 681) metal coordination : bond 0.00339 ( 4) metal coordination : angle 1.30997 ( 3) covalent geometry : bond 0.00321 ( 6700) covalent geometry : angle 0.66924 ( 9045) ********************** 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 115 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8355 (p90) cc_final: 0.8041 (p90) REVERT: A 273 LYS cc_start: 0.8290 (mmpt) cc_final: 0.7798 (mmpt) REVERT: A 431 MET cc_start: 0.7856 (tpt) cc_final: 0.7650 (tpt) REVERT: A 472 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7028 (tm) REVERT: A 498 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7803 (mt) REVERT: A 704 TYR cc_start: 0.8365 (t80) cc_final: 0.7984 (t80) REVERT: A 824 TYR cc_start: 0.8550 (t80) cc_final: 0.8264 (t80) outliers start: 26 outliers final: 21 residues processed: 103 average time/residue: 0.2072 time to fit residues: 28.2808 Evaluate side-chains 105 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 606 THR Chi-restraints excluded: chain A residue 718 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 815 THR 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: 1.9990 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 25 optimal weight: 4.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- 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 = 0.4077 r_free = 0.4077 target = 0.167980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135950 restraints weight = 9783.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.137486 restraints weight = 7281.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.139383 restraints weight = 5696.990| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 6704 Z= 0.139 Angle : 0.677 11.854 9048 Z= 0.328 Chirality : 0.042 0.138 999 Planarity : 0.004 0.038 1155 Dihedral : 6.255 84.695 929 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.12 % Favored : 94.76 % Rotamer: Outliers : 3.58 % Allowed : 18.71 % Favored : 77.72 % 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: -0.23 (0.30), residues: 801 helix: 0.62 (0.31), residues: 276 sheet: -0.10 (0.43), residues: 155 loop : -0.68 (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 0.015 0.001 PHE A 238 TYR 0.019 0.001 TYR A 582 ARG 0.006 0.000 ARG A 135 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 241) hydrogen bonds : angle 5.08693 ( 681) metal coordination : bond 0.00333 ( 4) metal coordination : angle 1.33306 ( 3) covalent geometry : bond 0.00330 ( 6700) covalent geometry : angle 0.67661 ( 9045) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2228.10 seconds wall clock time: 39 minutes 52.87 seconds (2392.87 seconds total)