Starting phenix.real_space_refine on Fri Aug 22 17:52:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9erd_19912/08_2025/9erd_19912.cif Found real_map, /net/cci-nas-00/data/ceres_data/9erd_19912/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9erd_19912/08_2025/9erd_19912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9erd_19912/08_2025/9erd_19912.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9erd_19912/08_2025/9erd_19912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9erd_19912/08_2025/9erd_19912.map" } resolution = 3.72 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.96, per 1000 atoms: 0.30 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: 0.60 Conformation dependent library (CDL) restraints added in 438.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.28 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: 1.24 Time building geometry restraints manager: 0.80 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: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.310 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.060 ------------------------------------------------------------------------------- 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 : 8.80 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG A 674 TYR 0.021 0.002 TYR A 539 PHE 0.010 0.002 PHE A 106 TRP 0.011 0.001 TRP A 699 HIS 0.004 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 6700) covalent geometry : angle 0.70661 ( 9045) hydrogen bonds : bond 0.21446 ( 241) hydrogen bonds : angle 7.80236 ( 681) metal coordination : bond 0.00615 ( 4) metal coordination : angle 1.87135 ( 3) *********************** 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 : 0.222 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: 0.1028 time to fit residues: 12.7871 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 : 0.280 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4041 r_free = 0.4041 target = 0.165222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.130233 restraints weight = 9779.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.133325 restraints weight = 6391.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135437 restraints weight = 4796.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136937 restraints weight = 3926.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137759 restraints weight = 3414.589| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6704 Z= 0.150 Angle : 0.653 10.949 9048 Z= 0.332 Chirality : 0.043 0.137 999 Planarity : 0.004 0.037 1155 Dihedral : 7.518 82.777 931 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.75 % Allowed : 12.52 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.30), residues: 801 helix: 0.24 (0.32), residues: 267 sheet: -0.56 (0.44), residues: 149 loop : -0.95 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 229 TYR 0.014 0.002 TYR A 539 PHE 0.013 0.002 PHE A 215 TRP 0.011 0.001 TRP A 699 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 6700) covalent geometry : angle 0.65308 ( 9045) hydrogen bonds : bond 0.04756 ( 241) hydrogen bonds : angle 5.57085 ( 681) metal coordination : bond 0.00639 ( 4) metal coordination : angle 1.34489 ( 3) *********************** 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 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8327 (p90) cc_final: 0.8037 (p90) REVERT: A 272 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8274 (ptp-170) REVERT: A 314 MET cc_start: 0.7365 (mpp) cc_final: 0.7009 (ptp) REVERT: A 351 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7482 (tpp) REVERT: A 562 ARG cc_start: 0.8024 (tmm-80) cc_final: 0.7632 (tmm-80) outliers start: 20 outliers final: 12 residues processed: 103 average time/residue: 0.0974 time to fit residues: 13.1053 Evaluate side-chains 96 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 412 LEU 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 8 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.160013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.127721 restraints weight = 10010.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128443 restraints weight = 7430.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.129767 restraints weight = 6040.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.130168 restraints weight = 4894.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.130486 restraints weight = 4623.069| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 6704 Z= 0.308 Angle : 0.786 11.958 9048 Z= 0.393 Chirality : 0.047 0.139 999 Planarity : 0.005 0.042 1155 Dihedral : 8.022 87.114 929 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 3.58 % Allowed : 14.03 % Favored : 82.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.29), residues: 801 helix: -0.23 (0.30), residues: 274 sheet: -0.83 (0.42), residues: 153 loop : -1.21 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 229 TYR 0.022 0.002 TYR A 629 PHE 0.018 0.002 PHE A 398 TRP 0.008 0.002 TRP A 110 HIS 0.009 0.002 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00740 ( 6700) covalent geometry : angle 0.78515 ( 9045) hydrogen bonds : bond 0.05057 ( 241) hydrogen bonds : angle 5.76886 ( 681) metal coordination : bond 0.01015 ( 4) metal coordination : angle 1.64157 ( 3) *********************** 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 108 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.9342 (pttp) cc_final: 0.9133 (pttp) REVERT: A 198 TYR cc_start: 0.8078 (p90) cc_final: 0.7854 (p90) REVERT: A 272 ARG cc_start: 0.8581 (ptp90) cc_final: 0.7859 (ptt-90) REVERT: A 273 LYS cc_start: 0.8064 (mmpt) cc_final: 0.7837 (mmpt) REVERT: A 472 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7099 (tm) REVERT: A 497 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8541 (mmtm) REVERT: A 498 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 562 ARG cc_start: 0.8223 (tmm-80) cc_final: 0.7809 (tmm-80) REVERT: A 824 TYR cc_start: 0.8494 (t80) cc_final: 0.8277 (t80) outliers start: 26 outliers final: 20 residues processed: 99 average time/residue: 0.1100 time to fit residues: 13.9491 Evaluate side-chains 98 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 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 472 LEU Chi-restraints excluded: chain A residue 497 LYS Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 698 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 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 68 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 46 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.162472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.130304 restraints weight = 9926.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131343 restraints weight = 7224.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132773 restraints weight = 5725.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.132946 restraints weight = 4577.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134869 restraints weight = 4352.882| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6704 Z= 0.185 Angle : 0.661 9.681 9048 Z= 0.331 Chirality : 0.044 0.135 999 Planarity : 0.004 0.036 1155 Dihedral : 7.283 84.096 929 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.13 % Allowed : 15.54 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.30), residues: 801 helix: 0.15 (0.31), residues: 274 sheet: -0.64 (0.42), residues: 153 loop : -1.13 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 229 TYR 0.015 0.002 TYR A 629 PHE 0.013 0.002 PHE A 103 TRP 0.009 0.001 TRP A 413 HIS 0.005 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 6700) covalent geometry : angle 0.66061 ( 9045) hydrogen bonds : bond 0.04253 ( 241) hydrogen bonds : angle 5.39400 ( 681) metal coordination : bond 0.00386 ( 4) metal coordination : angle 1.70856 ( 3) *********************** 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 115 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 85 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.7628 (mp0) cc_final: 0.7409 (mp0) REVERT: A 198 TYR cc_start: 0.8132 (p90) cc_final: 0.7927 (p90) REVERT: A 272 ARG cc_start: 0.8617 (ptp90) cc_final: 0.8129 (ptt-90) REVERT: A 405 LEU cc_start: 0.8419 (tp) cc_final: 0.8034 (tp) REVERT: A 472 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6974 (tm) REVERT: A 497 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8099 (mptt) REVERT: A 498 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8004 (mt) REVERT: A 534 ASP cc_start: 0.7948 (p0) cc_final: 0.7654 (p0) REVERT: A 655 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6696 (tt) REVERT: A 824 TYR cc_start: 0.8511 (t80) cc_final: 0.8254 (t80) outliers start: 30 outliers final: 20 residues processed: 104 average time/residue: 0.0950 time to fit residues: 13.1062 Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 138 THR Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 80 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.164831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.132201 restraints weight = 10032.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.133461 restraints weight = 7382.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.135323 restraints weight = 5703.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.135750 restraints weight = 4516.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136192 restraints weight = 4105.968| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1975 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= 0.141 Angle : 0.622 9.517 9048 Z= 0.310 Chirality : 0.043 0.133 999 Planarity : 0.004 0.033 1155 Dihedral : 6.848 81.303 929 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 4.40 % Allowed : 15.54 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.30), residues: 801 helix: 0.42 (0.31), residues: 275 sheet: -0.44 (0.42), residues: 151 loop : -1.01 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 229 TYR 0.032 0.002 TYR A 539 PHE 0.011 0.001 PHE A 103 TRP 0.010 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 6700) covalent geometry : angle 0.62146 ( 9045) hydrogen bonds : bond 0.03921 ( 241) hydrogen bonds : angle 5.17017 ( 681) metal coordination : bond 0.00274 ( 4) metal coordination : angle 1.12993 ( 3) *********************** 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: 32 poor density : 84 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 TYR cc_start: 0.8187 (p90) cc_final: 0.7925 (p90) REVERT: A 272 ARG cc_start: 0.8634 (ptp90) cc_final: 0.8124 (ptt-90) REVERT: A 351 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7489 (tpp) REVERT: A 405 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7935 (tp) REVERT: A 472 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7071 (tm) REVERT: A 534 ASP cc_start: 0.7843 (p0) cc_final: 0.7595 (p0) REVERT: A 655 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6636 (tt) REVERT: A 824 TYR cc_start: 0.8487 (t80) cc_final: 0.8228 (t80) outliers start: 32 outliers final: 24 residues processed: 103 average time/residue: 0.0928 time to fit residues: 12.3761 Evaluate side-chains 106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 78 time to evaluate : 0.261 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 735 ASP Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 865 VAL 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 45 optimal weight: 0.2980 chunk 36 optimal weight: 0.6980 chunk 30 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.4065 r_free = 0.4065 target = 0.167244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.133225 restraints weight = 9843.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.135793 restraints weight = 7217.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.138061 restraints weight = 4929.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138302 restraints weight = 3839.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138675 restraints weight = 3782.169| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6704 Z= 0.117 Angle : 0.625 13.049 9048 Z= 0.305 Chirality : 0.042 0.133 999 Planarity : 0.004 0.035 1155 Dihedral : 6.426 79.926 929 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.13 % Allowed : 17.19 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.30), residues: 801 helix: 0.62 (0.31), residues: 275 sheet: -0.14 (0.45), residues: 137 loop : -0.68 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 229 TYR 0.024 0.001 TYR A 539 PHE 0.009 0.001 PHE A 103 TRP 0.011 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 6700) covalent geometry : angle 0.62468 ( 9045) hydrogen bonds : bond 0.03664 ( 241) hydrogen bonds : angle 5.01718 ( 681) metal coordination : bond 0.00345 ( 4) metal coordination : angle 1.01283 ( 3) *********************** 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 118 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 88 time to evaluate : 0.251 Fit side-chains REVERT: A 198 TYR cc_start: 0.8400 (p90) cc_final: 0.8155 (p90) REVERT: A 273 LYS cc_start: 0.8281 (mmpt) cc_final: 0.7826 (mmpt) REVERT: A 472 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6999 (tm) REVERT: A 498 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7822 (mt) REVERT: A 534 ASP cc_start: 0.7711 (p0) cc_final: 0.7456 (p0) REVERT: A 797 ARG cc_start: 0.7876 (ttp-170) cc_final: 0.7254 (ttp-170) REVERT: A 824 TYR cc_start: 0.8536 (t80) cc_final: 0.8266 (t80) outliers start: 30 outliers final: 21 residues processed: 105 average time/residue: 0.0800 time to fit residues: 11.4198 Evaluate side-chains 103 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 80 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 246 LEU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 472 LEU 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 858 SER 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 44 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 chunk 79 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 72 optimal weight: 0.6980 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 = 0.4039 r_free = 0.4039 target = 0.164855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.132918 restraints weight = 9831.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132384 restraints weight = 7302.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134482 restraints weight = 6176.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.135066 restraints weight = 4773.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.135439 restraints weight = 4351.259| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 6704 Z= 0.170 Angle : 0.671 12.208 9048 Z= 0.329 Chirality : 0.043 0.161 999 Planarity : 0.004 0.043 1155 Dihedral : 6.610 85.706 929 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.62 % Favored : 94.26 % Rotamer: Outliers : 4.68 % Allowed : 16.78 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.32 (0.30), residues: 801 helix: 0.58 (0.32), residues: 274 sheet: -0.22 (0.45), residues: 137 loop : -0.72 (0.32), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 229 TYR 0.021 0.002 TYR A 582 PHE 0.011 0.001 PHE A 398 TRP 0.006 0.001 TRP A 413 HIS 0.005 0.001 HIS A 664 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 6700) covalent geometry : angle 0.67072 ( 9045) hydrogen bonds : bond 0.03875 ( 241) hydrogen bonds : angle 5.22002 ( 681) metal coordination : bond 0.00267 ( 4) metal coordination : angle 1.30592 ( 3) *********************** 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 114 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 80 time to evaluate : 0.240 Fit side-chains REVERT: A 198 TYR cc_start: 0.8299 (p90) cc_final: 0.8055 (p90) REVERT: A 273 LYS cc_start: 0.8305 (mmpt) cc_final: 0.7844 (mmpt) REVERT: A 472 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6968 (tm) REVERT: A 498 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7870 (mt) REVERT: A 797 ARG cc_start: 0.7881 (ttp-170) cc_final: 0.7256 (ttp-170) REVERT: A 824 TYR cc_start: 0.8532 (t80) cc_final: 0.8250 (t80) outliers start: 34 outliers final: 25 residues processed: 105 average time/residue: 0.0853 time to fit residues: 11.9258 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 : 0.155 ------------------------------------------------------------------------------- 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 297 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 53 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.165858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.134854 restraints weight = 9842.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135779 restraints weight = 7302.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138063 restraints weight = 5830.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138099 restraints weight = 4498.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.138409 restraints weight = 4256.283| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 6704 Z= 0.143 Angle : 0.665 11.999 9048 Z= 0.323 Chirality : 0.043 0.137 999 Planarity : 0.004 0.037 1155 Dihedral : 6.469 84.540 929 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.99 % Favored : 94.88 % Rotamer: Outliers : 4.26 % Allowed : 18.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.30), residues: 801 helix: 0.67 (0.32), residues: 274 sheet: -0.07 (0.47), residues: 132 loop : -0.66 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 135 TYR 0.017 0.001 TYR A 539 PHE 0.018 0.001 PHE A 238 TRP 0.009 0.001 TRP A 413 HIS 0.003 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 6700) covalent geometry : angle 0.66480 ( 9045) hydrogen bonds : bond 0.03654 ( 241) hydrogen bonds : angle 5.12909 ( 681) metal coordination : bond 0.00270 ( 4) metal coordination : angle 1.17282 ( 3) *********************** 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 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 80 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7807 (mmpt) REVERT: A 472 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7011 (tm) REVERT: A 498 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7804 (mt) REVERT: A 824 TYR cc_start: 0.8400 (t80) cc_final: 0.8107 (t80) outliers start: 31 outliers final: 25 residues processed: 102 average time/residue: 0.0772 time to fit residues: 10.5392 Evaluate side-chains 104 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 427 ILE 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 715 LEU 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 26 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.4052 r_free = 0.4052 target = 0.165763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.133382 restraints weight = 10005.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.134508 restraints weight = 7422.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136665 restraints weight = 5703.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.136752 restraints weight = 4482.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.137215 restraints weight = 4274.812| |-----------------------------------------------------------------------------| r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 6704 Z= 0.151 Angle : 0.684 11.734 9048 Z= 0.334 Chirality : 0.043 0.176 999 Planarity : 0.004 0.039 1155 Dihedral : 6.469 85.728 929 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 4.13 % Allowed : 18.98 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.30), residues: 801 helix: 0.55 (0.32), residues: 274 sheet: -0.15 (0.45), residues: 139 loop : -0.68 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 135 TYR 0.017 0.001 TYR A 198 PHE 0.020 0.002 PHE A 238 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 892 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 6700) covalent geometry : angle 0.68413 ( 9045) hydrogen bonds : bond 0.03669 ( 241) hydrogen bonds : angle 5.19243 ( 681) metal coordination : bond 0.00272 ( 4) metal coordination : angle 1.23398 ( 3) *********************** 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 111 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8249 (mmpt) cc_final: 0.7806 (mmpt) REVERT: A 472 LEU cc_start: 0.7430 (OUTLIER) cc_final: 0.7016 (tm) REVERT: A 498 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7808 (mt) REVERT: A 824 TYR cc_start: 0.8520 (t80) cc_final: 0.8216 (t80) outliers start: 30 outliers final: 24 residues processed: 102 average time/residue: 0.0845 time to fit residues: 11.4994 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 : 0.238 ------------------------------------------------------------------------------- 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 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 412 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 27 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 58 optimal weight: 0.0770 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- 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 = 0.4072 r_free = 0.4072 target = 0.167772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.133953 restraints weight = 9820.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136702 restraints weight = 7027.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.138288 restraints weight = 5089.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138625 restraints weight = 4073.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.138839 restraints weight = 3954.309| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6704 Z= 0.128 Angle : 0.678 11.805 9048 Z= 0.328 Chirality : 0.042 0.172 999 Planarity : 0.004 0.040 1155 Dihedral : 6.256 83.909 929 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.12 % Favored : 95.76 % Rotamer: Outliers : 3.58 % Allowed : 20.50 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.30), residues: 801 helix: 0.72 (0.32), residues: 274 sheet: 0.01 (0.45), residues: 144 loop : -0.65 (0.33), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 135 TYR 0.017 0.001 TYR A 198 PHE 0.012 0.001 PHE A 705 TRP 0.011 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 6700) covalent geometry : angle 0.67783 ( 9045) hydrogen bonds : bond 0.03548 ( 241) hydrogen bonds : angle 5.08029 ( 681) metal coordination : bond 0.00344 ( 4) metal coordination : angle 1.08253 ( 3) ********************** 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 110 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.249 Fit side-chains revert: symmetry clash REVERT: A 273 LYS cc_start: 0.8327 (mmpt) cc_final: 0.7847 (mmpt) REVERT: A 472 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6975 (tm) REVERT: A 824 TYR cc_start: 0.8581 (t80) cc_final: 0.8237 (t80) outliers start: 26 outliers final: 24 residues processed: 103 average time/residue: 0.0822 time to fit residues: 11.3712 Evaluate side-chains 106 residues out of total 727 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 308 LEU Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 HIS Chi-restraints excluded: chain A residue 412 LEU 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 555 VAL Chi-restraints excluded: chain A residue 588 SER 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 745 MET Chi-restraints excluded: chain A residue 815 THR Chi-restraints excluded: chain A residue 858 SER Chi-restraints excluded: chain A residue 881 VAL Chi-restraints excluded: chain A residue 887 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 4.9990 chunk 17 optimal weight: 0.0070 chunk 59 optimal weight: 0.6980 chunk 74 optimal weight: 0.2980 chunk 14 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 6.9990 chunk 63 optimal weight: 0.0980 overall best weight: 0.3598 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.170166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136994 restraints weight = 9827.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.139154 restraints weight = 7192.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.141268 restraints weight = 5243.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.141737 restraints weight = 4071.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.142117 restraints weight = 4058.041| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 6704 Z= 0.115 Angle : 0.650 11.914 9048 Z= 0.314 Chirality : 0.042 0.158 999 Planarity : 0.004 0.042 1155 Dihedral : 6.050 82.822 929 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.89 % Allowed : 20.91 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.30), residues: 801 helix: 0.86 (0.32), residues: 275 sheet: 0.13 (0.45), residues: 144 loop : -0.61 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 135 TYR 0.020 0.001 TYR A 539 PHE 0.013 0.001 PHE A 705 TRP 0.013 0.001 TRP A 413 HIS 0.003 0.000 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 6700) covalent geometry : angle 0.64969 ( 9045) hydrogen bonds : bond 0.03338 ( 241) hydrogen bonds : angle 4.95613 ( 681) metal coordination : bond 0.00426 ( 4) metal coordination : angle 1.00871 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1103.35 seconds wall clock time: 19 minutes 47.98 seconds (1187.98 seconds total)