Starting phenix.real_space_refine on Wed Mar 4 06:25:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2n_27143/03_2026/8d2n_27143.map" } resolution = 2.88 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= 0.000 sd= 0.005 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: 6 Type Number sf(0) Gaussians P 128 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 6676 2.51 5 N 2119 2.21 5 O 2470 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-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11414 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1105, 8716 Classifications: {'peptide': 1105} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 3, 'PCIS': 3, 'PTRANS': 59, 'TRANS': 1039} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1961 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 9, 'rna3p_pur': 42, 'rna3p_pyr': 37} Link IDs: {'rna2p': 13, 'rna3p': 78} Chain breaks: 1 Chain: "X" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 514 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "D" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 222 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.06, per 1000 atoms: 0.27 Number of scatterers: 11414 At special positions: 0 Unit cell: (102.3, 109.725, 120.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 20 16.00 P 128 15.00 Mg 1 11.99 O 2470 8.00 N 2119 7.00 C 6676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 578 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 575 " - pdb=" SG CYS A 613 " distance=2.04 Simple disulfide: pdb=" SG CYS A 578 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS A 610 " - pdb=" SG CYS A 613 " distance=2.03 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: 1.09 Conformation dependent library (CDL) restraints added in 516.6 milliseconds 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2074 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 46.9% alpha, 8.9% beta 43 base pairs and 79 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 Processing helix chain 'A' and resid 104 through 116 Processing helix chain 'A' and resid 120 through 138 Processing helix chain 'A' and resid 147 through 153 Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 180 through 192 Processing helix chain 'A' and resid 221 through 237 removed outlier: 3.695A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 251 Processing helix chain 'A' and resid 279 through 294 removed outlier: 3.730A pdb=" N GLN A 283 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A 294 " --> pdb=" O ALA A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 316 Processing helix chain 'A' and resid 326 through 330 removed outlier: 3.612A pdb=" N ILE A 330 " --> pdb=" O TRP A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 354 through 359 removed outlier: 3.916A pdb=" N GLN A 359 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 378 Processing helix chain 'A' and resid 381 through 391 Processing helix chain 'A' and resid 392 through 405 removed outlier: 3.589A pdb=" N ASP A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 430 removed outlier: 4.176A pdb=" N GLY A 430 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 458 through 468 removed outlier: 4.460A pdb=" N LYS A 464 " --> pdb=" O HIS A 460 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 467 " --> pdb=" O ARG A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 508 Processing helix chain 'A' and resid 526 through 539 removed outlier: 3.777A pdb=" N ALA A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 553 removed outlier: 3.732A pdb=" N ARG A 544 " --> pdb=" O LYS A 540 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 572 removed outlier: 3.660A pdb=" N LEU A 562 " --> pdb=" O SER A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.718A pdb=" N GLY A 598 " --> pdb=" O ARG A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 618 removed outlier: 4.123A pdb=" N LYS A 617 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 618 " --> pdb=" O LYS A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 618' Processing helix chain 'A' and resid 636 through 643 Processing helix chain 'A' and resid 653 through 669 removed outlier: 3.938A pdb=" N SER A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 703 Processing helix chain 'A' and resid 713 through 723 removed outlier: 3.809A pdb=" N GLU A 717 " --> pdb=" O GLY A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 731 Processing helix chain 'A' and resid 742 through 747 removed outlier: 3.684A pdb=" N LEU A 745 " --> pdb=" O THR A 742 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ARG A 747 " --> pdb=" O ARG A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 748 through 758 Processing helix chain 'A' and resid 761 through 777 Processing helix chain 'A' and resid 797 through 807 Processing helix chain 'A' and resid 809 through 819 Processing helix chain 'A' and resid 856 through 861 Processing helix chain 'A' and resid 864 through 876 Processing helix chain 'A' and resid 957 through 963 Processing helix chain 'A' and resid 981 through 986 Processing helix chain 'A' and resid 988 through 998 Processing helix chain 'A' and resid 1024 through 1033 removed outlier: 3.770A pdb=" N MET A1028 " --> pdb=" O GLY A1024 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR A1032 " --> pdb=" O MET A1028 " (cutoff:3.500A) Processing helix chain 'A' and resid 1057 through 1071 Processing helix chain 'A' and resid 1076 through 1086 Processing helix chain 'A' and resid 1094 through 1099 Processing sheet with id=AA1, first strand: chain 'A' and resid 706 through 710 removed outlier: 6.422A pdb=" N ILE A 513 " --> pdb=" O ALA A 708 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 710 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL A 515 " --> pdb=" O PHE A 710 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N TRP A 13 " --> pdb=" O SER A 512 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N VAL A 514 " --> pdb=" O TRP A 13 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU A 15 " --> pdb=" O VAL A 514 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLU A 516 " --> pdb=" O LEU A 15 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL A 17 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 24 " --> pdb=" O VAL A 43 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VAL A 43 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU A 26 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A 41 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ALA A 28 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N ILE A 39 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER A 30 " --> pdb=" O LYS A 37 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 846 through 849 Processing sheet with id=AA5, first strand: chain 'A' and resid 854 through 855 Processing sheet with id=AA6, first strand: chain 'A' and resid 899 through 900 Processing sheet with id=AA7, first strand: chain 'A' and resid 921 through 924 Processing sheet with id=AA8, first strand: chain 'A' and resid 949 through 956 removed outlier: 3.972A pdb=" N GLY A1004 " --> pdb=" O VAL A 939 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ARG A 941 " --> pdb=" O GLN A1002 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N GLN A1002 " --> pdb=" O ARG A 941 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1090 through 1093 removed outlier: 6.652A pdb=" N ASN A1050 " --> pdb=" O THR A1041 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU A1011 " --> pdb=" O ILE A1106 " (cutoff:3.500A) 377 hydrogen bonds defined for protein. 1089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 109 hydrogen bonds 198 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 79 stacking parallelities Total time for adding SS restraints: 3.43 Time building geometry restraints manager: 1.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3004 1.34 - 1.46: 3717 1.46 - 1.59: 4922 1.59 - 1.71: 248 1.71 - 1.84: 28 Bond restraints: 11919 Sorted by residual: bond pdb=" N SER A 524 " pdb=" CA SER A 524 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.77e-02 3.19e+03 5.88e+00 bond pdb=" N9 G B 95 " pdb=" C4 G B 95 " ideal model delta sigma weight residual 1.375 1.417 -0.042 2.00e-02 2.50e+03 4.37e+00 bond pdb=" CA VAL A 451 " pdb=" C VAL A 451 " ideal model delta sigma weight residual 1.523 1.545 -0.022 1.27e-02 6.20e+03 2.99e+00 bond pdb=" C3' DT X 23 " pdb=" O3' DT X 23 " ideal model delta sigma weight residual 1.422 1.473 -0.051 3.00e-02 1.11e+03 2.89e+00 bond pdb=" C SER A 522 " pdb=" N GLU A 523 " ideal model delta sigma weight residual 1.334 1.363 -0.029 1.79e-02 3.12e+03 2.64e+00 ... (remaining 11914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 16613 3.85 - 7.70: 137 7.70 - 11.55: 13 11.55 - 15.40: 1 15.40 - 19.25: 1 Bond angle restraints: 16765 Sorted by residual: angle pdb=" C PRO A 675 " pdb=" N GLU A 676 " pdb=" CA GLU A 676 " ideal model delta sigma weight residual 121.70 136.29 -14.59 1.80e+00 3.09e-01 6.57e+01 angle pdb=" C ALA A 260 " pdb=" N GLU A 261 " pdb=" CA GLU A 261 " ideal model delta sigma weight residual 121.54 132.85 -11.31 1.91e+00 2.74e-01 3.50e+01 angle pdb=" CA LEU A 757 " pdb=" CB LEU A 757 " pdb=" CG LEU A 757 " ideal model delta sigma weight residual 116.30 135.55 -19.25 3.50e+00 8.16e-02 3.03e+01 angle pdb=" CA ARG A 525 " pdb=" CB ARG A 525 " pdb=" CG ARG A 525 " ideal model delta sigma weight residual 114.10 123.58 -9.48 2.00e+00 2.50e-01 2.25e+01 angle pdb=" N GLU A 526 " pdb=" CA GLU A 526 " pdb=" C GLU A 526 " ideal model delta sigma weight residual 111.24 105.64 5.60 1.29e+00 6.01e-01 1.88e+01 ... (remaining 16760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 6715 33.90 - 67.80: 499 67.80 - 101.71: 51 101.71 - 135.61: 0 135.61 - 169.51: 2 Dihedral angle restraints: 7267 sinusoidal: 4071 harmonic: 3196 Sorted by residual: dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -4.54 -81.46 1 1.00e+01 1.00e-02 8.17e+01 dihedral pdb=" CB CYS A 578 " pdb=" SG CYS A 578 " pdb=" SG CYS A 610 " pdb=" CB CYS A 610 " ideal model delta sinusoidal sigma weight residual -86.00 -167.28 81.28 1 1.00e+01 1.00e-02 8.14e+01 dihedral pdb=" CB CYS A 575 " pdb=" SG CYS A 575 " pdb=" SG CYS A 613 " pdb=" CB CYS A 613 " ideal model delta sinusoidal sigma weight residual -86.00 -166.15 80.15 1 1.00e+01 1.00e-02 7.96e+01 ... (remaining 7264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1626 0.069 - 0.137: 270 0.137 - 0.206: 29 0.206 - 0.274: 3 0.274 - 0.343: 1 Chirality restraints: 1929 Sorted by residual: chirality pdb=" CG LEU A 84 " pdb=" CB LEU A 84 " pdb=" CD1 LEU A 84 " pdb=" CD2 LEU A 84 " both_signs ideal model delta sigma weight residual False -2.59 -2.25 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA ARG A 525 " pdb=" N ARG A 525 " pdb=" C ARG A 525 " pdb=" CB ARG A 525 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C1' G B 30 " pdb=" O4' G B 30 " pdb=" C2' G B 30 " pdb=" N9 G B 30 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1926 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 521 " -0.018 2.00e-02 2.50e+03 3.60e-02 1.29e+01 pdb=" C ALA A 521 " 0.062 2.00e-02 2.50e+03 pdb=" O ALA A 521 " -0.024 2.00e-02 2.50e+03 pdb=" N SER A 522 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 61 " -0.017 2.00e-02 2.50e+03 1.69e-02 6.42e+00 pdb=" N1 U B 61 " 0.044 2.00e-02 2.50e+03 pdb=" C2 U B 61 " -0.016 2.00e-02 2.50e+03 pdb=" O2 U B 61 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U B 61 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U B 61 " 0.000 2.00e-02 2.50e+03 pdb=" O4 U B 61 " 0.001 2.00e-02 2.50e+03 pdb=" C5 U B 61 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U B 61 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 45 " 0.028 2.00e-02 2.50e+03 1.64e-02 6.03e+00 pdb=" N1 U B 45 " -0.037 2.00e-02 2.50e+03 pdb=" C2 U B 45 " 0.009 2.00e-02 2.50e+03 pdb=" O2 U B 45 " -0.007 2.00e-02 2.50e+03 pdb=" N3 U B 45 " -0.000 2.00e-02 2.50e+03 pdb=" C4 U B 45 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 45 " 0.007 2.00e-02 2.50e+03 pdb=" C5 U B 45 " -0.000 2.00e-02 2.50e+03 pdb=" C6 U B 45 " -0.005 2.00e-02 2.50e+03 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 361 2.68 - 3.24: 9801 3.24 - 3.79: 20621 3.79 - 4.35: 26009 4.35 - 4.90: 39445 Nonbonded interactions: 96237 Sorted by model distance: nonbonded pdb=" OD2 ASP A 18 " pdb="MG MG A1201 " model vdw 2.129 2.170 nonbonded pdb=" O2 C B 83 " pdb=" N2 G B 101 " model vdw 2.253 2.496 nonbonded pdb=" OG SER A 59 " pdb=" OP1 C B 17 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU A 727 " pdb=" OG SER A 741 " model vdw 2.277 3.040 nonbonded pdb=" O VAL A 755 " pdb=" OG1 THR A 758 " model vdw 2.283 3.040 ... (remaining 96232 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.790 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 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 : 0.004 0.051 11924 Z= 0.229 Angle : 0.943 19.251 16775 Z= 0.493 Chirality : 0.051 0.343 1929 Planarity : 0.008 0.092 1716 Dihedral : 20.410 169.511 5178 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.83 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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 are not related in a simple way. whole: -1.94 (0.22), residues: 1097 helix: -1.00 (0.20), residues: 495 sheet: -1.10 (0.51), residues: 105 loop : -1.51 (0.24), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 711 TYR 0.025 0.003 TYR A 651 PHE 0.025 0.002 PHE A 282 TRP 0.033 0.002 TRP A1128 HIS 0.012 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00446 (11919) covalent geometry : angle 0.94118 (16765) SS BOND : bond 0.00442 ( 5) SS BOND : angle 2.43988 ( 10) hydrogen bonds : bond 0.07503 ( 486) hydrogen bonds : angle 5.70669 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.363 Fit side-chains REVERT: A 820 ARG cc_start: 0.6349 (mtm110) cc_final: 0.6145 (mtp180) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 1.0140 time to fit residues: 64.2533 Evaluate side-chains 39 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 53 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 overall best weight: 1.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 391 GLN A 642 GLN A 898 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.195916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.173457 restraints weight = 14672.006| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.16 r_work: 0.3774 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11924 Z= 0.175 Angle : 0.618 7.994 16775 Z= 0.319 Chirality : 0.039 0.220 1929 Planarity : 0.005 0.038 1716 Dihedral : 21.479 167.826 3093 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.77 % Allowed : 7.33 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.93 (0.24), residues: 1097 helix: 0.16 (0.23), residues: 497 sheet: -0.89 (0.56), residues: 85 loop : -1.31 (0.24), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 711 TYR 0.016 0.002 TYR A 986 PHE 0.016 0.001 PHE A 384 TRP 0.018 0.002 TRP A1128 HIS 0.007 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00375 (11919) covalent geometry : angle 0.61616 (16765) SS BOND : bond 0.00341 ( 5) SS BOND : angle 1.78028 ( 10) hydrogen bonds : bond 0.06138 ( 486) hydrogen bonds : angle 4.65352 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.380 Fit side-chains REVERT: A 650 MET cc_start: 0.1696 (mtt) cc_final: 0.1054 (pmm) REVERT: A 812 ASP cc_start: 0.7352 (t0) cc_final: 0.7146 (t0) REVERT: A 976 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7696 (pm20) REVERT: A 1028 MET cc_start: 0.7342 (ptt) cc_final: 0.7065 (ptp) outliers start: 7 outliers final: 3 residues processed: 51 average time/residue: 0.8805 time to fit residues: 47.7303 Evaluate side-chains 43 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 974 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 77 optimal weight: 8.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 117 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 898 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.191955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169230 restraints weight = 14650.212| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.27 r_work: 0.3770 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11924 Z= 0.264 Angle : 0.710 9.212 16775 Z= 0.364 Chirality : 0.044 0.234 1929 Planarity : 0.006 0.048 1716 Dihedral : 21.522 169.000 3093 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.42 % Allowed : 10.28 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.92 (0.24), residues: 1097 helix: 0.24 (0.24), residues: 494 sheet: -0.98 (0.54), residues: 85 loop : -1.35 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1048 TYR 0.019 0.002 TYR A 986 PHE 0.021 0.002 PHE A 282 TRP 0.016 0.002 TRP A 13 HIS 0.006 0.002 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00579 (11919) covalent geometry : angle 0.70964 (16765) SS BOND : bond 0.00400 ( 5) SS BOND : angle 1.50091 ( 10) hydrogen bonds : bond 0.06416 ( 486) hydrogen bonds : angle 4.78966 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.346 Fit side-chains REVERT: A 650 MET cc_start: 0.1645 (mtt) cc_final: 0.1172 (pmm) REVERT: A 686 TYR cc_start: 0.6981 (t80) cc_final: 0.6653 (t80) REVERT: A 976 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7608 (pm20) outliers start: 13 outliers final: 5 residues processed: 51 average time/residue: 0.9247 time to fit residues: 50.0244 Evaluate side-chains 43 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 24 optimal weight: 0.4980 chunk 44 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 82 optimal weight: 6.9990 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.193021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.170266 restraints weight = 14649.969| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.18 r_work: 0.3786 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11924 Z= 0.210 Angle : 0.640 7.744 16775 Z= 0.330 Chirality : 0.041 0.235 1929 Planarity : 0.005 0.060 1716 Dihedral : 21.417 169.122 3093 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.53 % Allowed : 12.58 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.80 (0.24), residues: 1097 helix: 0.33 (0.24), residues: 495 sheet: -0.94 (0.54), residues: 85 loop : -1.28 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.015 0.002 TYR A 986 PHE 0.020 0.002 PHE A 384 TRP 0.014 0.002 TRP A 13 HIS 0.004 0.001 HIS A 538 Details of bonding type rmsd covalent geometry : bond 0.00456 (11919) covalent geometry : angle 0.63905 (16765) SS BOND : bond 0.00373 ( 5) SS BOND : angle 1.42563 ( 10) hydrogen bonds : bond 0.05946 ( 486) hydrogen bonds : angle 4.61824 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 0.367 Fit side-chains REVERT: A 90 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6938 (mt-10) REVERT: A 686 TYR cc_start: 0.6864 (t80) cc_final: 0.6570 (t80) REVERT: A 976 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7599 (pm20) outliers start: 14 outliers final: 8 residues processed: 52 average time/residue: 0.9328 time to fit residues: 51.5119 Evaluate side-chains 48 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1076 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 97 optimal weight: 0.0970 chunk 36 optimal weight: 9.9990 overall best weight: 3.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 614 ASN A 702 ASN A 898 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.190531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.175786 restraints weight = 14774.998| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.02 r_work: 0.3800 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11924 Z= 0.279 Angle : 0.724 9.145 16775 Z= 0.371 Chirality : 0.045 0.244 1929 Planarity : 0.006 0.052 1716 Dihedral : 21.533 170.727 3093 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.97 % Allowed : 15.10 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -1.04 (0.24), residues: 1097 helix: 0.12 (0.23), residues: 494 sheet: -1.02 (0.53), residues: 85 loop : -1.40 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.017 0.003 TYR A 986 PHE 0.019 0.002 PHE A 384 TRP 0.017 0.002 TRP A 13 HIS 0.005 0.002 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00610 (11919) covalent geometry : angle 0.72369 (16765) SS BOND : bond 0.00440 ( 5) SS BOND : angle 1.51478 ( 10) hydrogen bonds : bond 0.06345 ( 486) hydrogen bonds : angle 4.82335 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 38 time to evaluate : 0.359 Fit side-chains REVERT: A 150 ASP cc_start: 0.6856 (t0) cc_final: 0.6617 (t0) REVERT: A 686 TYR cc_start: 0.6931 (t80) cc_final: 0.6703 (t80) REVERT: A 976 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7518 (pm20) outliers start: 18 outliers final: 9 residues processed: 51 average time/residue: 0.8344 time to fit residues: 45.4762 Evaluate side-chains 45 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1076 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 64 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 113 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.191965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.168926 restraints weight = 14698.187| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 0.91 r_work: 0.3698 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11924 Z= 0.208 Angle : 0.648 10.235 16775 Z= 0.333 Chirality : 0.041 0.237 1929 Planarity : 0.005 0.049 1716 Dihedral : 21.384 172.193 3093 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.19 % Allowed : 15.86 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.84 (0.24), residues: 1097 helix: 0.31 (0.24), residues: 494 sheet: -1.00 (0.54), residues: 85 loop : -1.30 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1048 TYR 0.014 0.002 TYR A 986 PHE 0.020 0.002 PHE A 384 TRP 0.014 0.002 TRP A 13 HIS 0.004 0.001 HIS A 936 Details of bonding type rmsd covalent geometry : bond 0.00451 (11919) covalent geometry : angle 0.64690 (16765) SS BOND : bond 0.00386 ( 5) SS BOND : angle 1.45409 ( 10) hydrogen bonds : bond 0.05823 ( 486) hydrogen bonds : angle 4.62950 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.352 Fit side-chains REVERT: A 461 ASN cc_start: 0.6295 (t0) cc_final: 0.6027 (t0) REVERT: A 686 TYR cc_start: 0.6933 (t80) cc_final: 0.6620 (t80) REVERT: A 976 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7454 (pm20) outliers start: 20 outliers final: 12 residues processed: 58 average time/residue: 0.8205 time to fit residues: 50.7793 Evaluate side-chains 53 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 883 LYS Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1128 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 72 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 90 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 59 optimal weight: 40.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.192092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.177453 restraints weight = 14627.292| |-----------------------------------------------------------------------------| r_work (start): 0.4189 rms_B_bonded: 1.01 r_work: 0.3794 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11924 Z= 0.205 Angle : 0.643 9.862 16775 Z= 0.330 Chirality : 0.041 0.236 1929 Planarity : 0.005 0.044 1716 Dihedral : 21.352 174.060 3093 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.30 % Allowed : 16.41 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.77 (0.24), residues: 1097 helix: 0.38 (0.24), residues: 493 sheet: -0.98 (0.54), residues: 85 loop : -1.28 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1048 TYR 0.015 0.002 TYR A1032 PHE 0.019 0.002 PHE A 384 TRP 0.013 0.002 TRP A 13 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00445 (11919) covalent geometry : angle 0.64214 (16765) SS BOND : bond 0.00370 ( 5) SS BOND : angle 1.44516 ( 10) hydrogen bonds : bond 0.05714 ( 486) hydrogen bonds : angle 4.57655 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 43 time to evaluate : 0.381 Fit side-chains REVERT: A 461 ASN cc_start: 0.5843 (t0) cc_final: 0.5625 (t0) REVERT: A 686 TYR cc_start: 0.6909 (t80) cc_final: 0.6645 (t80) REVERT: A 976 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7472 (pm20) outliers start: 21 outliers final: 12 residues processed: 60 average time/residue: 0.8652 time to fit residues: 55.1991 Evaluate side-chains 51 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 805 GLU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1128 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 0.0060 chunk 101 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 898 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.196384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.173080 restraints weight = 14714.987| |-----------------------------------------------------------------------------| r_work (start): 0.4135 rms_B_bonded: 1.10 r_work: 0.3731 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11924 Z= 0.124 Angle : 0.556 10.747 16775 Z= 0.288 Chirality : 0.037 0.232 1929 Planarity : 0.004 0.035 1716 Dihedral : 21.034 173.190 3093 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.42 % Allowed : 17.40 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.32 (0.25), residues: 1097 helix: 0.85 (0.24), residues: 488 sheet: -0.85 (0.54), residues: 85 loop : -1.10 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.012 0.001 TYR A 651 PHE 0.016 0.001 PHE A 384 TRP 0.010 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00259 (11919) covalent geometry : angle 0.55497 (16765) SS BOND : bond 0.00340 ( 5) SS BOND : angle 1.41156 ( 10) hydrogen bonds : bond 0.05273 ( 486) hydrogen bonds : angle 4.23725 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.354 Fit side-chains REVERT: A 461 ASN cc_start: 0.6246 (t0) cc_final: 0.6005 (t0) REVERT: A 676 GLU cc_start: 0.1030 (OUTLIER) cc_final: -0.0445 (pm20) REVERT: A 686 TYR cc_start: 0.6876 (t80) cc_final: 0.6569 (t80) REVERT: A 976 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7494 (pm20) REVERT: A 1068 ARG cc_start: 0.6006 (tpm170) cc_final: 0.4069 (ttm-80) outliers start: 13 outliers final: 6 residues processed: 59 average time/residue: 0.9201 time to fit residues: 57.5084 Evaluate side-chains 47 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 1076 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 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 = 0.4355 r_free = 0.4355 target = 0.192972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.169354 restraints weight = 14612.888| |-----------------------------------------------------------------------------| r_work (start): 0.4097 rms_B_bonded: 1.21 r_work: 0.3763 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11924 Z= 0.186 Angle : 0.609 7.484 16775 Z= 0.313 Chirality : 0.039 0.228 1929 Planarity : 0.005 0.047 1716 Dihedral : 21.105 172.027 3093 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.20 % Allowed : 18.05 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.40 (0.25), residues: 1097 helix: 0.72 (0.24), residues: 493 sheet: -0.79 (0.55), residues: 85 loop : -1.12 (0.25), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 820 TYR 0.013 0.002 TYR A 986 PHE 0.014 0.002 PHE A 384 TRP 0.011 0.001 TRP A 13 HIS 0.003 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00403 (11919) covalent geometry : angle 0.60800 (16765) SS BOND : bond 0.00319 ( 5) SS BOND : angle 1.41491 ( 10) hydrogen bonds : bond 0.05408 ( 486) hydrogen bonds : angle 4.37173 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.346 Fit side-chains REVERT: A 676 GLU cc_start: 0.1267 (OUTLIER) cc_final: -0.0373 (pm20) REVERT: A 686 TYR cc_start: 0.6910 (t80) cc_final: 0.6621 (t80) REVERT: A 976 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7561 (pm20) REVERT: A 1068 ARG cc_start: 0.6260 (tpm170) cc_final: 0.4379 (ttm-80) outliers start: 11 outliers final: 8 residues processed: 52 average time/residue: 0.9011 time to fit residues: 49.8014 Evaluate side-chains 51 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 SER Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 849 THR Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1128 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 5.9990 chunk 1 optimal weight: 0.0980 chunk 112 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 0.0010 chunk 116 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 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 = 0.4395 r_free = 0.4395 target = 0.197046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.174355 restraints weight = 14850.530| |-----------------------------------------------------------------------------| r_work (start): 0.4153 rms_B_bonded: 1.12 r_work: 0.3777 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11924 Z= 0.117 Angle : 0.545 9.059 16775 Z= 0.282 Chirality : 0.037 0.231 1929 Planarity : 0.004 0.057 1716 Dihedral : 20.914 170.050 3093 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.77 % Allowed : 18.38 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.10 (0.25), residues: 1097 helix: 1.04 (0.24), residues: 488 sheet: -0.68 (0.58), residues: 80 loop : -1.02 (0.25), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 820 TYR 0.013 0.001 TYR A 651 PHE 0.014 0.001 PHE A 384 TRP 0.010 0.001 TRP A 161 HIS 0.005 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00243 (11919) covalent geometry : angle 0.54419 (16765) SS BOND : bond 0.00269 ( 5) SS BOND : angle 1.44782 ( 10) hydrogen bonds : bond 0.05143 ( 486) hydrogen bonds : angle 4.12463 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2194 Ramachandran restraints generated. 1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.428 Fit side-chains REVERT: A 516 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7374 (pt0) REVERT: A 676 GLU cc_start: 0.1061 (OUTLIER) cc_final: -0.0433 (pm20) REVERT: A 686 TYR cc_start: 0.6862 (t80) cc_final: 0.6514 (t80) REVERT: A 820 ARG cc_start: 0.6938 (ttm110) cc_final: 0.6538 (ptp-170) REVERT: A 976 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7642 (pm20) REVERT: A 1068 ARG cc_start: 0.6096 (tpm170) cc_final: 0.4195 (ttm-80) outliers start: 7 outliers final: 4 residues processed: 50 average time/residue: 0.9592 time to fit residues: 50.8050 Evaluate side-chains 49 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 849 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 113 optimal weight: 10.0000 chunk 116 optimal weight: 7.9990 chunk 121 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 44 optimal weight: 8.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.193457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.169710 restraints weight = 14718.924| |-----------------------------------------------------------------------------| r_work (start): 0.4102 rms_B_bonded: 1.11 r_work: 0.3683 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11924 Z= 0.181 Angle : 0.603 8.421 16775 Z= 0.308 Chirality : 0.039 0.224 1929 Planarity : 0.005 0.051 1716 Dihedral : 21.029 167.866 3093 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.98 % Allowed : 18.60 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % 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 are not related in a simple way. whole: -0.24 (0.25), residues: 1097 helix: 0.84 (0.24), residues: 493 sheet: -0.67 (0.58), residues: 80 loop : -1.02 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 820 TYR 0.014 0.002 TYR A 651 PHE 0.013 0.001 PHE A 384 TRP 0.011 0.001 TRP A 13 HIS 0.003 0.001 HIS A 749 Details of bonding type rmsd covalent geometry : bond 0.00393 (11919) covalent geometry : angle 0.60184 (16765) SS BOND : bond 0.00303 ( 5) SS BOND : angle 1.42872 ( 10) hydrogen bonds : bond 0.05367 ( 486) hydrogen bonds : angle 4.29209 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2784.78 seconds wall clock time: 48 minutes 32.87 seconds (2912.87 seconds total)