Starting phenix.real_space_refine on Tue Jul 29 16:31:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_27143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_27143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_27143.map" model { file = "/net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_27143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2n_27143/07_2025/8d2n_27143.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.26, per 1000 atoms: 0.64 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: 2.72 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.37 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: 5.59 Time building geometry restraints manager: 3.26 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: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.110 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (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 TRP 0.033 0.002 TRP A1128 HIS 0.012 0.001 HIS A 538 PHE 0.025 0.002 PHE A 282 TYR 0.025 0.003 TYR A 651 ARG 0.020 0.001 ARG A 711 Details of bonding type rmsd hydrogen bonds : bond 0.07503 ( 486) hydrogen bonds : angle 5.70669 ( 1287) SS BOND : bond 0.00442 ( 5) SS BOND : angle 2.43988 ( 10) covalent geometry : bond 0.00446 (11919) covalent geometry : angle 0.94118 (16765) *********************** 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 : 1.108 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: 1.9999 time to fit residues: 127.6341 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 : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 62 optimal weight: 8.9990 chunk 49 optimal weight: 0.1980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 58 optimal weight: 20.0000 chunk 71 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- 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 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 = 0.4357 r_free = 0.4357 target = 0.193341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.170053 restraints weight = 14450.743| |-----------------------------------------------------------------------------| r_work (start): 0.4103 rms_B_bonded: 1.24 r_work: 0.3748 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11924 Z= 0.249 Angle : 0.707 8.820 16775 Z= 0.362 Chirality : 0.043 0.231 1929 Planarity : 0.006 0.041 1716 Dihedral : 21.597 168.911 3093 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.20 % Allowed : 7.77 % Favored : 91.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.23), residues: 1097 helix: -0.01 (0.23), residues: 494 sheet: -1.03 (0.54), residues: 85 loop : -1.39 (0.24), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1128 HIS 0.008 0.002 HIS A 538 PHE 0.017 0.002 PHE A 384 TYR 0.019 0.002 TYR A 986 ARG 0.006 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.06701 ( 486) hydrogen bonds : angle 4.85473 ( 1287) SS BOND : bond 0.00423 ( 5) SS BOND : angle 1.83548 ( 10) covalent geometry : bond 0.00542 (11919) covalent geometry : angle 0.70568 (16765) *********************** 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 59 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.986 Fit side-chains REVERT: A 150 ASP cc_start: 0.6907 (t0) cc_final: 0.6704 (t0) REVERT: A 474 ARG cc_start: 0.5909 (mmm160) cc_final: 0.5567 (mpt180) REVERT: A 820 ARG cc_start: 0.6980 (mtm110) cc_final: 0.6726 (mtp180) REVERT: A 976 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7680 (pm20) outliers start: 11 outliers final: 6 residues processed: 57 average time/residue: 2.3732 time to fit residues: 143.8481 Evaluate side-chains 49 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.867 ------------------------------------------------------------------------------- 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 273 LEU Chi-restraints excluded: chain A residue 872 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 25 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 chunk 119 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 39 optimal weight: 8.9990 chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- 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 = 0.4410 r_free = 0.4410 target = 0.198517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.176624 restraints weight = 14820.634| |-----------------------------------------------------------------------------| r_work (start): 0.4175 rms_B_bonded: 1.14 r_work: 0.3822 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11924 Z= 0.116 Angle : 0.541 6.971 16775 Z= 0.282 Chirality : 0.036 0.231 1929 Planarity : 0.004 0.034 1716 Dihedral : 21.154 167.980 3093 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.55 % Allowed : 10.50 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.24), residues: 1097 helix: 0.62 (0.24), residues: 492 sheet: -0.86 (0.55), residues: 85 loop : -1.15 (0.24), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS A 538 PHE 0.017 0.001 PHE A 384 TYR 0.011 0.001 TYR A 868 ARG 0.011 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05659 ( 486) hydrogen bonds : angle 4.34147 ( 1287) SS BOND : bond 0.00286 ( 5) SS BOND : angle 1.44982 ( 10) covalent geometry : bond 0.00238 (11919) covalent geometry : angle 0.54038 (16765) *********************** 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 56 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 1.091 Fit side-chains REVERT: A 820 ARG cc_start: 0.6939 (mtm110) cc_final: 0.6680 (mtp180) REVERT: A 976 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7668 (pm20) REVERT: A 1068 ARG cc_start: 0.6069 (tpm170) cc_final: 0.4278 (ttm-80) outliers start: 5 outliers final: 1 residues processed: 53 average time/residue: 1.9075 time to fit residues: 108.3734 Evaluate side-chains 45 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 44 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 103 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 82 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 108 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 = 0.4379 r_free = 0.4379 target = 0.195606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172710 restraints weight = 14683.503| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.16 r_work: 0.3727 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11924 Z= 0.159 Angle : 0.566 6.665 16775 Z= 0.294 Chirality : 0.038 0.222 1929 Planarity : 0.004 0.045 1716 Dihedral : 21.159 165.969 3093 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.09 % Allowed : 11.60 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.25), residues: 1097 helix: 0.71 (0.24), residues: 497 sheet: -0.79 (0.55), residues: 85 loop : -1.06 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 145 HIS 0.003 0.001 HIS A 538 PHE 0.014 0.001 PHE A 384 TYR 0.014 0.002 TYR A 986 ARG 0.006 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05654 ( 486) hydrogen bonds : angle 4.31032 ( 1287) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.37335 ( 10) covalent geometry : bond 0.00340 (11919) covalent geometry : angle 0.56531 (16765) *********************** 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 53 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.115 Fit side-chains REVERT: A 496 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 976 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7548 (pm20) outliers start: 10 outliers final: 3 residues processed: 50 average time/residue: 1.9294 time to fit residues: 103.0412 Evaluate side-chains 46 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 42 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 883 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 23 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 75 optimal weight: 8.9990 chunk 58 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 29 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 80 optimal weight: 0.0770 chunk 57 optimal weight: 20.0000 overall best weight: 3.5744 ------------------------------------------------------------------------------- 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 898 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.191908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169103 restraints weight = 14469.850| |-----------------------------------------------------------------------------| r_work (start): 0.4096 rms_B_bonded: 1.25 r_work: 0.3750 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2171 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= 0.263 Angle : 0.696 8.757 16775 Z= 0.357 Chirality : 0.043 0.231 1929 Planarity : 0.006 0.050 1716 Dihedral : 21.420 165.954 3093 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.75 % Allowed : 12.91 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1097 helix: 0.37 (0.23), residues: 494 sheet: -0.89 (0.54), residues: 85 loop : -1.20 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 13 HIS 0.005 0.002 HIS A 481 PHE 0.017 0.002 PHE A 384 TYR 0.018 0.002 TYR A 986 ARG 0.008 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.06281 ( 486) hydrogen bonds : angle 4.65783 ( 1287) SS BOND : bond 0.00392 ( 5) SS BOND : angle 1.45108 ( 10) covalent geometry : bond 0.00575 (11919) covalent geometry : angle 0.69517 (16765) *********************** 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 58 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.995 Fit side-chains REVERT: A 686 TYR cc_start: 0.7002 (t80) cc_final: 0.6770 (t80) REVERT: A 976 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7653 (pm20) outliers start: 16 outliers final: 6 residues processed: 55 average time/residue: 1.7774 time to fit residues: 104.4828 Evaluate side-chains 45 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 974 THR Chi-restraints excluded: chain A residue 976 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 91 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 chunk 97 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 = 0.4380 r_free = 0.4380 target = 0.195688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.165744 restraints weight = 14719.266| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 1.54 r_work: 0.3635 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3525 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11924 Z= 0.135 Angle : 0.551 7.088 16775 Z= 0.288 Chirality : 0.037 0.229 1929 Planarity : 0.004 0.042 1716 Dihedral : 21.090 165.860 3093 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.98 % Allowed : 14.55 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.25), residues: 1097 helix: 0.77 (0.24), residues: 489 sheet: -0.85 (0.54), residues: 85 loop : -1.00 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.003 0.001 HIS A 749 PHE 0.018 0.001 PHE A 384 TYR 0.012 0.001 TYR A 651 ARG 0.008 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05495 ( 486) hydrogen bonds : angle 4.27986 ( 1287) SS BOND : bond 0.00300 ( 5) SS BOND : angle 1.38644 ( 10) covalent geometry : bond 0.00284 (11919) covalent geometry : angle 0.54979 (16765) *********************** 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 57 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 1.005 Fit side-chains REVERT: A 676 GLU cc_start: 0.1015 (OUTLIER) cc_final: 0.0519 (mm-30) REVERT: A 686 TYR cc_start: 0.7067 (t80) cc_final: 0.6657 (t80) REVERT: A 976 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7535 (pm20) REVERT: A 1068 ARG cc_start: 0.5699 (tpm170) cc_final: 0.3906 (ttm-80) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 1.7529 time to fit residues: 103.3394 Evaluate side-chains 48 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 1.139 ------------------------------------------------------------------------------- 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 676 GLU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.193312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.169584 restraints weight = 14736.613| |-----------------------------------------------------------------------------| r_work (start): 0.4101 rms_B_bonded: 1.22 r_work: 0.3700 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11924 Z= 0.193 Angle : 0.607 8.158 16775 Z= 0.313 Chirality : 0.039 0.230 1929 Planarity : 0.005 0.054 1716 Dihedral : 21.162 164.944 3093 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.53 % Allowed : 14.11 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1097 helix: 0.63 (0.24), residues: 495 sheet: -0.84 (0.55), residues: 85 loop : -1.01 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 145 HIS 0.003 0.001 HIS A 481 PHE 0.016 0.002 PHE A 384 TYR 0.015 0.002 TYR A 986 ARG 0.007 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05661 ( 486) hydrogen bonds : angle 4.38350 ( 1287) SS BOND : bond 0.00329 ( 5) SS BOND : angle 1.38932 ( 10) covalent geometry : bond 0.00418 (11919) covalent geometry : angle 0.60574 (16765) *********************** 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 58 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 1.020 Fit side-chains REVERT: A 150 ASP cc_start: 0.6857 (t0) cc_final: 0.6606 (t0) REVERT: A 676 GLU cc_start: 0.1496 (OUTLIER) cc_final: 0.0800 (mm-30) REVERT: A 686 TYR cc_start: 0.6918 (t80) cc_final: 0.6673 (t80) REVERT: A 976 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7694 (pm20) outliers start: 14 outliers final: 5 residues processed: 55 average time/residue: 1.7593 time to fit residues: 103.5224 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 : 1.123 ------------------------------------------------------------------------------- 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 676 GLU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 93 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 117 optimal weight: 8.9990 chunk 95 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.194644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.171103 restraints weight = 14824.944| |-----------------------------------------------------------------------------| r_work (start): 0.4117 rms_B_bonded: 1.23 r_work: 0.3749 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11924 Z= 0.153 Angle : 0.570 8.275 16775 Z= 0.296 Chirality : 0.038 0.229 1929 Planarity : 0.004 0.041 1716 Dihedral : 21.082 164.359 3093 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.77 % Allowed : 15.65 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.24), residues: 1097 helix: 0.78 (0.24), residues: 489 sheet: -0.79 (0.55), residues: 85 loop : -0.98 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 13 HIS 0.004 0.001 HIS A 749 PHE 0.016 0.001 PHE A 384 TYR 0.013 0.002 TYR A1032 ARG 0.009 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05455 ( 486) hydrogen bonds : angle 4.28060 ( 1287) SS BOND : bond 0.00314 ( 5) SS BOND : angle 1.39073 ( 10) covalent geometry : bond 0.00328 (11919) covalent geometry : angle 0.56884 (16765) *********************** 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 52 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 1.065 Fit side-chains REVERT: A 150 ASP cc_start: 0.6889 (t0) cc_final: 0.6670 (t0) REVERT: A 676 GLU cc_start: 0.1401 (OUTLIER) cc_final: -0.0249 (pm20) REVERT: A 686 TYR cc_start: 0.6880 (t80) cc_final: 0.6619 (t80) REVERT: A 820 ARG cc_start: 0.7018 (mtm110) cc_final: 0.6664 (mtp180) REVERT: A 976 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7621 (pm20) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 1.8645 time to fit residues: 99.7892 Evaluate side-chains 48 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 676 GLU Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 96 optimal weight: 0.9980 chunk 104 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.0980 chunk 121 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4400 r_free = 0.4400 target = 0.197333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.174725 restraints weight = 14723.796| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 1.12 r_work: 0.3762 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11924 Z= 0.117 Angle : 0.523 8.329 16775 Z= 0.273 Chirality : 0.036 0.227 1929 Planarity : 0.004 0.031 1716 Dihedral : 20.904 162.350 3093 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.66 % Allowed : 15.97 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.25), residues: 1097 helix: 1.05 (0.24), residues: 489 sheet: -0.69 (0.58), residues: 80 loop : -0.91 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.013 0.001 PHE A 384 TYR 0.012 0.001 TYR A1032 ARG 0.008 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05234 ( 486) hydrogen bonds : angle 4.07620 ( 1287) SS BOND : bond 0.00290 ( 5) SS BOND : angle 1.39533 ( 10) covalent geometry : bond 0.00243 (11919) covalent geometry : angle 0.52224 (16765) *********************** 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: 6 poor density : 46 time to evaluate : 1.010 Fit side-chains REVERT: A 650 MET cc_start: 0.1352 (pp-130) cc_final: 0.0999 (ppp) REVERT: A 676 GLU cc_start: 0.0825 (OUTLIER) cc_final: -0.0385 (pm20) REVERT: A 820 ARG cc_start: 0.6899 (mtm110) cc_final: 0.6511 (mtp180) REVERT: A 976 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7485 (pm20) REVERT: A 1068 ARG cc_start: 0.6074 (tpm170) cc_final: 0.4179 (ttm-80) outliers start: 6 outliers final: 3 residues processed: 50 average time/residue: 1.7756 time to fit residues: 94.9160 Evaluate side-chains 47 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 43 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 974 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 6 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 66 optimal weight: 0.0030 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 overall best weight: 3.3998 ------------------------------------------------------------------------------- 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** A 898 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.192047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168710 restraints weight = 14600.857| |-----------------------------------------------------------------------------| r_work (start): 0.4091 rms_B_bonded: 0.95 r_work: 0.3686 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 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 : 0.005 0.049 11924 Z= 0.250 Angle : 0.665 8.055 16775 Z= 0.340 Chirality : 0.042 0.226 1929 Planarity : 0.005 0.045 1716 Dihedral : 21.211 160.867 3093 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.09 % Allowed : 15.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1097 helix: 0.58 (0.23), residues: 495 sheet: -0.74 (0.55), residues: 85 loop : -1.08 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 145 HIS 0.005 0.002 HIS A 481 PHE 0.014 0.002 PHE A 282 TYR 0.018 0.002 TYR A 986 ARG 0.008 0.001 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05939 ( 486) hydrogen bonds : angle 4.43416 ( 1287) SS BOND : bond 0.00357 ( 5) SS BOND : angle 1.41611 ( 10) covalent geometry : bond 0.00548 (11919) covalent geometry : angle 0.66427 (16765) ********************** 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 53 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 1.064 Fit side-chains REVERT: A 365 GLU cc_start: 0.4402 (tt0) cc_final: 0.3691 (tp30) REVERT: A 650 MET cc_start: 0.1530 (pp-130) cc_final: 0.1153 (ppp) REVERT: A 676 GLU cc_start: 0.1158 (OUTLIER) cc_final: -0.0275 (pm20) REVERT: A 686 TYR cc_start: 0.7036 (t80) cc_final: 0.6628 (t80) REVERT: A 976 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7487 (pm20) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 1.7367 time to fit residues: 97.8397 Evaluate side-chains 48 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 974 THR Chi-restraints excluded: chain A residue 976 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4392 r_free = 0.4392 target = 0.196702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.173617 restraints weight = 14673.431| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.14 r_work: 0.3748 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11924 Z= 0.120 Angle : 0.544 11.338 16775 Z= 0.281 Chirality : 0.037 0.230 1929 Planarity : 0.004 0.045 1716 Dihedral : 21.003 161.310 3093 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.88 % Allowed : 16.30 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1097 helix: 0.97 (0.24), residues: 489 sheet: -0.75 (0.58), residues: 80 loop : -0.97 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 PHE 0.016 0.001 PHE A 384 TYR 0.013 0.001 TYR A1032 ARG 0.009 0.000 ARG A1048 Details of bonding type rmsd hydrogen bonds : bond 0.05303 ( 486) hydrogen bonds : angle 4.12887 ( 1287) SS BOND : bond 0.00286 ( 5) SS BOND : angle 1.39927 ( 10) covalent geometry : bond 0.00249 (11919) covalent geometry : angle 0.54285 (16765) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6156.88 seconds wall clock time: 106 minutes 53.47 seconds (6413.47 seconds total)