Starting phenix.real_space_refine on Fri Sep 11 20:35:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.cif Found real_map, /net/cci-nas-00/data/ceres_data/8d2n_27143/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.cif" model { file = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8d2n_27143/09_2026/8d2n_27143.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.62, per 1000 atoms: 0.23 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: 1.01 Conformation dependent library (CDL) restraints added in 395.4 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: 1.09 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: 3.49 Time building geometry restraints manager: 1.40 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=" C1' DC X 21 " pdb=" N1 DC X 21 " ideal model delta sigma weight residual 1.468 1.534 -0.066 1.40e-02 5.10e+03 2.24e+01 bond pdb=" C1' DC X 25 " pdb=" N1 DC X 25 " ideal model delta sigma weight residual 1.468 1.531 -0.063 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C1' DC X 15 " pdb=" N1 DC X 15 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" C3' DA X 13 " pdb=" C2' DA X 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.16e+01 bond pdb=" C3' DT X 12 " pdb=" C2' DT X 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 ... (remaining 11914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.85: 16581 3.85 - 7.70: 168 7.70 - 11.55: 14 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=" N3 DT X 4 " pdb=" C4 DT X 4 " pdb=" O4 DT X 4 " ideal model delta sigma weight residual 119.90 123.21 -3.31 6.00e-01 2.78e+00 3.04e+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=" O4 DT X 4 " pdb=" C4 DT X 4 " pdb=" C5 DT X 4 " ideal model delta sigma weight residual 124.90 121.32 3.58 7.00e-01 2.04e+00 2.61e+01 ... (remaining 16760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.90: 6558 33.90 - 67.80: 579 67.80 - 101.71: 52 101.71 - 135.61: 0 135.61 - 169.51: 2 Dihedral angle restraints: 7191 sinusoidal: 3995 harmonic: 3196 Sorted by residual: dihedral pdb=" C4' A B 41 " pdb=" C3' A B 41 " pdb=" C2' A B 41 " pdb=" C1' A B 41 " ideal model delta sinusoidal sigma weight residual 36.34 -39.31 75.66 1 3.10e+00 1.04e-01 7.52e+02 dihedral pdb=" C4' U B 65 " pdb=" C3' U B 65 " pdb=" C2' U B 65 " pdb=" C1' U B 65 " ideal model delta sinusoidal sigma weight residual 36.35 -38.28 74.63 1 3.10e+00 1.04e-01 7.34e+02 dihedral pdb=" C4' A B 39 " pdb=" C3' A B 39 " pdb=" C2' A B 39 " pdb=" C1' A B 39 " ideal model delta sinusoidal sigma weight residual 36.35 -37.55 73.89 1 3.10e+00 1.04e-01 7.22e+02 ... (remaining 7188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1621 0.082 - 0.165: 178 0.165 - 0.247: 84 0.247 - 0.329: 40 0.329 - 0.412: 6 Chirality restraints: 1929 Sorted by residual: chirality pdb=" P C B 63 " pdb=" OP1 C B 63 " pdb=" OP2 C B 63 " pdb=" O5' C B 63 " both_signs ideal model delta sigma weight residual True 2.17 -2.58 -0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" P G B 97 " pdb=" OP1 G B 97 " pdb=" OP2 G B 97 " pdb=" O5' G B 97 " both_signs ideal model delta sigma weight residual True 2.17 -2.57 -0.40 2.00e-01 2.50e+01 4.01e+00 chirality pdb=" C2' A B 39 " pdb=" C3' A B 39 " pdb=" O2' A B 39 " pdb=" C1' A B 39 " both_signs ideal model delta sigma weight residual False -2.79 -2.41 -0.38 2.00e-01 2.50e+01 3.52e+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: 0.01 ========== 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.270 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.440 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11924 Z= 0.314 Angle : 1.040 19.251 16775 Z= 0.562 Chirality : 0.080 0.412 1929 Planarity : 0.008 0.092 1716 Dihedral : 21.382 169.511 5102 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/Z covalent geometry : bond 0.00493 / 0.31 (11919) covalent geometry : angle 1.03812 / 0.56 (16765) SS BOND : bond 0.00442 / 0.26 ( 5) SS BOND : angle 2.43988 / 1.53 ( 10) hydrogen bonds : bond 0.07503 / 5.41 ( 486) hydrogen bonds : angle 5.70669 / 4.21 ( 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 : 0.319 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: 0.8010 time to fit residues: 51.0422 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 : 0.353 ------------------------------------------------------------------------------- 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: 4.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 8.9990 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: 7.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 HIS 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 = 0.4395 r_free = 0.4395 target = 0.197336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.176948 restraints weight = 14748.709| |-----------------------------------------------------------------------------| r_work (start): 0.4181 rms_B_bonded: 1.25 r_work: 0.3865 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work: 0.3806 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11924 Z= 0.213 Angle : 1.050 17.612 16775 Z= 0.451 Chirality : 0.096 1.313 1929 Planarity : 0.005 0.036 1716 Dihedral : 21.873 163.960 3017 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.88 % Allowed : 7.33 % Favored : 91.79 % 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: -1.09 (0.23), residues: 1097 helix: 0.01 (0.23), residues: 496 sheet: -0.92 (0.56), residues: 85 loop : -1.38 (0.24), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 506 TYR 0.020 0.002 TYR A 440 PHE 0.016 0.001 PHE A 384 TRP 0.015 0.001 TRP A1128 HIS 0.009 0.001 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (11919) covalent geometry : angle 1.04976 / 0.45 (16765) SS BOND : bond 0.00326 / 0.18 ( 5) SS BOND : angle 1.74469 / 1.11 ( 10) hydrogen bonds : bond 0.06360 / 4.50 ( 486) hydrogen bonds : angle 4.77408 / 3.51 ( 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 52 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.354 Fit side-chains REVERT: A 650 MET cc_start: 0.1594 (mtt) cc_final: 0.0964 (ppp) REVERT: A 812 ASP cc_start: 0.7344 (t0) cc_final: 0.7134 (t0) REVERT: A 976 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7568 (pm20) outliers start: 8 outliers final: 4 residues processed: 50 average time/residue: 0.7635 time to fit residues: 40.8883 Evaluate side-chains 43 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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: 5.9990 chunk 72 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 GLN A 391 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 = 0.4325 r_free = 0.4325 target = 0.190627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.176060 restraints weight = 14641.597| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 1.00 r_work: 0.3798 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.078 11924 Z= 0.391 Angle : 1.107 15.329 16775 Z= 0.494 Chirality : 0.085 1.197 1929 Planarity : 0.008 0.072 1716 Dihedral : 22.301 168.591 3017 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 0.98 % Allowed : 12.04 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.84 % Cis-general : 0.29 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.34 (0.24), residues: 1097 helix: -0.17 (0.23), residues: 493 sheet: -1.20 (0.54), residues: 85 loop : -1.50 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.018 0.003 TYR A 986 PHE 0.024 0.003 PHE A 282 TRP 0.023 0.003 TRP A 13 HIS 0.009 0.002 HIS A 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00857 / 0.39 (11919) covalent geometry : angle 1.10642 / 0.49 (16765) SS BOND : bond 0.00456 / 0.28 ( 5) SS BOND : angle 1.57408 / 0.98 ( 10) hydrogen bonds : bond 0.07508 / 5.08 ( 486) hydrogen bonds : angle 5.10271 / 3.76 ( 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 49 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.361 Fit side-chains REVERT: A 686 TYR cc_start: 0.7053 (t80) cc_final: 0.6801 (t80) REVERT: A 976 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: A 1064 LEU cc_start: 0.7855 (mp) cc_final: 0.7647 (mp) outliers start: 9 outliers final: 5 residues processed: 45 average time/residue: 0.7480 time to fit residues: 36.0943 Evaluate side-chains 41 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 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: 0.9980 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 64 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 82 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4387 r_free = 0.4387 target = 0.196517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.174990 restraints weight = 14759.347| |-----------------------------------------------------------------------------| r_work (start): 0.4159 rms_B_bonded: 1.07 r_work: 0.3852 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11924 Z= 0.152 Angle : 0.813 11.899 16775 Z= 0.365 Chirality : 0.067 1.053 1929 Planarity : 0.005 0.069 1716 Dihedral : 22.005 164.318 3017 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 0.88 % Allowed : 12.91 % Favored : 86.21 % 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: -0.74 (0.24), residues: 1097 helix: 0.39 (0.24), residues: 495 sheet: -1.11 (0.53), residues: 85 loop : -1.22 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1048 TYR 0.012 0.002 TYR A 172 PHE 0.022 0.001 PHE A 384 TRP 0.009 0.001 TRP A 388 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (11919) covalent geometry : angle 0.81227 / 0.36 (16765) SS BOND : bond 0.00351 / 0.22 ( 5) SS BOND : angle 1.43145 / 0.91 ( 10) hydrogen bonds : bond 0.06157 / 4.32 ( 486) hydrogen bonds : angle 4.54346 / 3.35 ( 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 51 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.281 Fit side-chains REVERT: A 496 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8237 (tt) REVERT: A 650 MET cc_start: 0.1575 (mtt) cc_final: 0.1197 (pmm) REVERT: A 686 TYR cc_start: 0.6937 (t80) cc_final: 0.6600 (t80) REVERT: A 976 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7567 (pm20) REVERT: A 1068 ARG cc_start: 0.6203 (tpm170) cc_final: 0.4381 (ttm-80) outliers start: 8 outliers final: 3 residues processed: 48 average time/residue: 0.7723 time to fit residues: 39.4896 Evaluate side-chains 43 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 910 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 chunk 70 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4341 r_free = 0.4341 target = 0.192145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.169680 restraints weight = 14703.490| |-----------------------------------------------------------------------------| r_work (start): 0.4094 rms_B_bonded: 1.05 r_work: 0.3772 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work: 0.3701 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11924 Z= 0.299 Angle : 0.937 12.008 16775 Z= 0.421 Chirality : 0.073 1.022 1929 Planarity : 0.006 0.055 1716 Dihedral : 22.036 165.963 3017 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 1.64 % Allowed : 13.46 % Favored : 84.90 % 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: -1.01 (0.24), residues: 1097 helix: 0.17 (0.24), residues: 495 sheet: -1.13 (0.54), residues: 85 loop : -1.38 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1048 TYR 0.019 0.003 TYR A 986 PHE 0.018 0.002 PHE A 384 TRP 0.018 0.002 TRP A 13 HIS 0.006 0.002 HIS A 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.30 (11919) covalent geometry : angle 0.93641 / 0.42 (16765) SS BOND : bond 0.00361 / 0.22 ( 5) SS BOND : angle 1.39003 / 0.87 ( 10) hydrogen bonds : bond 0.06635 / 4.55 ( 486) hydrogen bonds : angle 4.78312 / 3.53 ( 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 54 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.292 Fit side-chains REVERT: A 150 ASP cc_start: 0.6890 (t0) cc_final: 0.6671 (t0) REVERT: A 650 MET cc_start: 0.1489 (mtt) cc_final: 0.1094 (pmm) REVERT: A 686 TYR cc_start: 0.7106 (t80) cc_final: 0.6755 (t80) REVERT: A 976 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7640 (pm20) outliers start: 15 outliers final: 8 residues processed: 49 average time/residue: 0.6822 time to fit residues: 36.0133 Evaluate side-chains 44 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 35 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 291 VAL Chi-restraints excluded: chain A residue 496 LEU Chi-restraints excluded: chain A residue 820 ARG Chi-restraints excluded: chain A residue 910 ASP 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 97 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 45 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4359 r_free = 0.4359 target = 0.194459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167943 restraints weight = 14799.402| |-----------------------------------------------------------------------------| r_work (start): 0.4074 rms_B_bonded: 1.51 r_work: 0.3634 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11924 Z= 0.142 Angle : 0.765 10.131 16775 Z= 0.345 Chirality : 0.062 0.861 1929 Planarity : 0.004 0.062 1716 Dihedral : 21.834 163.105 3017 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.09 % Allowed : 14.55 % 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 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: -0.57 (0.25), residues: 1097 helix: 0.62 (0.24), residues: 489 sheet: -1.01 (0.54), residues: 85 loop : -1.21 (0.25), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.011 0.001 TYR A 172 PHE 0.021 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/Z covalent geometry : bond 0.00284 / 0.14 (11919) covalent geometry : angle 0.76441 / 0.34 (16765) SS BOND : bond 0.00330 / 0.21 ( 5) SS BOND : angle 1.39144 / 0.89 ( 10) hydrogen bonds : bond 0.05904 / 4.17 ( 486) hydrogen bonds : angle 4.41348 / 3.27 ( 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 56 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.352 Fit side-chains REVERT: A 496 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (tt) REVERT: A 976 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: A 1068 ARG cc_start: 0.5963 (tpm170) cc_final: 0.4024 (ttm-80) outliers start: 10 outliers final: 3 residues processed: 52 average time/residue: 0.7941 time to fit residues: 44.0086 Evaluate side-chains 45 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 910 ASP Chi-restraints excluded: chain A residue 976 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 10.0000 chunk 41 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 51 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 39 optimal weight: 0.2980 chunk 90 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4333 r_free = 0.4333 target = 0.191894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.164309 restraints weight = 14698.309| |-----------------------------------------------------------------------------| r_work (start): 0.4032 rms_B_bonded: 1.55 r_work: 0.3575 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11924 Z= 0.212 Angle : 0.819 12.547 16775 Z= 0.368 Chirality : 0.065 0.964 1929 Planarity : 0.005 0.060 1716 Dihedral : 21.834 163.677 3017 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.31 % Allowed : 15.21 % Favored : 83.48 % 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: -0.63 (0.24), residues: 1097 helix: 0.51 (0.24), residues: 495 sheet: -0.98 (0.54), residues: 85 loop : -1.20 (0.25), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1048 TYR 0.016 0.002 TYR A 986 PHE 0.017 0.002 PHE A 384 TRP 0.012 0.001 TRP A 145 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.21 (11919) covalent geometry : angle 0.81814 / 0.37 (16765) SS BOND : bond 0.00319 / 0.19 ( 5) SS BOND : angle 1.37024 / 0.87 ( 10) hydrogen bonds : bond 0.06042 / 4.20 ( 486) hydrogen bonds : angle 4.50314 / 3.33 ( 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 54 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.377 Fit side-chains REVERT: A 676 GLU cc_start: 0.1211 (OUTLIER) cc_final: 0.0605 (mm-30) REVERT: A 976 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7427 (pm20) outliers start: 12 outliers final: 6 residues processed: 51 average time/residue: 0.7441 time to fit residues: 40.6370 Evaluate side-chains 48 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 849 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 974 THR Chi-restraints excluded: chain A residue 976 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 0.0670 chunk 101 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 121 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4370 r_free = 0.4370 target = 0.195462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.168805 restraints weight = 14819.275| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.55 r_work: 0.3620 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2157 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= 0.131 Angle : 0.722 9.725 16775 Z= 0.329 Chirality : 0.058 0.710 1929 Planarity : 0.004 0.057 1716 Dihedral : 21.676 161.880 3017 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.09 % Allowed : 16.30 % Favored : 82.60 % 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: -0.31 (0.25), residues: 1097 helix: 0.81 (0.24), residues: 488 sheet: -0.84 (0.55), residues: 85 loop : -1.06 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1048 TYR 0.010 0.002 TYR A 651 PHE 0.018 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/Z covalent geometry : bond 0.00260 / 0.13 (11919) covalent geometry : angle 0.72183 / 0.33 (16765) SS BOND : bond 0.00287 / 0.18 ( 5) SS BOND : angle 1.38024 / 0.88 ( 10) hydrogen bonds : bond 0.05738 / 4.07 ( 486) hydrogen bonds : angle 4.27743 / 3.17 ( 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 56 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.268 Fit side-chains REVERT: A 461 ASN cc_start: 0.6505 (t0) cc_final: 0.6263 (t0) REVERT: A 496 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8247 (tt) REVERT: A 676 GLU cc_start: 0.0958 (OUTLIER) cc_final: 0.0334 (mm-30) REVERT: A 976 GLU cc_start: 0.7849 (mt-10) cc_final: 0.7449 (pm20) REVERT: A 1068 ARG cc_start: 0.5970 (tpm170) cc_final: 0.4102 (ttm-80) outliers start: 10 outliers final: 4 residues processed: 53 average time/residue: 0.7526 time to fit residues: 42.6888 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 : 0.263 ------------------------------------------------------------------------------- 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 849 THR Chi-restraints excluded: chain A residue 910 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 48 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 108 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 55 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 75 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4348 r_free = 0.4348 target = 0.192399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.177427 restraints weight = 14534.393| |-----------------------------------------------------------------------------| r_work (start): 0.4188 rms_B_bonded: 1.00 r_work: 0.3806 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11924 Z= 0.274 Angle : 0.872 11.674 16775 Z= 0.394 Chirality : 0.067 0.787 1929 Planarity : 0.006 0.052 1716 Dihedral : 21.780 162.449 3017 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.42 % Allowed : 16.19 % Favored : 82.39 % 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: -0.64 (0.24), residues: 1097 helix: 0.46 (0.24), residues: 494 sheet: -0.85 (0.55), residues: 85 loop : -1.19 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1048 TYR 0.020 0.002 TYR A 986 PHE 0.016 0.002 PHE A 282 TRP 0.018 0.002 TRP A 145 HIS 0.005 0.002 HIS A 936 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.27 (11919) covalent geometry : angle 0.87201 / 0.39 (16765) SS BOND : bond 0.00348 / 0.22 ( 5) SS BOND : angle 1.39200 / 0.87 ( 10) hydrogen bonds : bond 0.06337 / 4.37 ( 486) hydrogen bonds : angle 4.57777 / 3.38 ( 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 55 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.351 Fit side-chains REVERT: A 461 ASN cc_start: 0.5979 (t0) cc_final: 0.5745 (t0) REVERT: A 676 GLU cc_start: 0.1814 (OUTLIER) cc_final: 0.0898 (mm-30) REVERT: A 686 TYR cc_start: 0.7097 (t80) cc_final: 0.6715 (t80) REVERT: A 976 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: A 1010 ASP cc_start: 0.8706 (OUTLIER) cc_final: 0.8100 (m-30) outliers start: 13 outliers final: 6 residues processed: 52 average time/residue: 0.7430 time to fit residues: 41.5003 Evaluate side-chains 49 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.304 ------------------------------------------------------------------------------- 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 849 THR 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 1010 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 0.0970 chunk 112 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4387 r_free = 0.4387 target = 0.196305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174989 restraints weight = 14774.331| |-----------------------------------------------------------------------------| r_work (start): 0.4161 rms_B_bonded: 1.29 r_work: 0.3816 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11924 Z= 0.141 Angle : 0.739 11.991 16775 Z= 0.336 Chirality : 0.058 0.605 1929 Planarity : 0.004 0.064 1716 Dihedral : 21.657 161.076 3017 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.20 % Allowed : 16.41 % Favored : 82.39 % 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: 0.79 (0.24), residues: 487 sheet: -0.85 (0.55), residues: 85 loop : -1.05 (0.25), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1048 TYR 0.012 0.002 TYR A 651 PHE 0.019 0.001 PHE A 384 TRP 0.011 0.001 TRP A 161 HIS 0.004 0.001 HIS A 749 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (11919) covalent geometry : angle 0.73892 / 0.34 (16765) SS BOND : bond 0.00287 / 0.17 ( 5) SS BOND : angle 1.38509 / 0.88 ( 10) hydrogen bonds : bond 0.05759 / 4.06 ( 486) hydrogen bonds : angle 4.32321 / 3.20 ( 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 54 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.249 Fit side-chains REVERT: A 461 ASN cc_start: 0.5936 (t0) cc_final: 0.5725 (t0) REVERT: A 676 GLU cc_start: 0.1695 (OUTLIER) cc_final: 0.0718 (mm-30) REVERT: A 686 TYR cc_start: 0.6978 (t80) cc_final: 0.6555 (t80) REVERT: A 976 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7557 (pm20) REVERT: A 1010 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8065 (m-30) REVERT: A 1068 ARG cc_start: 0.6304 (tpm170) cc_final: 0.4445 (ttm-80) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 0.7519 time to fit residues: 41.0044 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 : 0.347 ------------------------------------------------------------------------------- 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 849 THR Chi-restraints excluded: chain A residue 910 ASP Chi-restraints excluded: chain A residue 1010 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 63 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 113 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 94 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4389 r_free = 0.4389 target = 0.196524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.182059 restraints weight = 14677.661| |-----------------------------------------------------------------------------| r_work (start): 0.4238 rms_B_bonded: 0.97 r_work: 0.3872 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11924 Z= 0.144 Angle : 0.716 8.688 16775 Z= 0.327 Chirality : 0.056 0.536 1929 Planarity : 0.004 0.069 1716 Dihedral : 21.583 161.420 3017 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.09 % Allowed : 16.52 % Favored : 82.39 % 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: -0.20 (0.25), residues: 1097 helix: 0.88 (0.24), residues: 488 sheet: -0.74 (0.55), residues: 85 loop : -0.97 (0.25), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1048 TYR 0.011 0.002 TYR A 651 PHE 0.016 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/Z covalent geometry : bond 0.00293 / 0.14 (11919) covalent geometry : angle 0.71560 / 0.33 (16765) SS BOND : bond 0.00289 / 0.17 ( 5) SS BOND : angle 1.40546 / 0.90 ( 10) hydrogen bonds : bond 0.05683 / 4.02 ( 486) hydrogen bonds : angle 4.24127 / 3.13 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2592.84 seconds wall clock time: 45 minutes 8.35 seconds (2708.35 seconds total)