Starting phenix.real_space_refine on Wed Aug 5 00:29:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.map" model { file = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2026/8r34_18860.cif" } resolution = 2.62 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= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 52 5.16 5 Na 4 4.78 5 C 5174 2.51 5 N 1136 2.21 5 O 1386 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7762 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "B" Number of atoms: 3651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3651 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 20, 'TRANS': 464} Chain breaks: 1 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 199 Unusual residues: {' NA': 2, '3PH': 4, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 1.79, per 1000 atoms: 0.23 Number of scatterers: 7762 At special positions: 0 Unit cell: (93.725, 93.725, 74.98, 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 52 16.00 P 10 15.00 Na 4 11.00 O 1386 8.00 N 1136 7.00 C 5174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 388.2 milliseconds 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1792 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 0 sheets defined 80.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.662A pdb=" N PHE A 409 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 410 " --> pdb=" O LYS A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 411 through 430 Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA A 443 " --> pdb=" O HIS A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 473 Proline residue: A 467 - end of helix Processing helix chain 'A' and resid 485 through 498 removed outlier: 3.634A pdb=" N ALA A 496 " --> pdb=" O GLU A 492 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 497 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N TRP A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 518 removed outlier: 3.506A pdb=" N TYR A 518 " --> pdb=" O VAL A 514 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 533 removed outlier: 3.739A pdb=" N TRP A 527 " --> pdb=" O VAL A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 555 removed outlier: 3.751A pdb=" N TRP A 553 " --> pdb=" O PHE A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 567 Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 614 Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 619 through 646 removed outlier: 3.509A pdb=" N VAL A 626 " --> pdb=" O GLN A 622 " (cutoff:3.500A) Proline residue: A 629 - end of helix Processing helix chain 'A' and resid 664 through 683 Processing helix chain 'A' and resid 684 through 686 No H-bonds generated for 'chain 'A' and resid 684 through 686' Processing helix chain 'A' and resid 687 through 692 Processing helix chain 'A' and resid 693 through 698 removed outlier: 3.564A pdb=" N ILE A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 707 removed outlier: 3.903A pdb=" N ILE A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 718 Processing helix chain 'A' and resid 720 through 741 removed outlier: 3.568A pdb=" N VAL A 724 " --> pdb=" O PRO A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 755 removed outlier: 3.804A pdb=" N LYS A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 755 " --> pdb=" O GLN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 775 removed outlier: 3.699A pdb=" N THR A 775 " --> pdb=" O LEU A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 796 Proline residue: A 788 - end of helix Processing helix chain 'A' and resid 801 through 814 Processing helix chain 'A' and resid 824 through 832 removed outlier: 3.545A pdb=" N SER A 832 " --> pdb=" O VAL A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 852 removed outlier: 3.566A pdb=" N VAL A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 874 removed outlier: 3.919A pdb=" N VAL A 862 " --> pdb=" O ALA A 858 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYR A 867 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER A 872 " --> pdb=" O GLY A 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.707A pdb=" N PHE B 409 " --> pdb=" O PRO B 406 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE B 410 " --> pdb=" O LYS B 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 406 through 410' Processing helix chain 'B' and resid 411 through 430 Processing helix chain 'B' and resid 435 through 455 removed outlier: 3.592A pdb=" N ALA B 443 " --> pdb=" O HIS B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 473 Proline residue: B 467 - end of helix Processing helix chain 'B' and resid 485 through 496 removed outlier: 3.651A pdb=" N ALA B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 518 Processing helix chain 'B' and resid 519 through 533 removed outlier: 3.523A pdb=" N SER B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TRP B 527 " --> pdb=" O VAL B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 555 removed outlier: 3.749A pdb=" N TRP B 553 " --> pdb=" O PHE B 549 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 567 Processing helix chain 'B' and resid 567 through 572 Processing helix chain 'B' and resid 578 through 596 Processing helix chain 'B' and resid 603 through 614 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 619 through 646 Proline residue: B 629 - end of helix Processing helix chain 'B' and resid 664 through 683 Processing helix chain 'B' and resid 684 through 686 No H-bonds generated for 'chain 'B' and resid 684 through 686' Processing helix chain 'B' and resid 687 through 692 Processing helix chain 'B' and resid 693 through 698 removed outlier: 3.573A pdb=" N ILE B 697 " --> pdb=" O SER B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 707 removed outlier: 3.901A pdb=" N ILE B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 718 Processing helix chain 'B' and resid 720 through 741 removed outlier: 3.575A pdb=" N VAL B 724 " --> pdb=" O PRO B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 741 through 755 removed outlier: 3.754A pdb=" N LYS B 753 " --> pdb=" O ALA B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.723A pdb=" N THR B 775 " --> pdb=" O LEU B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 796 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 801 through 814 Processing helix chain 'B' and resid 824 through 832 removed outlier: 3.565A pdb=" N SER B 832 " --> pdb=" O VAL B 828 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 852 removed outlier: 3.553A pdb=" N VAL B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 852 through 874 removed outlier: 3.881A pdb=" N VAL B 862 " --> pdb=" O ALA B 858 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N TYR B 867 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 872 " --> pdb=" O GLY B 868 " (cutoff:3.500A) 508 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1168 1.33 - 1.45: 1899 1.45 - 1.57: 4685 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 7846 Sorted by residual: bond pdb=" O3 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.569 1.507 0.062 2.00e-02 2.50e+03 9.46e+00 bond pdb=" O3 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.41e+00 bond pdb=" O4 PO4 B 902 " pdb=" P PO4 B 902 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 8.89e+00 bond pdb=" O4 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.568 1.509 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O2 PO4 A 901 " pdb=" P PO4 A 901 " ideal model delta sigma weight residual 1.567 1.509 0.058 2.00e-02 2.50e+03 8.39e+00 ... (remaining 7841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 9900 1.12 - 2.24: 534 2.24 - 3.36: 86 3.36 - 4.49: 35 4.49 - 5.61: 19 Bond angle restraints: 10574 Sorted by residual: angle pdb=" C PHE A 656 " pdb=" N LYS A 657 " pdb=" CA LYS A 657 " ideal model delta sigma weight residual 121.61 127.22 -5.61 1.39e+00 5.18e-01 1.63e+01 angle pdb=" C ILE A 786 " pdb=" N ILE A 787 " pdb=" CA ILE A 787 " ideal model delta sigma weight residual 120.24 122.76 -2.52 6.30e-01 2.52e+00 1.60e+01 angle pdb=" C ILE B 786 " pdb=" N ILE B 787 " pdb=" CA ILE B 787 " ideal model delta sigma weight residual 120.24 122.54 -2.30 6.30e-01 2.52e+00 1.34e+01 angle pdb=" C ILE A 699 " pdb=" N ILE A 700 " pdb=" CA ILE A 700 " ideal model delta sigma weight residual 120.33 123.20 -2.87 8.00e-01 1.56e+00 1.29e+01 angle pdb=" C ILE B 699 " pdb=" N ILE B 700 " pdb=" CA ILE B 700 " ideal model delta sigma weight residual 120.33 123.07 -2.74 8.00e-01 1.56e+00 1.17e+01 ... (remaining 10569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 3847 16.20 - 32.40: 532 32.40 - 48.60: 201 48.60 - 64.80: 91 64.80 - 81.00: 5 Dihedral angle restraints: 4676 sinusoidal: 1894 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU A 755 " pdb=" C GLU A 755 " pdb=" N ASN A 756 " pdb=" CA ASN A 756 " ideal model delta harmonic sigma weight residual 180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CG ARG A 850 " pdb=" CD ARG A 850 " pdb=" NE ARG A 850 " pdb=" CZ ARG A 850 " ideal model delta sinusoidal sigma weight residual 180.00 -136.60 -43.40 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CA LYS A 735 " pdb=" CB LYS A 735 " pdb=" CG LYS A 735 " pdb=" CD LYS A 735 " ideal model delta sinusoidal sigma weight residual -180.00 -120.22 -59.78 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 4673 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 786 0.033 - 0.066: 357 0.066 - 0.099: 97 0.099 - 0.132: 20 0.132 - 0.164: 2 Chirality restraints: 1262 Sorted by residual: chirality pdb=" CG LEU A 408 " pdb=" CB LEU A 408 " pdb=" CD1 LEU A 408 " pdb=" CD2 LEU A 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" CG LEU B 408 " pdb=" CB LEU B 408 " pdb=" CD1 LEU B 408 " pdb=" CD2 LEU B 408 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.28e-01 chirality pdb=" CA ASN A 756 " pdb=" N ASN A 756 " pdb=" C ASN A 756 " pdb=" CB ASN A 756 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.25e-01 ... (remaining 1259 not shown) Planarity restraints: 1226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 719 " -0.029 5.00e-02 4.00e+02 4.43e-02 3.15e+00 pdb=" N PRO B 720 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 720 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 720 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 643 " 0.013 2.00e-02 2.50e+03 1.29e-02 2.91e+00 pdb=" CG PHE B 643 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE B 643 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 643 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 643 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 643 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 643 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 719 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO A 720 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 720 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 720 " -0.023 5.00e-02 4.00e+02 ... (remaining 1223 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 260 2.71 - 3.26: 7715 3.26 - 3.81: 12757 3.81 - 4.35: 17570 4.35 - 4.90: 28579 Nonbonded interactions: 66881 Sorted by model distance: nonbonded pdb=" O LEU B 860 " pdb=" OG1 THR B 864 " model vdw 2.167 3.040 nonbonded pdb=" O LEU A 860 " pdb=" OG1 THR A 864 " model vdw 2.202 3.040 nonbonded pdb=" O ILE B 601 " pdb=" O HOH B1001 " model vdw 2.223 3.040 nonbonded pdb=" O ILE A 601 " pdb=" O HOH A1001 " model vdw 2.227 3.040 nonbonded pdb=" O MET A 648 " pdb=" OG1 THR A 651 " model vdw 2.244 3.040 ... (remaining 66876 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 378 through 876 or resid 903 or resid 905 through 907)) selection = (chain 'B' and (resid 378 through 876 or resid 903 or resid 905 through 907)) } 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=0.00 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.480 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 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 0.062 7846 Z= 0.190 Angle : 0.647 5.608 10574 Z= 0.392 Chirality : 0.040 0.164 1262 Planarity : 0.005 0.044 1226 Dihedral : 18.597 81.003 2884 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.41 % Allowed : 24.94 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.27), residues: 962 helix: 0.71 (0.20), residues: 712 sheet: None (None), residues: 0 loop : -0.99 (0.35), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 836 TYR 0.013 0.001 TYR B 841 PHE 0.030 0.002 PHE B 643 TRP 0.009 0.001 TRP B 639 HIS 0.004 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.19 ( 7846) covalent geometry : angle 0.64714 / 0.39 (10574) hydrogen bonds : bond 0.17896 / 11.61 ( 508) hydrogen bonds : angle 7.95764 / 5.93 ( 1524) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.248 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.5710 time to fit residues: 63.6100 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 822 SER Chi-restraints excluded: chain A residue 832 SER Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 651 THR Chi-restraints excluded: chain B residue 685 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.0770 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122113 restraints weight = 7865.156| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.47 r_work: 0.3346 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7846 Z= 0.135 Angle : 0.536 5.588 10574 Z= 0.276 Chirality : 0.039 0.129 1262 Planarity : 0.005 0.041 1226 Dihedral : 13.622 59.667 1305 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.54 % Allowed : 23.16 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.27), residues: 962 helix: 1.26 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.81 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.010 0.001 TYR B 841 PHE 0.027 0.001 PHE B 643 TRP 0.008 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7846) covalent geometry : angle 0.53640 / 0.28 (10574) hydrogen bonds : bond 0.04219 / 2.71 ( 508) hydrogen bonds : angle 4.98724 / 3.68 ( 1524) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 89 time to evaluate : 0.273 Fit side-chains REVERT: A 431 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.5970 (tptt) REVERT: B 537 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7023 (ptp-170) REVERT: B 756 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7450 (m-40) REVERT: B 801 LYS cc_start: 0.6889 (OUTLIER) cc_final: 0.6479 (mttt) REVERT: B 850 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7267 (mpt180) outliers start: 28 outliers final: 11 residues processed: 106 average time/residue: 0.5478 time to fit residues: 61.8349 Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 843 SER Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 843 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.0970 chunk 57 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.150695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126239 restraints weight = 7778.205| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.33 r_work: 0.3410 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7846 Z= 0.125 Angle : 0.516 5.364 10574 Z= 0.261 Chirality : 0.039 0.141 1262 Planarity : 0.004 0.040 1226 Dihedral : 13.359 59.868 1296 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.05 % Allowed : 21.65 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.27), residues: 962 helix: 1.62 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.68 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.009 0.001 TYR B 518 PHE 0.026 0.001 PHE B 643 TRP 0.008 0.001 TRP A 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 7846) covalent geometry : angle 0.51556 / 0.26 (10574) hydrogen bonds : bond 0.03904 / 2.50 ( 508) hydrogen bonds : angle 4.66104 / 3.43 ( 1524) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.366 Fit side-chains REVERT: A 431 LYS cc_start: 0.6952 (OUTLIER) cc_final: 0.5974 (tptt) REVERT: B 537 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7015 (ptp-170) REVERT: B 756 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7381 (m-40) REVERT: B 801 LYS cc_start: 0.6820 (OUTLIER) cc_final: 0.6439 (mttt) REVERT: B 850 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.7260 (mpt180) REVERT: B 863 ILE cc_start: 0.8091 (OUTLIER) cc_final: 0.7801 (mp) outliers start: 32 outliers final: 14 residues processed: 104 average time/residue: 0.5785 time to fit residues: 63.8874 Evaluate side-chains 104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 863 ILE Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 25 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.146938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.122138 restraints weight = 7796.301| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.41 r_work: 0.3352 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7846 Z= 0.129 Angle : 0.514 5.375 10574 Z= 0.260 Chirality : 0.039 0.128 1262 Planarity : 0.004 0.038 1226 Dihedral : 13.176 59.843 1294 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.43 % Allowed : 21.01 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.27), residues: 962 helix: 1.79 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.57 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.009 0.001 TYR B 841 PHE 0.026 0.001 PHE B 643 TRP 0.007 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 7846) covalent geometry : angle 0.51437 / 0.26 (10574) hydrogen bonds : bond 0.03830 / 2.46 ( 508) hydrogen bonds : angle 4.54301 / 3.35 ( 1524) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.302 Fit side-chains REVERT: A 431 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6007 (tptt) REVERT: B 537 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6997 (ptp-170) REVERT: B 611 SER cc_start: 0.7982 (OUTLIER) cc_final: 0.7698 (p) REVERT: B 801 LYS cc_start: 0.6821 (OUTLIER) cc_final: 0.6485 (mttt) REVERT: B 850 ARG cc_start: 0.8440 (OUTLIER) cc_final: 0.7209 (mpt180) outliers start: 35 outliers final: 15 residues processed: 104 average time/residue: 0.5773 time to fit residues: 63.8319 Evaluate side-chains 104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 84 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.122339 restraints weight = 7796.802| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.45 r_work: 0.3349 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7846 Z= 0.135 Angle : 0.517 5.376 10574 Z= 0.262 Chirality : 0.039 0.135 1262 Planarity : 0.004 0.037 1226 Dihedral : 12.666 59.988 1286 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.80 % Allowed : 21.52 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.27), residues: 962 helix: 1.87 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 440 TYR 0.009 0.001 TYR B 841 PHE 0.027 0.001 PHE B 643 TRP 0.007 0.001 TRP A 553 HIS 0.003 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 ( 7846) covalent geometry : angle 0.51693 / 0.26 (10574) hydrogen bonds : bond 0.03839 / 2.46 ( 508) hydrogen bonds : angle 4.51089 / 3.32 ( 1524) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.251 Fit side-chains REVERT: A 431 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.5967 (tptt) REVERT: B 537 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6923 (ptp-170) REVERT: B 801 LYS cc_start: 0.6807 (OUTLIER) cc_final: 0.6462 (mttt) REVERT: B 850 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7147 (mpt180) outliers start: 30 outliers final: 14 residues processed: 94 average time/residue: 0.5568 time to fit residues: 55.3778 Evaluate side-chains 97 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 537 ARG Chi-restraints excluded: chain B residue 575 ASP Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 836 ARG Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.3980 chunk 22 optimal weight: 0.0060 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 0.0040 chunk 82 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.150940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125288 restraints weight = 7760.970| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.46 r_work: 0.3389 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7846 Z= 0.106 Angle : 0.482 5.287 10574 Z= 0.243 Chirality : 0.038 0.127 1262 Planarity : 0.004 0.035 1226 Dihedral : 12.175 59.979 1286 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.91 % Allowed : 22.15 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.27), residues: 962 helix: 2.10 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.46 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.007 0.001 TYR A 841 PHE 0.022 0.001 PHE A 643 TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 ( 7846) covalent geometry : angle 0.48214 / 0.24 (10574) hydrogen bonds : bond 0.03300 / 2.11 ( 508) hydrogen bonds : angle 4.28833 / 3.16 ( 1524) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.239 Fit side-chains REVERT: A 431 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.5947 (tptt) REVERT: A 875 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7389 (mmmt) REVERT: B 611 SER cc_start: 0.8008 (OUTLIER) cc_final: 0.7727 (p) REVERT: B 648 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.7169 (ptm) REVERT: B 801 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6407 (mttt) outliers start: 23 outliers final: 8 residues processed: 95 average time/residue: 0.5217 time to fit residues: 52.6450 Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 648 MET Chi-restraints excluded: chain B residue 756 ASN Chi-restraints excluded: chain B residue 801 LYS Chi-restraints excluded: chain B residue 822 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.149380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.123499 restraints weight = 7779.025| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.46 r_work: 0.3363 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7846 Z= 0.127 Angle : 0.512 5.376 10574 Z= 0.258 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.035 1226 Dihedral : 12.207 59.778 1282 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.66 % Allowed : 22.91 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.27), residues: 962 helix: 2.03 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.47 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 440 TYR 0.008 0.001 TYR B 518 PHE 0.025 0.001 PHE B 643 TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7846) covalent geometry : angle 0.51203 / 0.26 (10574) hydrogen bonds : bond 0.03675 / 2.35 ( 508) hydrogen bonds : angle 4.39748 / 3.24 ( 1524) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.389 Fit side-chains REVERT: A 431 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.5980 (tptt) REVERT: A 651 THR cc_start: 0.6458 (m) cc_final: 0.6195 (m) REVERT: A 875 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7374 (mmmt) outliers start: 21 outliers final: 8 residues processed: 91 average time/residue: 0.5420 time to fit residues: 52.4615 Evaluate side-chains 90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 822 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.121793 restraints weight = 7817.282| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.45 r_work: 0.3355 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7846 Z= 0.131 Angle : 0.517 5.378 10574 Z= 0.260 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.038 1226 Dihedral : 12.224 59.560 1282 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.15 % Allowed : 24.05 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.27), residues: 962 helix: 2.00 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 836 TYR 0.008 0.001 TYR B 518 PHE 0.027 0.001 PHE B 643 TRP 0.006 0.001 TRP A 553 HIS 0.003 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 7846) covalent geometry : angle 0.51663 / 0.26 (10574) hydrogen bonds : bond 0.03715 / 2.38 ( 508) hydrogen bonds : angle 4.42010 / 3.25 ( 1524) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.283 Fit side-chains REVERT: A 431 LYS cc_start: 0.7000 (OUTLIER) cc_final: 0.5999 (tptt) REVERT: A 651 THR cc_start: 0.6331 (m) cc_final: 0.6068 (m) REVERT: A 875 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7408 (mmmt) REVERT: B 875 LYS cc_start: 0.7736 (OUTLIER) cc_final: 0.7472 (mmmt) outliers start: 17 outliers final: 11 residues processed: 88 average time/residue: 0.5224 time to fit residues: 48.8633 Evaluate side-chains 93 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.6980 chunk 88 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.148918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123054 restraints weight = 7753.426| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.45 r_work: 0.3353 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7846 Z= 0.131 Angle : 0.517 5.372 10574 Z= 0.261 Chirality : 0.039 0.130 1262 Planarity : 0.004 0.037 1226 Dihedral : 12.201 59.558 1282 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.78 % Allowed : 23.54 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.27), residues: 962 helix: 2.00 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.48 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 836 TYR 0.008 0.001 TYR B 841 PHE 0.027 0.001 PHE B 643 TRP 0.006 0.001 TRP A 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 7846) covalent geometry : angle 0.51721 / 0.26 (10574) hydrogen bonds : bond 0.03709 / 2.37 ( 508) hydrogen bonds : angle 4.42510 / 3.26 ( 1524) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.211 Fit side-chains REVERT: A 431 LYS cc_start: 0.6992 (OUTLIER) cc_final: 0.6009 (tptt) REVERT: A 611 SER cc_start: 0.7961 (OUTLIER) cc_final: 0.7677 (p) REVERT: A 651 THR cc_start: 0.6231 (m) cc_final: 0.5972 (m) REVERT: A 875 LYS cc_start: 0.7761 (OUTLIER) cc_final: 0.7460 (mmmt) REVERT: B 611 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7676 (p) REVERT: B 850 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.5886 (mpt-90) REVERT: B 875 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7466 (mmmt) outliers start: 22 outliers final: 10 residues processed: 95 average time/residue: 0.4617 time to fit residues: 46.7926 Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121797 restraints weight = 7737.377| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.42 r_work: 0.3335 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3214 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7846 Z= 0.151 Angle : 0.542 5.424 10574 Z= 0.273 Chirality : 0.040 0.135 1262 Planarity : 0.004 0.038 1226 Dihedral : 12.425 59.826 1282 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.28 % Allowed : 24.18 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.27), residues: 962 helix: 1.89 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.50 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 836 TYR 0.009 0.001 TYR B 841 PHE 0.029 0.002 PHE B 643 TRP 0.006 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 7846) covalent geometry : angle 0.54186 / 0.27 (10574) hydrogen bonds : bond 0.03991 / 2.56 ( 508) hydrogen bonds : angle 4.53927 / 3.34 ( 1524) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1924 Ramachandran restraints generated. 962 Oldfield, 0 Emsley, 962 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.255 Fit side-chains REVERT: A 431 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.5976 (tptt) REVERT: A 611 SER cc_start: 0.7891 (OUTLIER) cc_final: 0.7609 (p) REVERT: A 651 THR cc_start: 0.6228 (m) cc_final: 0.5946 (m) REVERT: A 875 LYS cc_start: 0.7700 (OUTLIER) cc_final: 0.7389 (mmmt) REVERT: B 611 SER cc_start: 0.7907 (OUTLIER) cc_final: 0.7628 (p) REVERT: B 850 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.5999 (mpt-90) REVERT: B 875 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7441 (mmmt) outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 0.5302 time to fit residues: 50.5944 Evaluate side-chains 90 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 610 MET Chi-restraints excluded: chain A residue 611 SER Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 875 LYS Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 610 MET Chi-restraints excluded: chain B residue 611 SER Chi-restraints excluded: chain B residue 822 SER Chi-restraints excluded: chain B residue 850 ARG Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121840 restraints weight = 7785.173| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.42 r_work: 0.3331 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3210 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7846 Z= 0.154 Angle : 0.546 5.437 10574 Z= 0.275 Chirality : 0.040 0.136 1262 Planarity : 0.004 0.038 1226 Dihedral : 12.501 59.408 1282 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.90 % Allowed : 24.68 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.87 (0.27), residues: 962 helix: 1.84 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.55 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 836 TYR 0.009 0.001 TYR B 841 PHE 0.029 0.002 PHE B 643 TRP 0.006 0.001 TRP B 553 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 ( 7846) covalent geometry : angle 0.54574 / 0.28 (10574) hydrogen bonds : bond 0.04013 / 2.57 ( 508) hydrogen bonds : angle 4.56590 / 3.36 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2468.13 seconds wall clock time: 42 minutes 56.24 seconds (2576.24 seconds total)