Starting phenix.real_space_refine on Fri Aug 22 20:38:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_18860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_18860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_18860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_18860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r34_18860/08_2025/8r34_18860.map" } 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-2.0-5787/lib/python3.9/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: 2.02, per 1000 atoms: 0.26 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: 0.69 Conformation dependent library (CDL) restraints added in 303.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.25 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: 1.29 Time building geometry restraints manager: 0.90 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 - 17.40: 3923 17.40 - 34.80: 543 34.80 - 52.19: 193 52.19 - 69.59: 78 69.59 - 86.99: 11 Dihedral angle restraints: 4748 sinusoidal: 1966 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 4745 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: 3.640 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: 0.030 Set scattering table: 0.020 Process input model: 8.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 19.662 86.987 2956 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 aren 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 covalent geometry : bond 0.00390 ( 7846) covalent geometry : angle 0.64714 (10574) hydrogen bonds : bond 0.17896 ( 508) hydrogen bonds : angle 7.95764 ( 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 : 0.301 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.5624 time to fit residues: 62.6754 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 : 0.199 ------------------------------------------------------------------------------- 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... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.148245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.122034 restraints weight = 7866.444| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.48 r_work: 0.3342 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0785 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= 0.134 Angle : 0.537 5.584 10574 Z= 0.275 Chirality : 0.039 0.130 1262 Planarity : 0.005 0.041 1226 Dihedral : 16.397 83.710 1377 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.42 % Allowed : 23.16 % 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 aren not related in a simple way. whole: 1.08 (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 0.007 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7846) covalent geometry : angle 0.53699 (10574) hydrogen bonds : bond 0.04283 ( 508) hydrogen bonds : angle 5.00759 ( 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 116 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 89 time to evaluate : 0.193 Fit side-chains REVERT: A 431 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.5959 (tptt) REVERT: B 537 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7004 (ptp-170) REVERT: B 756 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 801 LYS cc_start: 0.6860 (OUTLIER) cc_final: 0.6449 (mttt) REVERT: B 850 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7238 (mpt180) outliers start: 27 outliers final: 10 residues processed: 106 average time/residue: 0.5261 time to fit residues: 59.1593 Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.201 ------------------------------------------------------------------------------- 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 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: 0.1980 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.120357 restraints weight = 7940.336| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.40 r_work: 0.3334 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7846 Z= 0.168 Angle : 0.563 5.476 10574 Z= 0.286 Chirality : 0.041 0.160 1262 Planarity : 0.005 0.042 1226 Dihedral : 16.121 79.073 1368 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 4.43 % Allowed : 21.14 % 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 aren not related in a simple way. whole: 1.30 (0.27), residues: 962 helix: 1.41 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 440 TYR 0.011 0.001 TYR B 841 PHE 0.029 0.002 PHE B 643 TRP 0.010 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 7846) covalent geometry : angle 0.56261 (10574) hydrogen bonds : bond 0.04468 ( 508) hydrogen bonds : angle 4.84304 ( 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 120 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.304 Fit side-chains REVERT: B 537 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6978 (ptp-170) REVERT: B 756 ASN cc_start: 0.7679 (OUTLIER) cc_final: 0.7365 (m-40) REVERT: B 801 LYS cc_start: 0.6780 (OUTLIER) cc_final: 0.6409 (mttt) REVERT: B 850 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7232 (mpt180) REVERT: B 863 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7731 (mp) outliers start: 35 outliers final: 16 residues processed: 104 average time/residue: 0.5293 time to fit residues: 58.5175 Evaluate side-chains 105 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 492 GLU Chi-restraints excluded: chain A residue 575 ASP 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 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 641 LEU 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: 0.8980 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121739 restraints weight = 7772.995| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.45 r_work: 0.3342 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7846 Z= 0.142 Angle : 0.528 5.419 10574 Z= 0.268 Chirality : 0.040 0.132 1262 Planarity : 0.004 0.040 1226 Dihedral : 15.633 79.244 1366 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.56 % Allowed : 21.39 % Favored : 74.05 % 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 aren not related in a simple way. whole: 1.60 (0.27), residues: 962 helix: 1.65 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.69 (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 0.027 0.001 PHE B 643 TRP 0.008 0.001 TRP B 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7846) covalent geometry : angle 0.52757 (10574) hydrogen bonds : bond 0.03994 ( 508) hydrogen bonds : angle 4.62562 ( 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 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.287 Fit side-chains REVERT: A 431 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.5969 (tptt) REVERT: B 537 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6998 (ptp-170) REVERT: B 611 SER cc_start: 0.7929 (OUTLIER) cc_final: 0.7639 (p) REVERT: B 801 LYS cc_start: 0.6847 (OUTLIER) cc_final: 0.6514 (mttt) REVERT: B 850 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7181 (mpt180) outliers start: 36 outliers final: 12 residues processed: 102 average time/residue: 0.5515 time to fit residues: 59.6119 Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 575 ASP Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain A residue 836 ARG 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 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: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.121378 restraints weight = 7799.162| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.42 r_work: 0.3336 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 7846 Z= 0.150 Angle : 0.540 5.406 10574 Z= 0.273 Chirality : 0.040 0.140 1262 Planarity : 0.004 0.039 1226 Dihedral : 15.041 81.769 1358 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.67 % Allowed : 22.78 % 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 aren not related in a simple way. whole: 1.68 (0.27), residues: 962 helix: 1.69 (0.19), residues: 724 sheet: None (None), residues: 0 loop : -0.63 (0.37), residues: 238 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 0.027 0.002 PHE B 643 TRP 0.008 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 7846) covalent geometry : angle 0.53996 (10574) hydrogen bonds : bond 0.04055 ( 508) hydrogen bonds : angle 4.61756 ( 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 113 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 84 time to evaluate : 0.304 Fit side-chains REVERT: A 431 LYS cc_start: 0.6969 (OUTLIER) cc_final: 0.5970 (tptt) REVERT: B 537 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.6835 (ptp-170) REVERT: B 801 LYS cc_start: 0.6764 (OUTLIER) cc_final: 0.6422 (mttt) REVERT: B 850 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7078 (mpt180) outliers start: 29 outliers final: 13 residues processed: 98 average time/residue: 0.4871 time to fit residues: 50.8283 Evaluate side-chains 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 0.0570 chunk 22 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.7102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.147126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.122656 restraints weight = 7762.104| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.36 r_work: 0.3364 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1259 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= 0.127 Angle : 0.513 5.339 10574 Z= 0.259 Chirality : 0.039 0.131 1262 Planarity : 0.004 0.037 1226 Dihedral : 14.474 83.882 1358 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.67 % Allowed : 22.53 % 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 aren not related in a simple way. whole: 1.94 (0.27), residues: 962 helix: 1.90 (0.19), residues: 720 sheet: None (None), residues: 0 loop : -0.53 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 440 TYR 0.008 0.001 TYR A 841 PHE 0.026 0.001 PHE B 643 TRP 0.007 0.001 TRP A 553 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7846) covalent geometry : angle 0.51250 (10574) hydrogen bonds : bond 0.03717 ( 508) hydrogen bonds : angle 4.47694 ( 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 109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 80 time to evaluate : 0.285 Fit side-chains REVERT: A 431 LYS cc_start: 0.6966 (OUTLIER) cc_final: 0.5984 (tptt) REVERT: A 875 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7411 (mmmt) REVERT: B 537 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6924 (ptp-170) REVERT: B 611 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7657 (p) REVERT: B 801 LYS cc_start: 0.6865 (OUTLIER) cc_final: 0.6535 (mttt) REVERT: B 850 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7153 (mpt180) outliers start: 29 outliers final: 14 residues processed: 94 average time/residue: 0.5790 time to fit residues: 57.8635 Evaluate side-chains 100 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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 575 ASP Chi-restraints excluded: chain A residue 610 MET 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 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 58 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 95 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 63 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.146493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.121906 restraints weight = 7793.944| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.37 r_work: 0.3354 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3232 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1308 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= 0.138 Angle : 0.530 5.371 10574 Z= 0.267 Chirality : 0.040 0.135 1262 Planarity : 0.004 0.037 1226 Dihedral : 14.256 86.101 1358 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.42 % Allowed : 22.78 % 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 aren not related in a simple way. whole: 1.91 (0.27), residues: 962 helix: 1.86 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.52 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.008 0.001 TYR A 841 PHE 0.027 0.002 PHE B 643 TRP 0.006 0.001 TRP B 553 HIS 0.003 0.002 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 7846) covalent geometry : angle 0.52978 (10574) hydrogen bonds : bond 0.03850 ( 508) hydrogen bonds : angle 4.50439 ( 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 107 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.210 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6008 (tptt) REVERT: A 875 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7412 (mmmt) REVERT: B 537 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.6938 (ptp-170) REVERT: B 801 LYS cc_start: 0.6861 (OUTLIER) cc_final: 0.6536 (mttt) REVERT: B 850 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7166 (mpt180) REVERT: B 875 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7410 (mmmt) outliers start: 27 outliers final: 19 residues processed: 94 average time/residue: 0.5707 time to fit residues: 56.8401 Evaluate side-chains 104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.175 ------------------------------------------------------------------------------- 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 575 ASP Chi-restraints excluded: chain A residue 610 MET 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 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 610 MET Chi-restraints excluded: chain B residue 641 LEU 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 873 VAL Chi-restraints excluded: chain B residue 875 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 0.0050 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 43 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.147342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121607 restraints weight = 7864.343| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 1.40 r_work: 0.3364 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1357 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= 0.123 Angle : 0.512 5.333 10574 Z= 0.257 Chirality : 0.039 0.130 1262 Planarity : 0.004 0.036 1226 Dihedral : 13.825 88.816 1358 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.42 % Allowed : 22.78 % 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 aren not related in a simple way. whole: 2.04 (0.27), residues: 962 helix: 1.96 (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 0.001 0.000 ARG A 440 TYR 0.008 0.001 TYR A 841 PHE 0.025 0.001 PHE B 643 TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7846) covalent geometry : angle 0.51152 (10574) hydrogen bonds : bond 0.03602 ( 508) hydrogen bonds : angle 4.41687 ( 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 109 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 82 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 431 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.5971 (tptt) REVERT: A 611 SER cc_start: 0.7887 (OUTLIER) cc_final: 0.7618 (p) REVERT: A 875 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7451 (mmmt) REVERT: B 412 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5793 (ttmt) REVERT: B 611 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 850 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.7085 (mpt180) REVERT: B 875 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7434 (mmmt) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 0.6029 time to fit residues: 64.1057 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 : 0.286 ------------------------------------------------------------------------------- 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 575 ASP 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 412 LYS Chi-restraints excluded: chain B residue 492 GLU 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 756 ASN 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 0.0470 chunk 82 optimal weight: 1.9990 chunk 70 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 43 optimal weight: 0.7980 chunk 88 optimal weight: 0.8980 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.149130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123423 restraints weight = 7747.172| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.44 r_work: 0.3367 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1451 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= 0.117 Angle : 0.505 5.307 10574 Z= 0.253 Chirality : 0.039 0.130 1262 Planarity : 0.004 0.036 1226 Dihedral : 13.453 88.156 1354 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.04 % Allowed : 23.67 % 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 aren not related in a simple way. whole: 2.14 (0.27), residues: 962 helix: 2.03 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.45 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 836 TYR 0.007 0.001 TYR A 841 PHE 0.025 0.001 PHE B 643 TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 7846) covalent geometry : angle 0.50504 (10574) hydrogen bonds : bond 0.03488 ( 508) hydrogen bonds : angle 4.37267 ( 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 106 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.296 Fit side-chains REVERT: A 431 LYS cc_start: 0.7038 (OUTLIER) cc_final: 0.6013 (tptt) REVERT: A 611 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7693 (p) REVERT: A 875 LYS cc_start: 0.7799 (OUTLIER) cc_final: 0.7485 (mmmt) REVERT: B 412 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.5915 (ttmt) REVERT: B 611 SER cc_start: 0.8136 (OUTLIER) cc_final: 0.7839 (p) REVERT: B 850 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7069 (mpt180) REVERT: B 875 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7484 (mmmt) outliers start: 24 outliers final: 9 residues processed: 97 average time/residue: 0.6054 time to fit residues: 62.2767 Evaluate side-chains 98 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.243 ------------------------------------------------------------------------------- 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 412 LYS 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: 2.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.121497 restraints weight = 7725.361| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.41 r_work: 0.3331 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1361 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= 0.160 Angle : 0.550 5.431 10574 Z= 0.278 Chirality : 0.041 0.138 1262 Planarity : 0.004 0.038 1226 Dihedral : 13.665 86.313 1354 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.53 % Allowed : 24.18 % 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 aren not related in a simple way. whole: 1.98 (0.27), residues: 962 helix: 1.91 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.39 (0.38), residues: 250 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 covalent geometry : bond 0.00383 ( 7846) covalent geometry : angle 0.54997 (10574) hydrogen bonds : bond 0.04059 ( 508) hydrogen bonds : angle 4.57708 ( 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 99 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.326 Fit side-chains REVERT: A 431 LYS cc_start: 0.7034 (OUTLIER) cc_final: 0.6006 (tptt) REVERT: A 497 MET cc_start: 0.8450 (mtt) cc_final: 0.7817 (mtt) REVERT: A 611 SER cc_start: 0.7838 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 651 THR cc_start: 0.6393 (m) cc_final: 0.6146 (m) REVERT: A 875 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7428 (mmmt) REVERT: B 412 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.5789 (ttmt) REVERT: B 611 SER cc_start: 0.7857 (OUTLIER) cc_final: 0.7567 (p) REVERT: B 850 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7020 (mpt180) REVERT: B 875 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7439 (mmmt) outliers start: 20 outliers final: 8 residues processed: 94 average time/residue: 0.6651 time to fit residues: 66.3137 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 412 LYS 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: 1.9990 chunk 47 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 0.1980 chunk 72 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.122404 restraints weight = 7782.736| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.43 r_work: 0.3351 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1404 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= 0.134 Angle : 0.526 5.373 10574 Z= 0.265 Chirality : 0.040 0.133 1262 Planarity : 0.004 0.037 1226 Dihedral : 13.542 83.984 1354 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.15 % Allowed : 24.56 % 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 aren not related in a simple way. whole: 1.97 (0.27), residues: 962 helix: 1.91 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.52 (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 A 841 PHE 0.027 0.001 PHE B 643 TRP 0.006 0.001 TRP B 639 HIS 0.003 0.001 HIS B 439 Details of bonding type rmsd covalent geometry : bond 0.00311 ( 7846) covalent geometry : angle 0.52642 (10574) hydrogen bonds : bond 0.03731 ( 508) hydrogen bonds : angle 4.47372 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.92 seconds wall clock time: 43 minutes 4.17 seconds (2584.17 seconds total)