Starting phenix.real_space_refine on Thu Jul 2 08:07:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r34_18860/07_2026/8r34_18860.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r34_18860/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8r34_18860/07_2026/8r34_18860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r34_18860/07_2026/8r34_18860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r34_18860/07_2026/8r34_18860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r34_18860/07_2026/8r34_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 197 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PH': 4, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 2 Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 197 Ad-hoc single atom residues: {' NA': 2} Unusual residues: {'3PH': 4, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 3} Chain breaks: 2 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: 1.70, per 1000 atoms: 0.22 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: 0.56 Conformation dependent library (CDL) restraints added in 384.5 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: 0.14 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: 1.04 Time building geometry restraints manager: 0.72 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: 0.03 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: 3.670 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.430 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.600 ------------------------------------------------------------------------------- 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 : 0.225 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 105 average time/residue: 0.4742 time to fit residues: 53.0241 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 : 0.265 ------------------------------------------------------------------------------- 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: 0.5980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.148411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.122199 restraints weight = 7862.655| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.47 r_work: 0.3345 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0787 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 : 0.534 5.532 10574 Z= 0.274 Chirality : 0.039 0.129 1262 Planarity : 0.005 0.040 1226 Dihedral : 13.622 59.596 1305 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.42 % Allowed : 23.29 % 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: 1.07 (0.27), residues: 962 helix: 1.25 (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 0.00293 / 0.13 ( 7846) covalent geometry : angle 0.53401 / 0.27 (10574) hydrogen bonds : bond 0.04292 / 2.75 ( 508) hydrogen bonds : angle 5.02389 / 3.70 ( 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 : 0.201 Fit side-chains REVERT: A 431 LYS cc_start: 0.6923 (OUTLIER) cc_final: 0.5948 (tptt) REVERT: B 537 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.6972 (ptp-170) REVERT: B 756 ASN cc_start: 0.7654 (OUTLIER) cc_final: 0.7449 (m-40) REVERT: B 801 LYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6453 (mttt) REVERT: B 850 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.7222 (mpt180) outliers start: 27 outliers final: 11 residues processed: 106 average time/residue: 0.4773 time to fit residues: 53.7737 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 : 0.210 ------------------------------------------------------------------------------- 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 610 MET 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: 2.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.146495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121638 restraints weight = 7931.956| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.40 r_work: 0.3347 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7846 Z= 0.145 Angle : 0.537 5.405 10574 Z= 0.273 Chirality : 0.040 0.157 1262 Planarity : 0.004 0.041 1226 Dihedral : 13.493 59.545 1296 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 4.18 % Allowed : 21.52 % 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: 1.41 (0.27), residues: 962 helix: 1.50 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.71 (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 0.002 PHE B 643 TRP 0.009 0.001 TRP A 553 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 ( 7846) covalent geometry : angle 0.53721 / 0.27 (10574) hydrogen bonds : bond 0.04178 / 2.68 ( 508) hydrogen bonds : angle 4.76724 / 3.51 ( 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 118 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.285 Fit side-chains REVERT: B 537 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6990 (ptp-170) REVERT: B 756 ASN cc_start: 0.7665 (OUTLIER) cc_final: 0.7363 (m-40) REVERT: B 801 LYS cc_start: 0.6859 (OUTLIER) cc_final: 0.6474 (mttt) REVERT: B 850 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.7168 (mpt180) REVERT: B 863 ILE cc_start: 0.8021 (OUTLIER) cc_final: 0.7773 (mp) outliers start: 33 outliers final: 14 residues processed: 102 average time/residue: 0.4615 time to fit residues: 50.1472 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.404 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 76 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.146457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.121798 restraints weight = 7960.027| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.39 r_work: 0.3398 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 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 0.024 7846 Z= 0.124 Angle : 0.508 5.353 10574 Z= 0.258 Chirality : 0.039 0.127 1262 Planarity : 0.004 0.038 1226 Dihedral : 13.206 59.251 1294 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 4.18 % Allowed : 21.52 % 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: 1.74 (0.27), residues: 962 helix: 1.74 (0.19), residues: 722 sheet: None (None), residues: 0 loop : -0.60 (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 B 518 PHE 0.025 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 0.00279 / 0.12 ( 7846) covalent geometry : angle 0.50805 / 0.26 (10574) hydrogen bonds : bond 0.03759 / 2.41 ( 508) hydrogen bonds : angle 4.54827 / 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 119 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 86 time to evaluate : 0.198 Fit side-chains REVERT: A 431 LYS cc_start: 0.6975 (OUTLIER) cc_final: 0.5989 (tptt) REVERT: A 875 LYS cc_start: 0.7599 (OUTLIER) cc_final: 0.7364 (mmmt) REVERT: B 537 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7040 (ptp-170) REVERT: B 801 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6558 (mttt) REVERT: B 850 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.7243 (mpt180) outliers start: 33 outliers final: 12 residues processed: 103 average time/residue: 0.4919 time to fit residues: 53.7216 Evaluate side-chains 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.178 ------------------------------------------------------------------------------- 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 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 89 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 94 optimal weight: 0.3980 chunk 78 optimal weight: 0.8980 chunk 59 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 = 0.3751 r_free = 0.3751 target = 0.147398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.121986 restraints weight = 7788.558| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.43 r_work: 0.3354 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1163 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= 0.134 Angle : 0.519 5.373 10574 Z= 0.263 Chirality : 0.039 0.132 1262 Planarity : 0.004 0.037 1226 Dihedral : 12.891 59.774 1290 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.80 % Allowed : 21.90 % 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: 1.88 (0.27), residues: 962 helix: 1.83 (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 0.008 0.001 TYR A 841 PHE 0.026 0.001 PHE B 643 TRP 0.007 0.001 TRP B 553 HIS 0.003 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7846) covalent geometry : angle 0.51906 / 0.26 (10574) hydrogen bonds : bond 0.03837 / 2.45 ( 508) hydrogen bonds : angle 4.52697 / 3.33 ( 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 111 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.280 Fit side-chains REVERT: A 431 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.5969 (tptt) REVERT: A 497 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7870 (mtt) REVERT: B 537 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6953 (ptp-170) REVERT: B 611 SER cc_start: 0.7956 (OUTLIER) cc_final: 0.7674 (p) REVERT: B 801 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6472 (mttt) REVERT: B 850 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7144 (mpt180) outliers start: 30 outliers final: 14 residues processed: 98 average time/residue: 0.5426 time to fit residues: 56.4280 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 : 0.202 ------------------------------------------------------------------------------- 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 497 MET 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=3.00 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 82 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.149523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.124227 restraints weight = 7758.885| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.43 r_work: 0.3382 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1301 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= 0.112 Angle : 0.491 5.296 10574 Z= 0.248 Chirality : 0.038 0.127 1262 Planarity : 0.004 0.035 1226 Dihedral : 12.328 59.991 1286 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.29 % Allowed : 22.28 % 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: 2.11 (0.27), residues: 962 helix: 2.01 (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 B 518 PHE 0.023 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 0.00246 / 0.11 ( 7846) covalent geometry : angle 0.49136 / 0.25 (10574) hydrogen bonds : bond 0.03438 / 2.19 ( 508) hydrogen bonds : angle 4.36176 / 3.21 ( 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: 26 poor density : 81 time to evaluate : 0.336 Fit side-chains REVERT: A 431 LYS cc_start: 0.6967 (OUTLIER) cc_final: 0.5972 (tptt) REVERT: A 875 LYS cc_start: 0.7767 (OUTLIER) cc_final: 0.7434 (mmmt) REVERT: B 801 LYS cc_start: 0.6829 (OUTLIER) cc_final: 0.6489 (mttt) outliers start: 26 outliers final: 11 residues processed: 93 average time/residue: 0.5005 time to fit residues: 49.4237 Evaluate side-chains 94 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 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 575 ASP Chi-restraints excluded: chain B residue 610 MET 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 873 VAL 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: 0.5980 chunk 57 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 63 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.147890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.123025 restraints weight = 7814.446| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.43 r_work: 0.3366 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1300 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 : 0.510 5.342 10574 Z= 0.256 Chirality : 0.039 0.137 1262 Planarity : 0.004 0.035 1226 Dihedral : 12.308 59.989 1286 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.66 % Allowed : 22.78 % 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: 2.13 (0.27), residues: 962 helix: 2.02 (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 0.001 0.000 ARG A 440 TYR 0.008 0.001 TYR B 841 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 0.00279 / 0.12 ( 7846) covalent geometry : angle 0.51041 / 0.26 (10574) hydrogen bonds : bond 0.03599 / 2.30 ( 508) hydrogen bonds : angle 4.38954 / 3.23 ( 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 104 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.320 Fit side-chains REVERT: A 431 LYS cc_start: 0.6976 (OUTLIER) cc_final: 0.6018 (tptt) REVERT: A 651 THR cc_start: 0.6557 (m) cc_final: 0.6294 (m) REVERT: B 801 LYS cc_start: 0.6950 (OUTLIER) cc_final: 0.6618 (mttt) outliers start: 21 outliers final: 14 residues processed: 95 average time/residue: 0.4628 time to fit residues: 46.7426 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 : 0.223 ------------------------------------------------------------------------------- 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 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 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 575 ASP Chi-restraints excluded: chain B residue 610 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 Chi-restraints excluded: chain B residue 873 VAL 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: 0.8980 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 34 optimal weight: 3.9990 chunk 43 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 16 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 = 0.3764 r_free = 0.3764 target = 0.148762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.123222 restraints weight = 7803.655| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.42 r_work: 0.3359 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1302 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 : 0.524 5.373 10574 Z= 0.264 Chirality : 0.040 0.131 1262 Planarity : 0.004 0.035 1226 Dihedral : 12.335 59.909 1282 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.06 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: 2.17 (0.27), residues: 962 helix: 2.06 (0.19), residues: 710 sheet: None (None), residues: 0 loop : -0.34 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 836 TYR 0.009 0.001 TYR B 518 PHE 0.026 0.001 PHE B 643 TRP 0.006 0.001 TRP B 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 0.52376 / 0.26 (10574) hydrogen bonds : bond 0.03772 / 2.41 ( 508) hydrogen bonds : angle 4.45369 / 3.28 ( 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 102 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.269 Fit side-chains REVERT: A 431 LYS cc_start: 0.6973 (OUTLIER) cc_final: 0.5967 (tptt) REVERT: A 651 THR cc_start: 0.6319 (m) cc_final: 0.6060 (m) REVERT: B 611 SER cc_start: 0.7972 (OUTLIER) cc_final: 0.7689 (p) REVERT: B 875 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.7446 (mmmt) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 0.4804 time to fit residues: 46.9526 Evaluate side-chains 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 408 LEU 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 740 SER Chi-restraints excluded: chain A residue 836 ARG 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 575 ASP 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 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: 0.7980 chunk 82 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 32 optimal weight: 0.0980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 chunk 43 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3789 r_free = 0.3789 target = 0.151019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125407 restraints weight = 7754.233| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 1.45 r_work: 0.3378 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3258 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1446 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= 0.108 Angle : 0.493 5.295 10574 Z= 0.247 Chirality : 0.038 0.129 1262 Planarity : 0.004 0.034 1226 Dihedral : 12.062 59.914 1282 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.77 % Allowed : 24.43 % 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: 2.24 (0.27), residues: 962 helix: 2.12 (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 0.000 ARG B 836 TYR 0.006 0.001 TYR B 841 PHE 0.022 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/Z covalent geometry : bond 0.00237 / 0.11 ( 7846) covalent geometry : angle 0.49329 / 0.25 (10574) hydrogen bonds : bond 0.03327 / 2.12 ( 508) hydrogen bonds : angle 4.29540 / 3.16 ( 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 95 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.285 Fit side-chains REVERT: A 431 LYS cc_start: 0.6999 (OUTLIER) cc_final: 0.5987 (tptt) REVERT: A 651 THR cc_start: 0.6182 (m) cc_final: 0.5879 (m) REVERT: B 611 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7810 (p) REVERT: B 875 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7472 (mmmt) outliers start: 14 outliers final: 8 residues processed: 90 average time/residue: 0.4603 time to fit residues: 44.1410 Evaluate side-chains 91 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 740 SER Chi-restraints excluded: chain A residue 836 ARG Chi-restraints excluded: chain B residue 408 LEU 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 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: 4.9990 chunk 34 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 6 optimal weight: 0.0670 chunk 74 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 1.5724 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.145715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.119984 restraints weight = 7751.849| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.41 r_work: 0.3320 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 7846 Z= 0.203 Angle : 0.597 5.954 10574 Z= 0.302 Chirality : 0.043 0.148 1262 Planarity : 0.004 0.037 1226 Dihedral : 12.696 59.847 1282 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.90 % Allowed : 24.56 % 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: 1.77 (0.27), residues: 962 helix: 1.74 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.42 (0.38), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 836 TYR 0.010 0.001 TYR B 841 PHE 0.034 0.002 PHE B 643 TRP 0.007 0.001 TRP B 527 HIS 0.004 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.20 ( 7846) covalent geometry : angle 0.59726 / 0.30 (10574) hydrogen bonds : bond 0.04576 / 2.95 ( 508) hydrogen bonds : angle 4.75043 / 3.49 ( 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 92 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.231 Fit side-chains REVERT: A 431 LYS cc_start: 0.7005 (OUTLIER) cc_final: 0.6004 (tptt) REVERT: A 651 THR cc_start: 0.6232 (m) cc_final: 0.5962 (m) REVERT: B 611 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7602 (p) REVERT: B 850 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.6337 (mpt-90) REVERT: B 875 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7426 (mmmt) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.5497 time to fit residues: 50.5131 Evaluate side-chains 86 residues out of total 790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LYS Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 836 ARG 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: 0.9990 chunk 47 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.147989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.122413 restraints weight = 7792.074| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.42 r_work: 0.3346 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1324 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= 0.140 Angle : 0.535 5.398 10574 Z= 0.270 Chirality : 0.040 0.133 1262 Planarity : 0.004 0.036 1226 Dihedral : 12.519 59.627 1282 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.52 % Allowed : 25.32 % Favored : 73.16 % 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: 1.97 (0.27), residues: 962 helix: 1.91 (0.19), residues: 712 sheet: None (None), residues: 0 loop : -0.42 (0.37), residues: 250 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 0.002 HIS B 439 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 ( 7846) covalent geometry : angle 0.53543 / 0.27 (10574) hydrogen bonds : bond 0.03871 / 2.48 ( 508) hydrogen bonds : angle 4.54276 / 3.34 ( 1524) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2129.08 seconds wall clock time: 37 minutes 12.27 seconds (2232.27 seconds total)