Starting phenix.real_space_refine on Wed Jun 3 10:56:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.cif Found real_map, /net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.map" model { file = "/net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9obw_70301/06_2026/9obw_70301.cif" } resolution = 3.15 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= 0.001 sd= 0.030 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 4 5.49 5 Mg 1 5.21 5 S 28 5.16 5 C 2513 2.51 5 N 556 2.21 5 O 660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3762 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 853 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 909 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "C" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 856 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 2 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2, 'GLU:plan': 3, 'PHE:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 909 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 4, 'TRANS': 124} Chain breaks: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 155 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 5, 'GLU:plan': 3, 'TYR:plan': 2, 'GLN:plan1': 2, 'ASP:plan': 2, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 84 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' MG': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 52 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 1.13, per 1000 atoms: 0.30 Number of scatterers: 3762 At special positions: 0 Unit cell: (86.456, 71.904, 65.912, 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 28 16.00 P 4 15.00 Mg 1 11.99 O 660 8.00 N 556 7.00 C 2513 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: 0.27 Conformation dependent library (CDL) restraints added in 165.9 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 74.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 559 through 583 removed outlier: 3.603A pdb=" N VAL A 570 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N HIS A 571 " --> pdb=" O GLY A 567 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL A 575 " --> pdb=" O HIS A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 616 removed outlier: 3.617A pdb=" N MET A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 656 removed outlier: 3.774A pdb=" N ILE A 631 " --> pdb=" O PHE A 627 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 632 " --> pdb=" O SER A 628 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N MET A 641 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A 642 " --> pdb=" O GLY A 638 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 644 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 838 removed outlier: 5.636A pdb=" N GLY A 815 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N VAL A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 819 " --> pdb=" O GLY A 815 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 825 " --> pdb=" O ALA A 821 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 826 " --> pdb=" O GLY A 822 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 832 " --> pdb=" O ILE A 828 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE A 833 " --> pdb=" O PHE A 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 577 removed outlier: 3.727A pdb=" N TRP B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE B 575 " --> pdb=" O ALA B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 601 through 614 removed outlier: 3.645A pdb=" N VAL B 613 " --> pdb=" O LEU B 609 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE B 614 " --> pdb=" O TRP B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 651 removed outlier: 3.553A pdb=" N MET B 631 " --> pdb=" O THR B 627 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 648 " --> pdb=" O ALA B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 843 Processing helix chain 'C' and resid 559 through 581 removed outlier: 3.564A pdb=" N VAL C 570 " --> pdb=" O VAL C 566 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS C 571 " --> pdb=" O GLY C 567 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 572 " --> pdb=" O LEU C 568 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA C 574 " --> pdb=" O VAL C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 603 through 616 removed outlier: 3.603A pdb=" N MET C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 626 through 656 removed outlier: 3.754A pdb=" N ILE C 631 " --> pdb=" O PHE C 627 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU C 632 " --> pdb=" O SER C 628 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET C 641 " --> pdb=" O ALA C 637 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 642 " --> pdb=" O GLY C 638 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE C 643 " --> pdb=" O PHE C 639 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 644 " --> pdb=" O ALA C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 838 removed outlier: 3.891A pdb=" N LEU C 819 " --> pdb=" O GLY C 815 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 825 " --> pdb=" O ALA C 821 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA C 826 " --> pdb=" O GLY C 822 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 829 " --> pdb=" O VAL C 825 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE C 832 " --> pdb=" O ILE C 828 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 577 removed outlier: 3.739A pdb=" N TRP D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU D 567 " --> pdb=" O PHE D 563 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 575 " --> pdb=" O ALA D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 601 through 614 removed outlier: 3.739A pdb=" N VAL D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE D 614 " --> pdb=" O TRP D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 625 through 651 removed outlier: 3.543A pdb=" N MET D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 648 " --> pdb=" O ALA D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 819 through 845 removed outlier: 3.532A pdb=" N TYR D 823 " --> pdb=" O ALA D 819 " (cutoff:3.500A) 261 hydrogen bonds defined for protein. 783 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: 0.52 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 547 1.32 - 1.44: 1037 1.44 - 1.56: 2160 1.56 - 1.68: 8 1.68 - 1.80: 56 Bond restraints: 3808 Sorted by residual: bond pdb=" C GLN C 556 " pdb=" O GLN C 556 " ideal model delta sigma weight residual 1.244 1.235 0.008 1.00e-02 1.00e+04 7.10e-01 bond pdb=" CB PRO D 553 " pdb=" CG PRO D 553 " ideal model delta sigma weight residual 1.492 1.451 0.041 5.00e-02 4.00e+02 6.60e-01 bond pdb=" CB PRO B 553 " pdb=" CG PRO B 553 " ideal model delta sigma weight residual 1.492 1.452 0.040 5.00e-02 4.00e+02 6.56e-01 bond pdb=" C GLU B 552 " pdb=" N PRO B 553 " ideal model delta sigma weight residual 1.334 1.346 -0.011 1.51e-02 4.39e+03 5.73e-01 bond pdb=" C GLU D 552 " pdb=" N PRO D 553 " ideal model delta sigma weight residual 1.334 1.346 -0.011 1.51e-02 4.39e+03 5.67e-01 ... (remaining 3803 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.07: 5003 1.07 - 2.15: 124 2.15 - 3.22: 27 3.22 - 4.29: 5 4.29 - 5.36: 4 Bond angle restraints: 5163 Sorted by residual: angle pdb=" C MET C 555 " pdb=" N GLN C 556 " pdb=" CA GLN C 556 " ideal model delta sigma weight residual 120.26 123.72 -3.46 1.34e+00 5.57e-01 6.68e+00 angle pdb=" N GLU B 552 " pdb=" CA GLU B 552 " pdb=" C GLU B 552 " ideal model delta sigma weight residual 109.81 115.17 -5.36 2.21e+00 2.05e-01 5.89e+00 angle pdb=" N GLU D 552 " pdb=" CA GLU D 552 " pdb=" C GLU D 552 " ideal model delta sigma weight residual 109.81 115.00 -5.19 2.21e+00 2.05e-01 5.52e+00 angle pdb=" N ILE D 815 " pdb=" CA ILE D 815 " pdb=" C ILE D 815 " ideal model delta sigma weight residual 112.98 110.11 2.87 1.25e+00 6.40e-01 5.27e+00 angle pdb=" C PHE D 614 " pdb=" N ASN D 615 " pdb=" CA ASN D 615 " ideal model delta sigma weight residual 121.54 125.72 -4.18 1.91e+00 2.74e-01 4.80e+00 ... (remaining 5158 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.58: 2038 15.58 - 31.15: 102 31.15 - 46.73: 38 46.73 - 62.31: 17 62.31 - 77.88: 5 Dihedral angle restraints: 2200 sinusoidal: 768 harmonic: 1432 Sorted by residual: dihedral pdb=" CA SER B 617 " pdb=" C SER B 617 " pdb=" N VAL B 618 " pdb=" CA VAL B 618 " ideal model delta harmonic sigma weight residual -180.00 -164.65 -15.35 0 5.00e+00 4.00e-02 9.42e+00 dihedral pdb=" CA LEU C 819 " pdb=" CB LEU C 819 " pdb=" CG LEU C 819 " pdb=" CD1 LEU C 819 " ideal model delta sinusoidal sigma weight residual 180.00 128.57 51.43 3 1.50e+01 4.44e-03 9.01e+00 dihedral pdb=" N ASN B 615 " pdb=" CA ASN B 615 " pdb=" CB ASN B 615 " pdb=" CG ASN B 615 " ideal model delta sinusoidal sigma weight residual -180.00 -128.60 -51.40 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 2197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 354 0.027 - 0.055: 197 0.055 - 0.082: 56 0.082 - 0.109: 6 0.109 - 0.136: 5 Chirality restraints: 618 Sorted by residual: chirality pdb=" CA PRO D 553 " pdb=" N PRO D 553 " pdb=" C PRO D 553 " pdb=" CB PRO D 553 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.65e-01 chirality pdb=" CA PRO B 553 " pdb=" N PRO B 553 " pdb=" C PRO B 553 " pdb=" CB PRO B 553 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA PRO A 557 " pdb=" N PRO A 557 " pdb=" C PRO A 557 " pdb=" CB PRO A 557 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 615 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 552 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 553 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 553 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 553 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 552 " 0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO D 553 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO D 553 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 553 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 556 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 557 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 557 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 557 " 0.018 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 1324 2.87 - 3.38: 3453 3.38 - 3.89: 5364 3.89 - 4.39: 6584 4.39 - 4.90: 11230 Nonbonded interactions: 27955 Sorted by model distance: nonbonded pdb=" O PRO A 624 " pdb=" NH1 ARG A 630 " model vdw 2.367 3.120 nonbonded pdb=" NZ LYS B 629 " pdb=" O13 POV B 902 " model vdw 2.380 3.120 nonbonded pdb=" O21 POV C 901 " pdb=" O31 POV C 901 " model vdw 2.397 2.432 nonbonded pdb=" ND2 ASN B 615 " pdb=" O HOH B1001 " model vdw 2.453 3.120 nonbonded pdb=" OG1 THR C 809 " pdb=" N PHE C 810 " model vdw 2.498 3.120 ... (remaining 27950 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 552 through 580 or (resid 581 through 583 and (name N or n \ ame CA or name C or name O or name CB )) or resid 584 through 901)) selection = (chain 'C' and (resid 552 through 582 or (resid 583 and (name N or name CA or na \ me C or name O or name CB )) or resid 584 through 901)) } ncs_group { reference = (chain 'B' and resid 546 through 845) selection = (chain 'D' and resid 546 through 845) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.350 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.890 Find NCS groups from input model: 0.080 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 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 0.041 3808 Z= 0.163 Angle : 0.465 5.363 5163 Z= 0.255 Chirality : 0.035 0.136 618 Planarity : 0.004 0.045 604 Dihedral : 13.146 77.884 1264 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.31 % Favored : 97.48 % Rotamer: Outliers : 0.62 % Allowed : 3.40 % Favored : 95.99 % 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: -1.96 (0.33), residues: 476 helix: -1.15 (0.24), residues: 356 sheet: None (None), residues: 0 loop : -1.17 (0.50), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.003 0.001 TYR B 646 PHE 0.009 0.001 PHE B 642 TRP 0.011 0.001 TRP D 607 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.16 ( 3808) covalent geometry : angle 0.46516 / 0.25 ( 5163) hydrogen bonds : bond 0.30923 / 20.23 ( 261) hydrogen bonds : angle 7.18417 / 5.11 ( 783) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.142 Fit side-chains REVERT: A 634 MET cc_start: 0.8752 (mtm) cc_final: 0.8517 (mtt) REVERT: C 604 SER cc_start: 0.8476 (p) cc_final: 0.8213 (t) outliers start: 2 outliers final: 2 residues processed: 68 average time/residue: 0.0381 time to fit residues: 3.7740 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 61 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 ASN B 616 ASN C 812 ASN D 615 ASN D 616 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.152179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.116722 restraints weight = 4086.714| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.64 r_work: 0.2944 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3808 Z= 0.147 Angle : 0.496 8.839 5163 Z= 0.263 Chirality : 0.036 0.127 618 Planarity : 0.005 0.045 604 Dihedral : 13.969 79.836 672 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.47 % Favored : 98.32 % Rotamer: Outliers : 2.16 % Allowed : 8.64 % Favored : 89.20 % 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: 0.09 (0.37), residues: 476 helix: 0.45 (0.26), residues: 370 sheet: None (None), residues: 0 loop : -1.00 (0.56), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.003 0.001 TYR C 578 PHE 0.013 0.001 PHE A 639 TRP 0.010 0.001 TRP A 563 HIS 0.002 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 3808) covalent geometry : angle 0.49582 / 0.26 ( 5163) hydrogen bonds : bond 0.06520 / 4.34 ( 261) hydrogen bonds : angle 3.69826 / 2.67 ( 783) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.089 Fit side-chains REVERT: D 606 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8370 (mp) outliers start: 7 outliers final: 4 residues processed: 58 average time/residue: 0.0390 time to fit residues: 3.3168 Evaluate side-chains 56 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain D residue 574 VAL Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 821 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.151541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.112906 restraints weight = 3976.231| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.74 r_work: 0.2906 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3808 Z= 0.145 Angle : 0.474 7.250 5163 Z= 0.247 Chirality : 0.036 0.130 618 Planarity : 0.004 0.046 604 Dihedral : 13.712 76.349 672 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.10 % Favored : 97.69 % Rotamer: Outliers : 2.78 % Allowed : 9.26 % Favored : 87.96 % 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: 0.79 (0.37), residues: 476 helix: 1.04 (0.26), residues: 368 sheet: None (None), residues: 0 loop : -1.10 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.004 0.001 TYR C 578 PHE 0.014 0.001 PHE A 639 TRP 0.010 0.001 TRP C 563 HIS 0.001 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 ( 3808) covalent geometry : angle 0.47438 / 0.25 ( 5163) hydrogen bonds : bond 0.05889 / 3.90 ( 261) hydrogen bonds : angle 3.40180 / 2.44 ( 783) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.116 Fit side-chains REVERT: D 606 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8331 (mp) outliers start: 9 outliers final: 6 residues processed: 59 average time/residue: 0.0396 time to fit residues: 3.4202 Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 818 MET Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 1.9990 chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 37 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.150368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.111466 restraints weight = 4001.994| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 1.75 r_work: 0.2884 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3808 Z= 0.166 Angle : 0.492 7.239 5163 Z= 0.257 Chirality : 0.037 0.135 618 Planarity : 0.004 0.046 604 Dihedral : 13.816 75.022 672 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.31 % Favored : 97.48 % Rotamer: Outliers : 3.09 % Allowed : 9.88 % Favored : 87.04 % 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: 0.87 (0.37), residues: 476 helix: 1.13 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.23 (0.51), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR C 578 PHE 0.014 0.001 PHE A 639 TRP 0.010 0.001 TRP B 607 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.17 ( 3808) covalent geometry : angle 0.49217 / 0.26 ( 5163) hydrogen bonds : bond 0.05960 / 3.95 ( 261) hydrogen bonds : angle 3.38400 / 2.43 ( 783) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.119 Fit side-chains REVERT: D 606 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8304 (mp) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.0339 time to fit residues: 3.0690 Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3640 r_free = 0.3640 target = 0.152294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.113634 restraints weight = 3965.742| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.74 r_work: 0.2911 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3808 Z= 0.128 Angle : 0.448 7.480 5163 Z= 0.232 Chirality : 0.035 0.125 618 Planarity : 0.004 0.046 604 Dihedral : 13.560 75.412 672 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.47 % Favored : 98.32 % Rotamer: Outliers : 3.40 % Allowed : 10.49 % Favored : 86.11 % 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: 1.17 (0.37), residues: 476 helix: 1.36 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.17 (0.50), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.004 0.001 TYR A 578 PHE 0.014 0.001 PHE A 639 TRP 0.009 0.001 TRP A 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 3808) covalent geometry : angle 0.44813 / 0.23 ( 5163) hydrogen bonds : bond 0.05118 / 3.39 ( 261) hydrogen bonds : angle 3.18205 / 2.29 ( 783) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.110 Fit side-chains REVERT: D 570 SER cc_start: 0.8267 (m) cc_final: 0.8052 (m) REVERT: D 606 ILE cc_start: 0.8569 (OUTLIER) cc_final: 0.8291 (mp) outliers start: 11 outliers final: 8 residues processed: 61 average time/residue: 0.0314 time to fit residues: 2.8201 Evaluate side-chains 62 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 45 optimal weight: 0.4980 chunk 29 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.154476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.114315 restraints weight = 4041.417| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 1.84 r_work: 0.2924 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3808 Z= 0.108 Angle : 0.434 9.923 5163 Z= 0.220 Chirality : 0.034 0.122 618 Planarity : 0.004 0.045 604 Dihedral : 13.143 77.545 672 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.26 % Favored : 98.53 % Rotamer: Outliers : 3.70 % Allowed : 10.49 % Favored : 85.80 % 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: 1.46 (0.38), residues: 476 helix: 1.57 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.08 (0.51), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.003 0.001 TYR A 578 PHE 0.014 0.001 PHE A 639 TRP 0.008 0.001 TRP C 563 HIS 0.001 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 3808) covalent geometry : angle 0.43389 / 0.22 ( 5163) hydrogen bonds : bond 0.04413 / 2.92 ( 261) hydrogen bonds : angle 2.97803 / 2.16 ( 783) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.137 Fit side-chains REVERT: D 570 SER cc_start: 0.8256 (m) cc_final: 0.8031 (m) REVERT: D 606 ILE cc_start: 0.8592 (OUTLIER) cc_final: 0.8306 (mp) outliers start: 12 outliers final: 9 residues processed: 58 average time/residue: 0.0405 time to fit residues: 3.4386 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 627 THR Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 12 optimal weight: 0.0670 chunk 17 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 overall best weight: 0.2716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.158146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.119293 restraints weight = 4038.935| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.77 r_work: 0.2991 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3808 Z= 0.088 Angle : 0.402 8.917 5163 Z= 0.204 Chirality : 0.033 0.115 618 Planarity : 0.004 0.044 604 Dihedral : 12.707 79.796 672 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 3.09 % Allowed : 10.80 % Favored : 86.11 % 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: 2.00 (0.39), residues: 476 helix: 1.83 (0.27), residues: 376 sheet: None (None), residues: 0 loop : -0.58 (0.60), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 630 TYR 0.002 0.000 TYR A 578 PHE 0.020 0.001 PHE C 654 TRP 0.007 0.001 TRP C 563 HIS 0.001 0.000 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00174 / 0.09 ( 3808) covalent geometry : angle 0.40169 / 0.20 ( 5163) hydrogen bonds : bond 0.03593 / 2.37 ( 261) hydrogen bonds : angle 2.75176 / 2.01 ( 783) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.141 Fit side-chains REVERT: D 570 SER cc_start: 0.8275 (m) cc_final: 0.8049 (m) REVERT: D 606 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8336 (mp) outliers start: 10 outliers final: 8 residues processed: 60 average time/residue: 0.0355 time to fit residues: 3.1597 Evaluate side-chains 63 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 627 THR Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 35 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.149709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.110318 restraints weight = 4080.258| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.78 r_work: 0.2863 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 3808 Z= 0.197 Angle : 0.531 8.368 5163 Z= 0.276 Chirality : 0.038 0.142 618 Planarity : 0.004 0.046 604 Dihedral : 13.820 79.213 672 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 2.78 % Allowed : 11.73 % Favored : 85.49 % 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: 1.25 (0.37), residues: 476 helix: 1.45 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.27 (0.50), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 630 TYR 0.005 0.001 TYR C 578 PHE 0.016 0.002 PHE C 654 TRP 0.011 0.002 TRP A 563 HIS 0.003 0.001 HIS C 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 ( 3808) covalent geometry : angle 0.53065 / 0.28 ( 5163) hydrogen bonds : bond 0.06171 / 4.09 ( 261) hydrogen bonds : angle 3.28242 / 2.34 ( 783) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.140 Fit side-chains REVERT: D 606 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8371 (mp) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.0371 time to fit residues: 3.2566 Evaluate side-chains 65 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 39 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.152831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.113544 restraints weight = 4048.376| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.78 r_work: 0.2910 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3808 Z= 0.120 Angle : 0.441 8.387 5163 Z= 0.228 Chirality : 0.035 0.125 618 Planarity : 0.004 0.044 604 Dihedral : 13.275 80.417 672 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.78 % Allowed : 11.73 % Favored : 85.49 % 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: 1.48 (0.38), residues: 476 helix: 1.61 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.18 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.003 0.001 TYR C 578 PHE 0.016 0.001 PHE C 654 TRP 0.009 0.001 TRP C 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 ( 3808) covalent geometry : angle 0.44068 / 0.23 ( 5163) hydrogen bonds : bond 0.04729 / 3.13 ( 261) hydrogen bonds : angle 3.04425 / 2.19 ( 783) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.126 Fit side-chains REVERT: D 570 SER cc_start: 0.8296 (m) cc_final: 0.8070 (m) REVERT: D 606 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8341 (mp) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0391 time to fit residues: 3.1791 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.153731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.112789 restraints weight = 4090.889| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.90 r_work: 0.2903 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 3808 Z= 0.114 Angle : 0.434 8.367 5163 Z= 0.225 Chirality : 0.035 0.124 618 Planarity : 0.004 0.045 604 Dihedral : 13.131 80.845 672 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.78 % Allowed : 11.42 % Favored : 85.80 % 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: 1.59 (0.38), residues: 476 helix: 1.69 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.13 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 630 TYR 0.003 0.001 TYR A 578 PHE 0.016 0.001 PHE C 654 TRP 0.009 0.001 TRP C 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 3808) covalent geometry : angle 0.43439 / 0.22 ( 5163) hydrogen bonds : bond 0.04574 / 3.03 ( 261) hydrogen bonds : angle 3.00033 / 2.16 ( 783) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.097 Fit side-chains REVERT: D 570 SER cc_start: 0.8247 (m) cc_final: 0.8025 (m) REVERT: D 606 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8271 (mp) outliers start: 9 outliers final: 8 residues processed: 56 average time/residue: 0.0310 time to fit residues: 2.5739 Evaluate side-chains 61 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 SER Chi-restraints excluded: chain B residue 570 SER Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 824 MET Chi-restraints excluded: chain D residue 606 ILE Chi-restraints excluded: chain D residue 615 ASN Chi-restraints excluded: chain D residue 815 ILE Chi-restraints excluded: chain D residue 821 VAL Chi-restraints excluded: chain D residue 824 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 41 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 11 optimal weight: 20.0000 chunk 12 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 615 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.152930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.114128 restraints weight = 3998.064| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.76 r_work: 0.2910 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3808 Z= 0.132 Angle : 0.450 8.211 5163 Z= 0.233 Chirality : 0.035 0.129 618 Planarity : 0.004 0.044 604 Dihedral : 13.211 80.960 672 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.78 % Allowed : 11.42 % Favored : 85.80 % 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: 1.52 (0.37), residues: 476 helix: 1.64 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -1.20 (0.52), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 630 TYR 0.004 0.001 TYR C 578 PHE 0.015 0.001 PHE C 654 TRP 0.009 0.001 TRP C 563 HIS 0.002 0.001 HIS A 571 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 3808) covalent geometry : angle 0.44986 / 0.23 ( 5163) hydrogen bonds : bond 0.04888 / 3.23 ( 261) hydrogen bonds : angle 3.04791 / 2.19 ( 783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1081.53 seconds wall clock time: 19 minutes 48.29 seconds (1188.29 seconds total)