Starting phenix.real_space_refine on Fri Sep 11 10:15:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mjo_48318/09_2026/9mjo_48318.map" } resolution = 2.45 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= 0.011 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: 5 Type Number sf(0) Gaussians S 70 5.16 5 Na 4 4.78 5 C 5806 2.51 5 N 1322 2.21 5 O 1436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8638 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 4198 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4190 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 538, 4190 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 4287 Chain: "A" Number of atoms: 4198 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 538, 4190 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 Conformer: "B" Number of residues, atoms: 538, 4190 Classifications: {'peptide': 538} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 26, 'TRANS': 511} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 77 Planarities with less than four sites: {'GLN:plan1': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 43 bond proxies already assigned to first conformer: 4287 Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Unusual residues: {' NA': 2, 'CLR': 4, 'CO3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 118 Unusual residues: {' NA': 2, 'CLR': 4, 'CO3': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.75, per 1000 atoms: 0.43 Number of scatterers: 8638 At special positions: 0 Unit cell: (80.025, 131.175, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 70 16.00 Na 4 11.00 O 1436 8.00 N 1322 7.00 C 5806 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 667 " - pdb=" SG CYS B 715 " distance=2.03 Simple disulfide: pdb=" SG CYS B 669 " - pdb=" SG CYS B 703 " distance=2.03 Simple disulfide: pdb=" SG CYS A 667 " - pdb=" SG CYS A 715 " distance=2.03 Simple disulfide: pdb=" SG CYS A 669 " - pdb=" SG CYS A 703 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 670.8 milliseconds 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 6 sheets defined 73.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 483 through 494 Processing helix chain 'B' and resid 498 through 503 Processing helix chain 'B' and resid 506 through 535 removed outlier: 3.962A pdb=" N SER B 522 " --> pdb=" O CYS B 518 " (cutoff:3.500A) Proline residue: B 523 - end of helix Processing helix chain 'B' and resid 540 through 559 Processing helix chain 'B' and resid 569 through 587 Processing helix chain 'B' and resid 589 through 611 Processing helix chain 'B' and resid 612 through 620 Processing helix chain 'B' and resid 621 through 651 removed outlier: 4.189A pdb=" N SER B 648 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU B 649 " --> pdb=" O PHE B 645 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA B 650 " --> pdb=" O GLU B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 665 removed outlier: 3.506A pdb=" N LEU B 662 " --> pdb=" O LEU B 659 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N THR B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 665 " --> pdb=" O LEU B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 706 Processing helix chain 'B' and resid 724 through 746 Processing helix chain 'B' and resid 747 through 749 No H-bonds generated for 'chain 'B' and resid 747 through 749' Processing helix chain 'B' and resid 753 through 763 Processing helix chain 'B' and resid 763 through 780 Processing helix chain 'B' and resid 811 through 817 removed outlier: 4.071A pdb=" N ILE B 815 " --> pdb=" O TRP B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 840 removed outlier: 4.313A pdb=" N LEU B 823 " --> pdb=" O ILE B 819 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR B 835 " --> pdb=" O ASP B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 841 through 845 Processing helix chain 'B' and resid 851 through 869 Processing helix chain 'B' and resid 877 through 887 Processing helix chain 'B' and resid 911 through 923 Processing helix chain 'B' and resid 926 through 931 Processing helix chain 'B' and resid 934 through 949 removed outlier: 3.626A pdb=" N LEU B 938 " --> pdb=" O PRO B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 961 Processing helix chain 'B' and resid 972 through 978 removed outlier: 3.501A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N HIS B 977 " --> pdb=" O ILE B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 979 through 1003 Processing helix chain 'B' and resid 1011 through 1023 removed outlier: 4.296A pdb=" N ALA B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1024 through 1026 No H-bonds generated for 'chain 'B' and resid 1024 through 1026' Processing helix chain 'B' and resid 1028 through 1036 Processing helix chain 'B' and resid 1040 through 1045 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 506 through 535 removed outlier: 3.961A pdb=" N SER A 522 " --> pdb=" O CYS A 518 " (cutoff:3.500A) Proline residue: A 523 - end of helix Processing helix chain 'A' and resid 540 through 559 Processing helix chain 'A' and resid 569 through 587 Processing helix chain 'A' and resid 589 through 611 Processing helix chain 'A' and resid 612 through 620 Processing helix chain 'A' and resid 621 through 651 removed outlier: 4.190A pdb=" N SER A 648 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLU A 649 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.506A pdb=" N LEU A 662 " --> pdb=" O LEU A 659 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR A 663 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR A 665 " --> pdb=" O LEU A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 706 Processing helix chain 'A' and resid 724 through 746 Processing helix chain 'A' and resid 747 through 749 No H-bonds generated for 'chain 'A' and resid 747 through 749' Processing helix chain 'A' and resid 753 through 763 Processing helix chain 'A' and resid 763 through 780 Processing helix chain 'A' and resid 811 through 817 removed outlier: 4.072A pdb=" N ILE A 815 " --> pdb=" O TRP A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 840 removed outlier: 4.314A pdb=" N LEU A 823 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N THR A 835 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 845 Processing helix chain 'A' and resid 851 through 869 Processing helix chain 'A' and resid 877 through 887 Processing helix chain 'A' and resid 911 through 923 Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 934 through 949 removed outlier: 3.626A pdb=" N LEU A 938 " --> pdb=" O PRO A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 961 Processing helix chain 'A' and resid 972 through 978 removed outlier: 3.501A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 1003 Processing helix chain 'A' and resid 1011 through 1023 removed outlier: 4.296A pdb=" N ALA A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1028 through 1036 Processing helix chain 'A' and resid 1040 through 1045 Processing sheet with id=AA1, first strand: chain 'B' and resid 566 through 567 Processing sheet with id=AA2, first strand: chain 'B' and resid 668 through 670 Processing sheet with id=AA3, first strand: chain 'B' and resid 889 through 891 removed outlier: 6.600A pdb=" N LEU B 890 " --> pdb=" O LEU B 904 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 566 through 567 Processing sheet with id=AA5, first strand: chain 'A' and resid 668 through 670 Processing sheet with id=AA6, first strand: chain 'A' and resid 889 through 891 removed outlier: 6.601A pdb=" N LEU A 890 " --> pdb=" O LEU A 904 " (cutoff:3.500A) 546 hydrogen bonds defined for protein. 1558 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: 2.07 Time building geometry restraints manager: 1.11 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: 1354 1.33 - 1.45: 2290 1.45 - 1.57: 5116 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 8868 Sorted by residual: bond pdb=" N VAL A 572 " pdb=" CA VAL A 572 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.17e-02 7.31e+03 8.80e+00 bond pdb=" N ASN B 840 " pdb=" CA ASN B 840 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.27e+00 bond pdb=" N VAL B 572 " pdb=" CA VAL B 572 " ideal model delta sigma weight residual 1.461 1.495 -0.034 1.17e-02 7.31e+03 8.20e+00 bond pdb=" N VAL A 773 " pdb=" CA VAL A 773 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 8.11e+00 bond pdb=" N ASN A 840 " pdb=" CA ASN A 840 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.10e-02 8.26e+03 7.97e+00 ... (remaining 8863 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 11645 1.40 - 2.80: 364 2.80 - 4.20: 75 4.20 - 5.60: 12 5.60 - 7.01: 2 Bond angle restraints: 12098 Sorted by residual: angle pdb=" C THR B 569 " pdb=" CA THR B 569 " pdb=" CB THR B 569 " ideal model delta sigma weight residual 110.51 117.52 -7.01 1.89e+00 2.80e-01 1.37e+01 angle pdb=" C THR A 569 " pdb=" CA THR A 569 " pdb=" CB THR A 569 " ideal model delta sigma weight residual 110.51 117.51 -7.00 1.89e+00 2.80e-01 1.37e+01 angle pdb=" N LEU B 770 " pdb=" CA LEU B 770 " pdb=" CB LEU B 770 " ideal model delta sigma weight residual 110.01 104.86 5.15 1.45e+00 4.76e-01 1.26e+01 angle pdb=" N LEU A 770 " pdb=" CA LEU A 770 " pdb=" CB LEU A 770 " ideal model delta sigma weight residual 110.01 104.95 5.06 1.45e+00 4.76e-01 1.22e+01 angle pdb=" N GLN A 664 " pdb=" CA GLN A 664 " pdb=" C GLN A 664 " ideal model delta sigma weight residual 111.87 107.16 4.71 1.41e+00 5.03e-01 1.12e+01 ... (remaining 12093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 5099 16.36 - 32.72: 397 32.72 - 49.08: 72 49.08 - 65.44: 16 65.44 - 81.80: 6 Dihedral angle restraints: 5590 sinusoidal: 2456 harmonic: 3134 Sorted by residual: dihedral pdb=" CB CYS B 667 " pdb=" SG CYS B 667 " pdb=" SG CYS B 715 " pdb=" CB CYS B 715 " ideal model delta sinusoidal sigma weight residual 93.00 139.24 -46.24 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CB CYS A 667 " pdb=" SG CYS A 667 " pdb=" SG CYS A 715 " pdb=" CB CYS A 715 " ideal model delta sinusoidal sigma weight residual 93.00 139.21 -46.21 1 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" CA GLN B 832 " pdb=" C GLN B 832 " pdb=" N GLN B 833 " pdb=" CA GLN B 833 " ideal model delta harmonic sigma weight residual -180.00 -163.30 -16.70 0 5.00e+00 4.00e-02 1.12e+01 ... (remaining 5587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1059 0.043 - 0.086: 304 0.086 - 0.130: 77 0.130 - 0.173: 12 0.173 - 0.216: 4 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA LEU B 871 " pdb=" N LEU B 871 " pdb=" C LEU B 871 " pdb=" CB LEU B 871 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LEU A 871 " pdb=" N LEU A 871 " pdb=" C LEU A 871 " pdb=" CB LEU A 871 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA LEU A 770 " pdb=" N LEU A 770 " pdb=" C LEU A 770 " pdb=" CB LEU A 770 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 ... (remaining 1453 not shown) Planarity restraints: 1412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 908 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C GLU A 908 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU A 908 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 909 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 908 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C GLU B 908 " 0.041 2.00e-02 2.50e+03 pdb=" O GLU B 908 " -0.016 2.00e-02 2.50e+03 pdb=" N GLN B 909 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 829 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.26e+00 pdb=" C PHE A 829 " -0.036 2.00e-02 2.50e+03 pdb=" O PHE A 829 " 0.013 2.00e-02 2.50e+03 pdb=" N MET A 830 " 0.012 2.00e-02 2.50e+03 ... (remaining 1409 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 164 2.70 - 3.25: 9026 3.25 - 3.80: 14411 3.80 - 4.35: 19165 4.35 - 4.90: 31296 Nonbonded interactions: 74062 Sorted by model distance: nonbonded pdb=" OE1 GLU B 576 " pdb=" OH TYR B 590 " model vdw 2.155 3.040 nonbonded pdb=" OE1 GLU A 576 " pdb=" OH TYR A 590 " model vdw 2.155 3.040 nonbonded pdb=" OG1 THR A 835 " pdb="NA NA A1206 " model vdw 2.343 2.470 nonbonded pdb=" OG1 THR B 835 " pdb="NA NA B1206 " model vdw 2.343 2.470 nonbonded pdb=" O LEU A 732 " pdb=" OG1 THR A 736 " model vdw 2.344 3.040 ... (remaining 74057 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: 0.02 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'A' } 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=0.30 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: 6.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.280 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:9.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 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 0.037 8872 Z= 0.239 Angle : 0.596 7.006 12106 Z= 0.368 Chirality : 0.044 0.216 1456 Planarity : 0.005 0.032 1412 Dihedral : 12.118 81.801 3550 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % 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: 1.55 (0.26), residues: 1062 helix: 1.31 (0.20), residues: 690 sheet: 0.30 (0.95), residues: 20 loop : 0.75 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 622 TYR 0.006 0.001 TYR A 665 PHE 0.018 0.002 PHE A 986 TRP 0.006 0.001 TRP B1034 HIS 0.001 0.000 HIS B 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.24 ( 8868) covalent geometry : angle 0.59562 / 0.37 (12098) SS BOND : bond 0.00350 / 0.18 ( 4) SS BOND : angle 0.55976 / 0.26 ( 8) hydrogen bonds : bond 0.12174 / 7.84 ( 546) hydrogen bonds : angle 5.53033 / 4.08 ( 1558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.335 Fit side-chains REVERT: A 481 ARG cc_start: 0.7054 (mtm110) cc_final: 0.6783 (mtm110) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.4847 time to fit residues: 66.4947 Evaluate side-chains 99 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 0.0770 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 664 GLN A 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.113918 restraints weight = 16578.534| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.38 r_work: 0.3210 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 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 : 0.004 0.029 8872 Z= 0.156 Angle : 0.512 5.095 12106 Z= 0.267 Chirality : 0.041 0.134 1456 Planarity : 0.005 0.041 1412 Dihedral : 5.310 59.287 1666 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.44 % Allowed : 5.15 % Favored : 94.41 % 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: 1.89 (0.26), residues: 1062 helix: 1.59 (0.19), residues: 698 sheet: -0.08 (0.90), residues: 20 loop : 0.84 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.010 0.001 TYR A 665 PHE 0.019 0.002 PHE A 917 TRP 0.007 0.001 TRP B1034 HIS 0.003 0.001 HIS B 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 8868) covalent geometry : angle 0.51244 / 0.27 (12098) SS BOND : bond 0.00474 / 0.24 ( 4) SS BOND : angle 0.53455 / 0.24 ( 8) hydrogen bonds : bond 0.04328 / 2.95 ( 546) hydrogen bonds : angle 4.22019 / 3.12 ( 1558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 114 time to evaluate : 0.511 Fit side-chains REVERT: B 491 LYS cc_start: 0.7223 (mttm) cc_final: 0.6843 (mttt) REVERT: B 909 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.6025 (pp30) REVERT: A 481 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6265 (mtm110) REVERT: A 491 LYS cc_start: 0.7234 (mttm) cc_final: 0.6859 (mttt) REVERT: A 909 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.6033 (pp30) outliers start: 4 outliers final: 0 residues processed: 116 average time/residue: 0.5416 time to fit residues: 67.3872 Evaluate side-chains 96 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 94 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 37 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.1980 chunk 59 optimal weight: 0.0980 chunk 92 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.140372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.115241 restraints weight = 14919.204| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.27 r_work: 0.3231 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8872 Z= 0.128 Angle : 0.473 5.099 12106 Z= 0.246 Chirality : 0.040 0.135 1456 Planarity : 0.004 0.038 1412 Dihedral : 5.229 57.797 1666 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.77 % Allowed : 7.35 % Favored : 91.89 % 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: 1.99 (0.26), residues: 1062 helix: 1.66 (0.19), residues: 702 sheet: -0.05 (0.91), residues: 20 loop : 0.91 (0.37), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 594 TYR 0.007 0.001 TYR B 665 PHE 0.016 0.002 PHE A 733 TRP 0.005 0.001 TRP A 728 HIS 0.002 0.000 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 8868) covalent geometry : angle 0.47274 / 0.25 (12098) SS BOND : bond 0.00348 / 0.18 ( 4) SS BOND : angle 0.41997 / 0.19 ( 8) hydrogen bonds : bond 0.04000 / 2.73 ( 546) hydrogen bonds : angle 4.14528 / 3.06 ( 1558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 117 time to evaluate : 0.329 Fit side-chains REVERT: B 481 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6901 (mtm110) REVERT: B 491 LYS cc_start: 0.7217 (mttm) cc_final: 0.6891 (mttt) REVERT: B 521 MET cc_start: 0.8094 (tpt) cc_final: 0.7589 (tpt) REVERT: B 831 ASP cc_start: 0.8436 (t0) cc_final: 0.7988 (t0) REVERT: B 909 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.6085 (pp30) REVERT: A 481 ARG cc_start: 0.6738 (mtm110) cc_final: 0.6267 (mtm110) REVERT: A 491 LYS cc_start: 0.7245 (mttm) cc_final: 0.6924 (mttt) REVERT: A 521 MET cc_start: 0.8103 (tpt) cc_final: 0.7599 (tpt) REVERT: A 831 ASP cc_start: 0.8400 (t0) cc_final: 0.8100 (t0) REVERT: A 909 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.6105 (pp30) outliers start: 7 outliers final: 0 residues processed: 121 average time/residue: 0.4886 time to fit residues: 63.9183 Evaluate side-chains 106 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 7 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3654 r_free = 0.3654 target = 0.138323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.113265 restraints weight = 14904.675| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.26 r_work: 0.3205 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 8872 Z= 0.157 Angle : 0.499 5.129 12106 Z= 0.259 Chirality : 0.041 0.136 1456 Planarity : 0.005 0.040 1412 Dihedral : 5.474 58.966 1666 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.99 % Allowed : 7.35 % Favored : 91.67 % 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: 1.87 (0.26), residues: 1062 helix: 1.59 (0.19), residues: 702 sheet: -0.24 (0.82), residues: 20 loop : 0.79 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 502 TYR 0.009 0.001 TYR A 665 PHE 0.019 0.002 PHE A 733 TRP 0.005 0.001 TRP B 728 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 ( 8868) covalent geometry : angle 0.49925 / 0.26 (12098) SS BOND : bond 0.00789 / 0.41 ( 4) SS BOND : angle 0.71909 / 0.34 ( 8) hydrogen bonds : bond 0.04242 / 2.89 ( 546) hydrogen bonds : angle 4.16455 / 3.08 ( 1558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 110 time to evaluate : 0.330 Fit side-chains REVERT: B 481 ARG cc_start: 0.7128 (mtm110) cc_final: 0.6894 (mtm110) REVERT: B 491 LYS cc_start: 0.7211 (mttm) cc_final: 0.6714 (mtmm) REVERT: B 521 MET cc_start: 0.8166 (tpt) cc_final: 0.7589 (tpt) REVERT: B 831 ASP cc_start: 0.8395 (t0) cc_final: 0.7865 (t0) REVERT: B 909 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.6190 (pp30) REVERT: A 481 ARG cc_start: 0.6763 (mtm110) cc_final: 0.6279 (mtm110) REVERT: A 491 LYS cc_start: 0.7219 (mttm) cc_final: 0.6724 (mtmm) REVERT: A 521 MET cc_start: 0.8182 (tpt) cc_final: 0.7569 (tpt) REVERT: A 909 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.6190 (pp30) outliers start: 9 outliers final: 0 residues processed: 114 average time/residue: 0.5420 time to fit residues: 66.1124 Evaluate side-chains 111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 66 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.7238 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.137997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.113049 restraints weight = 14865.958| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.26 r_work: 0.3202 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8872 Z= 0.158 Angle : 0.504 5.124 12106 Z= 0.261 Chirality : 0.041 0.137 1456 Planarity : 0.005 0.041 1412 Dihedral : 5.605 58.683 1666 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.77 % Allowed : 8.99 % Favored : 90.24 % 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: 1.80 (0.26), residues: 1062 helix: 1.56 (0.19), residues: 702 sheet: -0.16 (0.83), residues: 20 loop : 0.70 (0.36), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.009 0.001 TYR B 665 PHE 0.019 0.002 PHE B 917 TRP 0.005 0.001 TRP A 728 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 8868) covalent geometry : angle 0.50345 / 0.26 (12098) SS BOND : bond 0.00713 / 0.37 ( 4) SS BOND : angle 0.97398 / 0.46 ( 8) hydrogen bonds : bond 0.04258 / 2.90 ( 546) hydrogen bonds : angle 4.17004 / 3.08 ( 1558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 108 time to evaluate : 0.335 Fit side-chains REVERT: B 481 ARG cc_start: 0.7163 (mtm110) cc_final: 0.6939 (mtm110) REVERT: B 491 LYS cc_start: 0.7197 (mttm) cc_final: 0.6719 (mtmm) REVERT: B 831 ASP cc_start: 0.8389 (t0) cc_final: 0.7858 (t0) REVERT: B 909 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.6160 (pp30) REVERT: A 481 ARG cc_start: 0.6816 (mtm110) cc_final: 0.6329 (mtm110) REVERT: A 491 LYS cc_start: 0.7197 (mttm) cc_final: 0.6723 (mtmm) REVERT: A 533 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.6044 (mm-30) REVERT: A 831 ASP cc_start: 0.8443 (t0) cc_final: 0.7914 (t0) REVERT: A 909 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.6162 (pp30) outliers start: 7 outliers final: 2 residues processed: 112 average time/residue: 0.5391 time to fit residues: 64.7536 Evaluate side-chains 111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 106 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 65 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.139938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.114996 restraints weight = 14838.444| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.27 r_work: 0.3227 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8872 Z= 0.122 Angle : 0.468 5.068 12106 Z= 0.242 Chirality : 0.039 0.136 1456 Planarity : 0.004 0.039 1412 Dihedral : 5.496 58.662 1666 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.66 % Allowed : 8.99 % Favored : 90.35 % 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 (0.26), residues: 1062 helix: 1.67 (0.19), residues: 704 sheet: -0.05 (0.85), residues: 20 loop : 0.80 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 502 TYR 0.007 0.001 TYR A 665 PHE 0.016 0.002 PHE B 917 TRP 0.004 0.001 TRP A 728 HIS 0.002 0.000 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 8868) covalent geometry : angle 0.46713 / 0.24 (12098) SS BOND : bond 0.00533 / 0.27 ( 4) SS BOND : angle 0.93371 / 0.44 ( 8) hydrogen bonds : bond 0.03878 / 2.64 ( 546) hydrogen bonds : angle 4.07767 / 3.01 ( 1558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.316 Fit side-chains REVERT: B 481 ARG cc_start: 0.7109 (mtm110) cc_final: 0.6898 (mtm110) REVERT: B 487 ILE cc_start: 0.7735 (mm) cc_final: 0.7493 (mt) REVERT: B 491 LYS cc_start: 0.7177 (mttm) cc_final: 0.6636 (mtmt) REVERT: B 533 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.6003 (mm-30) REVERT: B 831 ASP cc_start: 0.8248 (t0) cc_final: 0.7807 (t0) REVERT: B 909 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.6142 (pp30) REVERT: A 481 ARG cc_start: 0.6749 (mtm110) cc_final: 0.6286 (mtm110) REVERT: A 487 ILE cc_start: 0.7701 (mm) cc_final: 0.7457 (mt) REVERT: A 491 LYS cc_start: 0.7182 (mttm) cc_final: 0.6638 (mtmt) REVERT: A 533 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6020 (mm-30) REVERT: A 831 ASP cc_start: 0.8356 (t0) cc_final: 0.7898 (t0) REVERT: A 909 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.6116 (pp30) outliers start: 6 outliers final: 2 residues processed: 129 average time/residue: 0.4934 time to fit residues: 68.5808 Evaluate side-chains 124 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.138027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.114101 restraints weight = 11583.656| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.98 r_work: 0.3223 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8872 Z= 0.155 Angle : 0.508 5.980 12106 Z= 0.260 Chirality : 0.041 0.139 1456 Planarity : 0.005 0.041 1412 Dihedral : 5.681 59.184 1666 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.88 % Allowed : 8.77 % Favored : 90.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.26), residues: 1062 helix: 1.59 (0.19), residues: 706 sheet: -0.21 (0.83), residues: 20 loop : 0.64 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.008 0.001 TYR B 665 PHE 0.019 0.002 PHE B 917 TRP 0.006 0.001 TRP B 728 HIS 0.002 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 ( 8868) covalent geometry : angle 0.50798 / 0.26 (12098) SS BOND : bond 0.00731 / 0.38 ( 4) SS BOND : angle 0.94601 / 0.44 ( 8) hydrogen bonds : bond 0.04212 / 2.87 ( 546) hydrogen bonds : angle 4.12909 / 3.05 ( 1558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.255 Fit side-chains REVERT: B 481 ARG cc_start: 0.7114 (mtm110) cc_final: 0.6892 (mtm110) REVERT: B 487 ILE cc_start: 0.7652 (mm) cc_final: 0.7413 (mt) REVERT: B 491 LYS cc_start: 0.7178 (mttm) cc_final: 0.6718 (mtmm) REVERT: B 533 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5979 (mm-30) REVERT: B 831 ASP cc_start: 0.8257 (t0) cc_final: 0.7813 (t0) REVERT: B 909 GLN cc_start: 0.8688 (OUTLIER) cc_final: 0.6168 (pp30) REVERT: A 481 ARG cc_start: 0.6733 (mtm110) cc_final: 0.6281 (mtm110) REVERT: A 487 ILE cc_start: 0.7635 (mm) cc_final: 0.7390 (mt) REVERT: A 491 LYS cc_start: 0.7185 (mttm) cc_final: 0.6725 (mtmm) REVERT: A 533 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: A 831 ASP cc_start: 0.8337 (t0) cc_final: 0.7796 (t0) REVERT: A 909 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.6241 (pp30) outliers start: 8 outliers final: 2 residues processed: 116 average time/residue: 0.5171 time to fit residues: 64.3711 Evaluate side-chains 122 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 116 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 43 optimal weight: 1.9990 chunk 98 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 100 optimal weight: 0.7980 chunk 34 optimal weight: 0.0970 chunk 89 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 664 GLN A 664 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114643 restraints weight = 12581.136| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.07 r_work: 0.3230 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8872 Z= 0.136 Angle : 0.491 6.386 12106 Z= 0.251 Chirality : 0.040 0.136 1456 Planarity : 0.005 0.040 1412 Dihedral : 5.654 58.925 1666 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.88 % Allowed : 9.10 % Favored : 90.02 % 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: 1.93 (0.26), residues: 1062 helix: 1.68 (0.19), residues: 704 sheet: -0.12 (0.84), residues: 20 loop : 0.71 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.008 0.001 TYR B 665 PHE 0.017 0.002 PHE B 917 TRP 0.005 0.001 TRP A 728 HIS 0.002 0.000 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 8868) covalent geometry : angle 0.49057 / 0.25 (12098) SS BOND : bond 0.00622 / 0.32 ( 4) SS BOND : angle 0.89730 / 0.42 ( 8) hydrogen bonds : bond 0.04003 / 2.72 ( 546) hydrogen bonds : angle 4.07778 / 3.01 ( 1558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.341 Fit side-chains REVERT: B 481 ARG cc_start: 0.7115 (mtm110) cc_final: 0.6894 (mtm110) REVERT: B 487 ILE cc_start: 0.7667 (mm) cc_final: 0.7420 (mt) REVERT: B 491 LYS cc_start: 0.7192 (mttm) cc_final: 0.6663 (mtmt) REVERT: B 533 GLU cc_start: 0.6819 (OUTLIER) cc_final: 0.5996 (mm-30) REVERT: B 831 ASP cc_start: 0.8251 (t0) cc_final: 0.7716 (t0) REVERT: B 909 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.6196 (pp30) REVERT: A 481 ARG cc_start: 0.6724 (mtm110) cc_final: 0.6276 (mtm110) REVERT: A 487 ILE cc_start: 0.7670 (mm) cc_final: 0.7416 (mt) REVERT: A 491 LYS cc_start: 0.7167 (mttm) cc_final: 0.6638 (mtmt) REVERT: A 533 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.6042 (mm-30) REVERT: A 909 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.6184 (pp30) outliers start: 8 outliers final: 4 residues processed: 120 average time/residue: 0.4910 time to fit residues: 63.3319 Evaluate side-chains 126 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 55 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 82 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 64 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 664 GLN A 809 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.141139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115624 restraints weight = 17731.283| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.47 r_work: 0.3227 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8872 Z= 0.110 Angle : 0.462 6.304 12106 Z= 0.236 Chirality : 0.039 0.135 1456 Planarity : 0.004 0.038 1412 Dihedral : 5.493 59.660 1666 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.99 % Allowed : 9.65 % Favored : 89.36 % 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 (0.26), residues: 1062 helix: 1.83 (0.19), residues: 704 sheet: -0.04 (0.84), residues: 20 loop : 0.81 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 502 TYR 0.008 0.001 TYR B 852 PHE 0.015 0.001 PHE B 917 TRP 0.003 0.001 TRP A 728 HIS 0.002 0.000 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8868) covalent geometry : angle 0.46123 / 0.24 (12098) SS BOND : bond 0.00366 / 0.19 ( 4) SS BOND : angle 0.77212 / 0.35 ( 8) hydrogen bonds : bond 0.03635 / 2.48 ( 546) hydrogen bonds : angle 3.99481 / 2.94 ( 1558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 122 time to evaluate : 0.330 Fit side-chains REVERT: B 481 ARG cc_start: 0.7179 (mtm110) cc_final: 0.6969 (mtm110) REVERT: B 487 ILE cc_start: 0.7755 (mm) cc_final: 0.7492 (mt) REVERT: B 491 LYS cc_start: 0.7177 (mttm) cc_final: 0.6624 (mtmt) REVERT: B 533 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6039 (mt-10) REVERT: B 646 GLU cc_start: 0.7014 (mt-10) cc_final: 0.6802 (pt0) REVERT: B 909 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.6129 (pp30) REVERT: A 481 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6347 (mtm110) REVERT: A 487 ILE cc_start: 0.7726 (mm) cc_final: 0.7468 (mt) REVERT: A 491 LYS cc_start: 0.7163 (mttm) cc_final: 0.6621 (mtmt) REVERT: A 533 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6066 (mt-10) REVERT: A 646 GLU cc_start: 0.7008 (mt-10) cc_final: 0.6797 (pt0) REVERT: A 909 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.6106 (pp30) outliers start: 9 outliers final: 4 residues processed: 127 average time/residue: 0.5292 time to fit residues: 72.1219 Evaluate side-chains 118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 110 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 9 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 49 optimal weight: 0.4980 chunk 103 optimal weight: 0.0370 chunk 10 optimal weight: 0.6980 overall best weight: 0.3856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.140781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.115860 restraints weight = 14864.911| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.27 r_work: 0.3238 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3110 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3110 r_free = 0.3110 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8872 Z= 0.115 Angle : 0.474 7.976 12106 Z= 0.241 Chirality : 0.039 0.135 1456 Planarity : 0.004 0.043 1412 Dihedral : 5.500 59.940 1666 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 10.42 % Favored : 88.71 % 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 (0.26), residues: 1062 helix: 1.82 (0.19), residues: 704 sheet: -0.16 (0.84), residues: 20 loop : 0.82 (0.36), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 502 TYR 0.006 0.001 TYR B 517 PHE 0.016 0.001 PHE A 733 TRP 0.005 0.001 TRP A 728 HIS 0.001 0.000 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 8868) covalent geometry : angle 0.47376 / 0.24 (12098) SS BOND : bond 0.00537 / 0.28 ( 4) SS BOND : angle 0.74996 / 0.34 ( 8) hydrogen bonds : bond 0.03718 / 2.53 ( 546) hydrogen bonds : angle 3.97132 / 2.93 ( 1558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2124 Ramachandran restraints generated. 1062 Oldfield, 0 Emsley, 1062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 112 time to evaluate : 0.273 Fit side-chains REVERT: B 481 ARG cc_start: 0.7127 (mtm110) cc_final: 0.6921 (mtm110) REVERT: B 487 ILE cc_start: 0.7758 (mm) cc_final: 0.7507 (mt) REVERT: B 491 LYS cc_start: 0.7173 (mttm) cc_final: 0.6643 (mtmt) REVERT: B 533 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6094 (mt-10) REVERT: B 909 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.6167 (pp30) REVERT: A 481 ARG cc_start: 0.6740 (mtm110) cc_final: 0.6290 (mtm110) REVERT: A 487 ILE cc_start: 0.7745 (mm) cc_final: 0.7502 (mt) REVERT: A 491 LYS cc_start: 0.7184 (mttm) cc_final: 0.6648 (mtmt) REVERT: A 533 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: A 909 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.6252 (pp30) outliers start: 8 outliers final: 4 residues processed: 116 average time/residue: 0.5180 time to fit residues: 64.6910 Evaluate side-chains 116 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 108 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 533 GLU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 806 LEU Chi-restraints excluded: chain B residue 909 GLN Chi-restraints excluded: chain A residue 533 GLU Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 806 LEU Chi-restraints excluded: chain A residue 909 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 809 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.137338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.111531 restraints weight = 19437.121| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.55 r_work: 0.3170 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8872 Z= 0.171 Angle : 0.540 9.087 12106 Z= 0.274 Chirality : 0.042 0.144 1456 Planarity : 0.005 0.042 1412 Dihedral : 5.851 59.686 1666 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.88 % Allowed : 10.64 % Favored : 88.49 % 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: 1.79 (0.26), residues: 1062 helix: 1.59 (0.19), residues: 706 sheet: -0.32 (0.83), residues: 20 loop : 0.62 (0.36), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 502 TYR 0.009 0.001 TYR A 751 PHE 0.020 0.002 PHE A 733 TRP 0.006 0.001 TRP A 728 HIS 0.003 0.001 HIS A 884 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.17 ( 8868) covalent geometry : angle 0.53979 / 0.27 (12098) SS BOND : bond 0.00788 / 0.40 ( 4) SS BOND : angle 0.77473 / 0.36 ( 8) hydrogen bonds : bond 0.04342 / 2.95 ( 546) hydrogen bonds : angle 4.10658 / 3.04 ( 1558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3631.37 seconds wall clock time: 62 minutes 28.93 seconds (3748.93 seconds total)