Starting phenix.real_space_refine on Thu Aug 6 10:49:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2t_44114/08_2026/9b2t_44114.map" } resolution = 2.99 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= 0.017 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 P 314 5.49 5 S 27 5.16 5 C 8588 2.51 5 N 2815 2.21 5 O 3450 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15194 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 3196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3196 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "J" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 3241 Classifications: {'DNA': 157} Link IDs: {'rna3p': 156} Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 757 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "K" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2636 Classifications: {'peptide': 329} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 316} Time building chain proxies: 3.51, per 1000 atoms: 0.23 Number of scatterers: 15194 At special positions: 0 Unit cell: (82.45, 170.72, 134.83, 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 27 16.00 P 314 15.00 O 3450 8.00 N 2815 7.00 C 8588 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: 1.32 Conformation dependent library (CDL) restraints added in 382.4 milliseconds 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 14 sheets defined 61.6% alpha, 7.2% beta 144 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.683A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.569A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.317A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.627A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.619A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.614A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.810A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.601A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.592A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.458A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.597A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.576A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.510A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.797A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 474 through 479 removed outlier: 3.799A pdb=" N CYS K 478 " --> pdb=" O PRO K 474 " (cutoff:3.500A) Processing helix chain 'K' and resid 481 through 486 removed outlier: 3.557A pdb=" N ARG K 486 " --> pdb=" O GLU K 482 " (cutoff:3.500A) Processing helix chain 'K' and resid 528 through 546 removed outlier: 3.529A pdb=" N ILE K 532 " --> pdb=" O THR K 528 " (cutoff:3.500A) Proline residue: K 534 - end of helix removed outlier: 3.645A pdb=" N SER K 546 " --> pdb=" O LEU K 542 " (cutoff:3.500A) Processing helix chain 'K' and resid 570 through 584 Processing helix chain 'K' and resid 621 through 644 removed outlier: 3.752A pdb=" N ALA K 625 " --> pdb=" O SER K 621 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 712 removed outlier: 4.287A pdb=" N PHE K 711 " --> pdb=" O ASP K 707 " (cutoff:3.500A) Processing helix chain 'K' and resid 716 through 728 removed outlier: 4.125A pdb=" N ASP K 720 " --> pdb=" O ASP K 716 " (cutoff:3.500A) Processing helix chain 'K' and resid 739 through 755 removed outlier: 3.826A pdb=" N LEU K 743 " --> pdb=" O TYR K 739 " (cutoff:3.500A) Processing helix chain 'K' and resid 764 through 781 Processing helix chain 'K' and resid 782 through 784 No H-bonds generated for 'chain 'K' and resid 782 through 784' Processing helix chain 'K' and resid 786 through 794 Processing helix chain 'K' and resid 795 through 798 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.560A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.247A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.820A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.888A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.513A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.381A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.569A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 488 through 492 removed outlier: 5.357A pdb=" N LYS K 489 " --> pdb=" O GLN K 500 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N GLN K 500 " --> pdb=" O LYS K 489 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU K 599 " --> pdb=" O ILE K 515 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU K 604 " --> pdb=" O SER K 561 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SER K 561 " --> pdb=" O GLU K 604 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU K 606 " --> pdb=" O LEU K 559 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N LEU K 559 " --> pdb=" O GLU K 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 610 through 611 removed outlier: 3.849A pdb=" N ILE K 610 " --> pdb=" O LEU K 657 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 664 through 669 Processing sheet with id=AB5, first strand: chain 'K' and resid 693 through 695 506 hydrogen bonds defined for protein. 1491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 376 hydrogen bonds 752 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3684 1.34 - 1.46: 4712 1.46 - 1.58: 7050 1.58 - 1.70: 626 1.70 - 1.82: 44 Bond restraints: 16116 Sorted by residual: bond pdb=" C1' DC I -48 " pdb=" N1 DC I -48 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DT J 67 " pdb=" C2' DT J 67 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 bond pdb=" C3' DT I 62 " pdb=" C2' DT I 62 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.85e+00 bond pdb=" C3' DG J 48 " pdb=" C2' DG J 48 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.18e+00 bond pdb=" C3' DA J 71 " pdb=" C2' DA J 71 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.92e+00 ... (remaining 16111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 23044 3.18 - 6.37: 58 6.37 - 9.55: 6 9.55 - 12.73: 1 12.73 - 15.92: 2 Bond angle restraints: 23111 Sorted by residual: angle pdb=" CA LEU K 629 " pdb=" CB LEU K 629 " pdb=" CG LEU K 629 " ideal model delta sigma weight residual 116.30 132.22 -15.92 3.50e+00 8.16e-02 2.07e+01 angle pdb=" N3 DT J 54 " pdb=" C4 DT J 54 " pdb=" O4 DT J 54 " ideal model delta sigma weight residual 119.90 122.61 -2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.03e+01 angle pdb=" N3 DT I 38 " pdb=" C4 DT I 38 " pdb=" O4 DT I 38 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 ... (remaining 23106 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 7297 35.59 - 71.18: 1567 71.18 - 106.76: 13 106.76 - 142.35: 0 142.35 - 177.94: 4 Dihedral angle restraints: 8881 sinusoidal: 5693 harmonic: 3188 Sorted by residual: dihedral pdb=" CA ARG K 486 " pdb=" C ARG K 486 " pdb=" N CYS K 487 " pdb=" CA CYS K 487 " ideal model delta harmonic sigma weight residual 180.00 -154.55 -25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA VAL K 498 " pdb=" C VAL K 498 " pdb=" N PHE K 499 " pdb=" CA PHE K 499 " ideal model delta harmonic sigma weight residual -180.00 -155.05 -24.95 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" C4' DT I -65 " pdb=" C3' DT I -65 " pdb=" O3' DT I -65 " pdb=" P DC I -64 " ideal model delta sinusoidal sigma weight residual 220.00 42.06 177.94 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8878 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1619 0.035 - 0.070: 674 0.070 - 0.105: 267 0.105 - 0.140: 58 0.140 - 0.175: 3 Chirality restraints: 2621 Sorted by residual: chirality pdb=" C3' DT I -65 " pdb=" C4' DT I -65 " pdb=" O3' DT I -65 " pdb=" C2' DT I -65 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.56 -0.17 2.00e-01 2.50e+01 6.94e-01 chirality pdb=" CA ILE K 513 " pdb=" N ILE K 513 " pdb=" C ILE K 513 " pdb=" CB ILE K 513 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 2618 not shown) Planarity restraints: 1839 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE K 499 " -0.018 2.00e-02 2.50e+03 1.52e-02 4.06e+00 pdb=" CG PHE K 499 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE K 499 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE K 499 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE K 499 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE K 499 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE K 499 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" CG ASP B 24 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.009 2.00e-02 2.50e+03 1.79e-02 3.22e+00 pdb=" C GLU H 110 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.010 2.00e-02 2.50e+03 ... (remaining 1836 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 460 2.68 - 3.24: 12573 3.24 - 3.79: 25907 3.79 - 4.35: 34045 4.35 - 4.90: 49667 Nonbonded interactions: 122652 Sorted by model distance: nonbonded pdb=" O ASN G 73 " pdb=" ND2 ASN G 73 " model vdw 2.131 3.120 nonbonded pdb=" OP2 DG I -58 " pdb=" OG1 THR K 757 " model vdw 2.164 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR G 76 " model vdw 2.183 3.040 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.313 3.120 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.320 3.120 ... (remaining 122647 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' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 118) } ncs_group { reference = (chain 'D' and resid 26 through 121) selection = chain 'H' } 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: 6.380 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.350 Find NCS groups from input model: 0.140 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:10.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 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 : 0.006 0.045 16116 Z= 0.497 Angle : 0.734 15.917 23111 Z= 0.616 Chirality : 0.044 0.175 2621 Planarity : 0.004 0.039 1839 Dihedral : 27.107 177.939 6821 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.24 % Allowed : 30.06 % Favored : 67.70 % 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: 1.58 (0.26), residues: 1080 helix: 2.46 (0.21), residues: 632 sheet: 0.01 (0.66), residues: 52 loop : -1.23 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 30 TYR 0.009 0.001 TYR F 51 PHE 0.033 0.002 PHE K 499 TRP 0.012 0.001 TRP K 652 HIS 0.002 0.001 HIS K 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.50 (16116) covalent geometry : angle 0.73417 / 0.62 (23111) hydrogen bonds : bond 0.12002 / 13.40 ( 882) hydrogen bonds : angle 4.08918 / 5.30 ( 2243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 500 GLN cc_start: 0.8226 (mm110) cc_final: 0.7721 (mm110) outliers start: 21 outliers final: 19 residues processed: 163 average time/residue: 0.7210 time to fit residues: 127.4309 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0060 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 27 GLN K 783 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.129760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.090329 restraints weight = 27625.974| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.92 r_work: 0.3053 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.0615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16116 Z= 0.152 Angle : 0.591 11.080 23111 Z= 0.350 Chirality : 0.042 0.322 2621 Planarity : 0.004 0.038 1839 Dihedral : 29.226 179.599 4659 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.41 % Allowed : 26.97 % Favored : 69.62 % 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: 1.66 (0.26), residues: 1080 helix: 2.57 (0.21), residues: 645 sheet: -0.15 (0.62), residues: 52 loop : -1.41 (0.27), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.007 0.001 TYR F 51 PHE 0.026 0.001 PHE K 499 TRP 0.009 0.001 TRP K 652 HIS 0.005 0.001 HIS K 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.15 (16116) covalent geometry : angle 0.59138 / 0.35 (23111) hydrogen bonds : bond 0.06223 / 6.83 ( 882) hydrogen bonds : angle 3.41973 / 4.51 ( 2243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.8052 (t0) cc_final: 0.7816 (t160) REVERT: K 499 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7503 (t80) outliers start: 32 outliers final: 13 residues processed: 168 average time/residue: 0.6099 time to fit residues: 111.4867 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 612 LEU Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 742 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 4 optimal weight: 10.0000 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.128939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088081 restraints weight = 27744.674| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.82 r_work: 0.3037 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16116 Z= 0.155 Angle : 0.591 12.534 23111 Z= 0.344 Chirality : 0.043 0.321 2621 Planarity : 0.004 0.041 1839 Dihedral : 29.432 179.132 4639 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.62 % Allowed : 26.12 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1080 helix: 2.67 (0.21), residues: 643 sheet: -0.10 (0.60), residues: 52 loop : -1.42 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.009 0.001 TYR F 51 PHE 0.020 0.002 PHE K 499 TRP 0.010 0.001 TRP K 652 HIS 0.006 0.001 HIS K 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.16 (16116) covalent geometry : angle 0.59104 / 0.34 (23111) hydrogen bonds : bond 0.06207 / 6.86 ( 882) hydrogen bonds : angle 3.31211 / 4.40 ( 2243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8464 (OUTLIER) cc_final: 0.8218 (tt0) REVERT: G 73 ASN cc_start: 0.8102 (t0) cc_final: 0.7832 (t160) REVERT: K 499 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.7364 (t80) REVERT: K 513 ILE cc_start: 0.8179 (pp) cc_final: 0.7318 (mp) outliers start: 34 outliers final: 17 residues processed: 159 average time/residue: 0.6090 time to fit residues: 105.3464 Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 135 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 764 THR Chi-restraints excluded: chain K residue 791 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 117 optimal weight: 0.0170 chunk 42 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.129567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.088828 restraints weight = 27779.433| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.77 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.0921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16116 Z= 0.140 Angle : 0.583 11.818 23111 Z= 0.339 Chirality : 0.042 0.321 2621 Planarity : 0.004 0.041 1839 Dihedral : 29.440 179.831 4639 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.20 % Allowed : 26.01 % Favored : 70.79 % 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: 1.85 (0.26), residues: 1080 helix: 2.75 (0.21), residues: 643 sheet: 0.04 (0.60), residues: 52 loop : -1.39 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 779 TYR 0.008 0.001 TYR F 51 PHE 0.019 0.001 PHE K 499 TRP 0.007 0.001 TRP K 652 HIS 0.006 0.001 HIS K 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.14 (16116) covalent geometry : angle 0.58296 / 0.34 (23111) hydrogen bonds : bond 0.05847 / 6.46 ( 882) hydrogen bonds : angle 3.24317 / 4.32 ( 2243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7878 (pm20) REVERT: G 73 ASN cc_start: 0.7993 (t0) cc_final: 0.7761 (t0) REVERT: K 499 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7353 (t80) outliers start: 30 outliers final: 19 residues processed: 159 average time/residue: 0.6449 time to fit residues: 111.3733 Evaluate side-chains 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 764 THR Chi-restraints excluded: chain K residue 788 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 10.0000 chunk 107 optimal weight: 30.0000 chunk 119 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.127458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.087793 restraints weight = 27680.657| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.89 r_work: 0.2984 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16116 Z= 0.183 Angle : 0.613 12.514 23111 Z= 0.351 Chirality : 0.044 0.321 2621 Planarity : 0.004 0.043 1839 Dihedral : 29.545 178.157 4639 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.84 % Allowed : 25.59 % Favored : 70.58 % 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: 1.71 (0.26), residues: 1080 helix: 2.65 (0.21), residues: 642 sheet: -0.05 (0.60), residues: 54 loop : -1.46 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.010 0.001 TYR F 51 PHE 0.017 0.002 PHE K 499 TRP 0.009 0.001 TRP K 652 HIS 0.005 0.001 HIS K 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.18 (16116) covalent geometry : angle 0.61253 / 0.35 (23111) hydrogen bonds : bond 0.06840 / 7.56 ( 882) hydrogen bonds : angle 3.33292 / 4.48 ( 2243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 138 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8434 (ptmt) REVERT: E 59 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7858 (pm20) REVERT: G 73 ASN cc_start: 0.8196 (t0) cc_final: 0.7951 (t0) REVERT: K 499 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7258 (t80) REVERT: K 513 ILE cc_start: 0.8109 (pp) cc_final: 0.7166 (mp) outliers start: 36 outliers final: 24 residues processed: 161 average time/residue: 0.5982 time to fit residues: 104.4154 Evaluate side-chains 164 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 596 ASP Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 686 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 764 THR Chi-restraints excluded: chain K residue 788 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 28 optimal weight: 10.0000 chunk 66 optimal weight: 0.4980 chunk 82 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 133 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.128166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.088465 restraints weight = 27559.575| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.04 r_work: 0.2993 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16116 Z= 0.155 Angle : 0.616 16.648 23111 Z= 0.349 Chirality : 0.043 0.322 2621 Planarity : 0.004 0.044 1839 Dihedral : 29.547 179.442 4639 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.05 % Allowed : 25.37 % Favored : 70.58 % 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: 1.72 (0.26), residues: 1080 helix: 2.65 (0.21), residues: 640 sheet: -0.08 (0.58), residues: 59 loop : -1.43 (0.27), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 30 TYR 0.010 0.001 TYR F 51 PHE 0.016 0.001 PHE K 499 TRP 0.008 0.001 TRP K 652 HIS 0.004 0.001 HIS K 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.16 (16116) covalent geometry : angle 0.61610 / 0.35 (23111) hydrogen bonds : bond 0.06422 / 7.09 ( 882) hydrogen bonds : angle 3.28899 / 4.42 ( 2243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 136 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: G 73 ASN cc_start: 0.8223 (t0) cc_final: 0.7978 (t0) REVERT: K 483 LYS cc_start: 0.0887 (OUTLIER) cc_final: 0.0585 (ptpt) REVERT: K 499 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.7268 (t80) outliers start: 38 outliers final: 21 residues processed: 160 average time/residue: 0.6626 time to fit residues: 114.9105 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 483 LYS Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 596 ASP Chi-restraints excluded: chain K residue 598 GLN Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.0980 chunk 27 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 101 optimal weight: 0.0070 chunk 134 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 98 optimal weight: 0.9990 overall best weight: 0.5800 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.128959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.089985 restraints weight = 27376.136| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.81 r_work: 0.3020 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 16116 Z= 0.143 Angle : 0.601 12.796 23111 Z= 0.343 Chirality : 0.043 0.323 2621 Planarity : 0.004 0.047 1839 Dihedral : 29.532 179.675 4639 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.88 % Allowed : 26.23 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.74 (0.26), residues: 1080 helix: 2.63 (0.21), residues: 644 sheet: 0.18 (0.58), residues: 57 loop : -1.43 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.013 0.001 TYR F 51 PHE 0.030 0.002 PHE K 645 TRP 0.007 0.001 TRP K 652 HIS 0.002 0.001 HIS K 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (16116) covalent geometry : angle 0.60146 / 0.34 (23111) hydrogen bonds : bond 0.05948 / 6.57 ( 882) hydrogen bonds : angle 3.22427 / 4.33 ( 2243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 139 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: G 73 ASN cc_start: 0.8169 (t0) cc_final: 0.7907 (t0) REVERT: K 499 PHE cc_start: 0.7727 (OUTLIER) cc_final: 0.7289 (t80) REVERT: K 513 ILE cc_start: 0.8112 (pp) cc_final: 0.7151 (mp) outliers start: 27 outliers final: 19 residues processed: 155 average time/residue: 0.6654 time to fit residues: 111.4965 Evaluate side-chains 157 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 136 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 596 ASP Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 110 optimal weight: 9.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.128622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088649 restraints weight = 27654.397| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.00 r_work: 0.3022 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16116 Z= 0.151 Angle : 0.604 12.515 23111 Z= 0.343 Chirality : 0.043 0.320 2621 Planarity : 0.004 0.047 1839 Dihedral : 29.553 179.758 4638 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.67 % Allowed : 26.23 % Favored : 71.11 % 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: 1.76 (0.26), residues: 1080 helix: 2.67 (0.21), residues: 644 sheet: 0.18 (0.59), residues: 57 loop : -1.47 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 96 TYR 0.007 0.001 TYR C 50 PHE 0.014 0.001 PHE K 499 TRP 0.010 0.001 TRP K 652 HIS 0.002 0.001 HIS K 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.15 (16116) covalent geometry : angle 0.60360 / 0.34 (23111) hydrogen bonds : bond 0.06025 / 6.67 ( 882) hydrogen bonds : angle 3.21724 / 4.37 ( 2243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7899 (pm20) REVERT: G 73 ASN cc_start: 0.8146 (t0) cc_final: 0.7905 (t0) REVERT: K 499 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7216 (t80) outliers start: 25 outliers final: 18 residues processed: 151 average time/residue: 0.7190 time to fit residues: 117.5607 Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 686 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 0.5980 chunk 27 optimal weight: 9.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 630 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.088009 restraints weight = 27622.000| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.08 r_work: 0.3029 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16116 Z= 0.158 Angle : 0.617 14.439 23111 Z= 0.348 Chirality : 0.043 0.318 2621 Planarity : 0.004 0.045 1839 Dihedral : 29.577 179.795 4636 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.67 % Allowed : 26.44 % Favored : 70.90 % 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: 1.70 (0.26), residues: 1080 helix: 2.64 (0.21), residues: 644 sheet: 0.13 (0.59), residues: 52 loop : -1.52 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.008 0.001 TYR F 51 PHE 0.014 0.002 PHE K 499 TRP 0.011 0.001 TRP K 652 HIS 0.003 0.001 HIS K 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (16116) covalent geometry : angle 0.61734 / 0.35 (23111) hydrogen bonds : bond 0.06143 / 6.80 ( 882) hydrogen bonds : angle 3.24326 / 4.35 ( 2243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: G 73 ASN cc_start: 0.8183 (t0) cc_final: 0.7900 (t160) REVERT: K 499 PHE cc_start: 0.7612 (OUTLIER) cc_final: 0.7195 (t80) REVERT: K 513 ILE cc_start: 0.8113 (pp) cc_final: 0.7196 (mp) outliers start: 25 outliers final: 20 residues processed: 148 average time/residue: 0.6942 time to fit residues: 111.4018 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 612 LEU Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 686 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 764 THR Chi-restraints excluded: chain K residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.1980 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 110 optimal weight: 0.5980 chunk 9 optimal weight: 9.9990 chunk 112 optimal weight: 30.0000 chunk 79 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.128583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.088497 restraints weight = 27714.923| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.02 r_work: 0.3034 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 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 : 0.002 0.036 16116 Z= 0.144 Angle : 0.615 12.634 23111 Z= 0.347 Chirality : 0.043 0.318 2621 Planarity : 0.004 0.046 1839 Dihedral : 29.571 179.788 4636 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.67 % Allowed : 26.44 % Favored : 70.90 % 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: 1.73 (0.26), residues: 1080 helix: 2.66 (0.21), residues: 644 sheet: 0.13 (0.59), residues: 52 loop : -1.50 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.008 0.001 TYR F 51 PHE 0.014 0.001 PHE K 797 TRP 0.010 0.001 TRP K 652 HIS 0.003 0.001 HIS K 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.14 (16116) covalent geometry : angle 0.61476 / 0.35 (23111) hydrogen bonds : bond 0.05978 / 6.61 ( 882) hydrogen bonds : angle 3.22948 / 4.33 ( 2243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2160 Ramachandran restraints generated. 1080 Oldfield, 0 Emsley, 1080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 59 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: G 73 ASN cc_start: 0.8147 (t0) cc_final: 0.7857 (t160) REVERT: K 513 ILE cc_start: 0.8132 (pp) cc_final: 0.7249 (mp) outliers start: 25 outliers final: 21 residues processed: 146 average time/residue: 0.6517 time to fit residues: 103.1452 Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 130 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 605 PHE Chi-restraints excluded: chain K residue 612 LEU Chi-restraints excluded: chain K residue 651 HIS Chi-restraints excluded: chain K residue 656 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 686 ILE Chi-restraints excluded: chain K residue 742 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 764 THR Chi-restraints excluded: chain K residue 791 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.1980 chunk 119 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 20.0000 chunk 95 optimal weight: 0.4980 chunk 21 optimal weight: 9.9990 chunk 55 optimal weight: 0.0670 chunk 114 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.128391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.088396 restraints weight = 27334.255| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.98 r_work: 0.3036 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16116 Z= 0.150 Angle : 0.603 12.522 23111 Z= 0.343 Chirality : 0.043 0.316 2621 Planarity : 0.004 0.046 1839 Dihedral : 29.567 179.887 4636 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.77 % Allowed : 26.33 % Favored : 70.90 % 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: 1.73 (0.26), residues: 1080 helix: 2.68 (0.21), residues: 644 sheet: 0.23 (0.58), residues: 52 loop : -1.53 (0.27), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.008 0.001 TYR F 51 PHE 0.018 0.001 PHE K 797 TRP 0.010 0.001 TRP K 652 HIS 0.005 0.001 HIS K 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (16116) covalent geometry : angle 0.60320 / 0.34 (23111) hydrogen bonds : bond 0.05942 / 6.58 ( 882) hydrogen bonds : angle 3.20400 / 4.30 ( 2243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.12 seconds wall clock time: 92 minutes 45.05 seconds (5565.05 seconds total)