Starting phenix.real_space_refine on Fri Jul 3 15:48:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2t_44114/07_2026/9b2t_44114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2t_44114/07_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_44114/07_2026/9b2t_44114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2t_44114/07_2026/9b2t_44114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2t_44114/07_2026/9b2t_44114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2t_44114/07_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-dev-6108/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: 2.49, per 1000 atoms: 0.16 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: 1.10 Conformation dependent library (CDL) restraints added in 327.9 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: 1.62 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: 3.00 Time building geometry restraints manager: 1.48 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: 23045 3.18 - 6.37: 57 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: 3.900 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 13.510 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:5.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.630 ------------------------------------------------------------------------------- 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 : 0.728 15.917 23111 Z= 0.611 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 0.72829 / 0.61 (23111) hydrogen bonds : bond 0.12002 / 13.33 ( 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 : 0.338 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: 0.6192 time to fit residues: 109.2609 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 : 0.306 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.129779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.090193 restraints weight = 27648.329| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.94 r_work: 0.3057 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16116 Z= 0.149 Angle : 0.583 10.910 23111 Z= 0.347 Chirality : 0.042 0.312 2621 Planarity : 0.004 0.039 1839 Dihedral : 29.275 179.923 4659 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.41 % Allowed : 26.33 % 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: 1.69 (0.26), residues: 1080 helix: 2.60 (0.21), residues: 643 sheet: -0.13 (0.61), residues: 52 loop : -1.38 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 648 TYR 0.007 0.001 TYR F 51 PHE 0.028 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 0.00242 / 0.15 (16116) covalent geometry : angle 0.58302 / 0.35 (23111) hydrogen bonds : bond 0.06080 / 6.65 ( 882) hydrogen bonds : angle 3.39999 / 4.49 ( 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 : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.8001 (t0) cc_final: 0.7742 (t160) REVERT: K 499 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7494 (t80) outliers start: 32 outliers final: 13 residues processed: 169 average time/residue: 0.5935 time to fit residues: 108.9382 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 : 0.273 ------------------------------------------------------------------------------- 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: 0.6980 chunk 46 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 118 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.127263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.086696 restraints weight = 27574.141| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.04 r_work: 0.2976 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0907 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= 0.184 Angle : 0.612 12.454 23111 Z= 0.355 Chirality : 0.044 0.296 2621 Planarity : 0.004 0.041 1839 Dihedral : 29.565 177.567 4639 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.37 % Allowed : 25.37 % 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: 1.60 (0.26), residues: 1080 helix: 2.56 (0.21), residues: 643 sheet: -0.06 (0.60), residues: 52 loop : -1.50 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 30 TYR 0.011 0.001 TYR F 51 PHE 0.023 0.002 PHE K 556 TRP 0.011 0.001 TRP K 652 HIS 0.007 0.001 HIS K 630 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (16116) covalent geometry : angle 0.61205 / 0.35 (23111) hydrogen bonds : bond 0.07078 / 7.79 ( 882) hydrogen bonds : angle 3.40658 / 4.54 ( 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 179 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 138 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (tt0) REVERT: G 73 ASN cc_start: 0.8218 (t0) cc_final: 0.7971 (t0) REVERT: K 499 PHE cc_start: 0.7883 (OUTLIER) cc_final: 0.7443 (t80) REVERT: K 513 ILE cc_start: 0.8155 (pp) cc_final: 0.7311 (mp) REVERT: K 612 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8920 (mm) outliers start: 41 outliers final: 22 residues processed: 163 average time/residue: 0.6287 time to fit residues: 111.2213 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 119 THR 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 E residue 80 THR 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 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 612 LEU 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 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: 9.9990 chunk 126 optimal weight: 0.9980 chunk 117 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 11 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 83 optimal weight: 0.0980 chunk 78 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.128867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.087964 restraints weight = 27711.162| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.81 r_work: 0.3040 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.0969 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= 0.139 Angle : 0.585 11.381 23111 Z= 0.340 Chirality : 0.042 0.304 2621 Planarity : 0.004 0.040 1839 Dihedral : 29.561 179.807 4639 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.20 % Allowed : 26.12 % Favored : 70.68 % 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: 1080 helix: 2.71 (0.21), residues: 643 sheet: 0.06 (0.60), residues: 52 loop : -1.46 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 648 TYR 0.009 0.001 TYR F 51 PHE 0.019 0.001 PHE K 499 TRP 0.007 0.001 TRP K 652 HIS 0.013 0.001 HIS K 778 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.14 (16116) covalent geometry : angle 0.58504 / 0.34 (23111) hydrogen bonds : bond 0.06048 / 6.64 ( 882) hydrogen bonds : angle 3.26008 / 4.35 ( 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 174 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.8076 (t0) cc_final: 0.7836 (t0) REVERT: K 499 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7312 (t80) REVERT: K 612 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8919 (mm) REVERT: K 645 PHE cc_start: 0.6963 (t80) cc_final: 0.6729 (p90) outliers start: 30 outliers final: 18 residues processed: 161 average time/residue: 0.6481 time to fit residues: 112.8245 Evaluate side-chains 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 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 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 742 VAL Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 55 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 107 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 113 optimal weight: 0.5980 chunk 132 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 670 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.127875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.088318 restraints weight = 27780.016| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.86 r_work: 0.2992 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16116 Z= 0.164 Angle : 0.596 12.582 23111 Z= 0.344 Chirality : 0.043 0.300 2621 Planarity : 0.004 0.042 1839 Dihedral : 29.610 179.243 4639 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.94 % Allowed : 25.91 % Favored : 70.15 % 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: 1.68 (0.26), residues: 1080 helix: 2.58 (0.21), residues: 645 sheet: 0.12 (0.59), residues: 57 loop : -1.46 (0.28), residues: 378 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 0.016 0.001 PHE K 499 TRP 0.008 0.001 TRP K 652 HIS 0.005 0.001 HIS K 794 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (16116) covalent geometry : angle 0.59602 / 0.34 (23111) hydrogen bonds : bond 0.06463 / 7.12 ( 882) hydrogen bonds : angle 3.32402 / 4.45 ( 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 172 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8459 (ptmt) REVERT: F 93 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8375 (tt0) REVERT: G 73 ASN cc_start: 0.8223 (t0) cc_final: 0.7999 (t0) REVERT: K 499 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7258 (t80) REVERT: K 513 ILE cc_start: 0.8140 (pp) cc_final: 0.7211 (mp) outliers start: 37 outliers final: 21 residues processed: 159 average time/residue: 0.6333 time to fit residues: 109.0376 Evaluate side-chains 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 93 GLN 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 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 764 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: 3.9990 chunk 82 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 7 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.127781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.087423 restraints weight = 27504.543| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.12 r_work: 0.2997 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16116 Z= 0.167 Angle : 0.596 12.272 23111 Z= 0.344 Chirality : 0.043 0.300 2621 Planarity : 0.004 0.043 1839 Dihedral : 29.639 179.350 4639 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.52 % Allowed : 25.69 % 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: 1.68 (0.26), residues: 1080 helix: 2.58 (0.21), residues: 644 sheet: 0.32 (0.58), residues: 57 loop : -1.50 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 30 TYR 0.009 0.001 TYR F 51 PHE 0.015 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 0.00318 / 0.17 (16116) covalent geometry : angle 0.59582 / 0.34 (23111) hydrogen bonds : bond 0.06518 / 7.17 ( 882) hydrogen bonds : angle 3.30100 / 4.45 ( 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 169 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8406 (ptmt) REVERT: G 73 ASN cc_start: 0.8234 (t0) cc_final: 0.8004 (t0) REVERT: K 499 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7314 (t80) outliers start: 33 outliers final: 20 residues processed: 157 average time/residue: 0.6452 time to fit residues: 109.2881 Evaluate side-chains 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 93 GLN 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 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 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 764 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 75 optimal weight: 0.0770 chunk 27 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 134 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 118 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.1342 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.127794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.087977 restraints weight = 27248.134| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.94 r_work: 0.3002 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.1278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16116 Z= 0.161 Angle : 0.598 12.272 23111 Z= 0.343 Chirality : 0.043 0.300 2621 Planarity : 0.004 0.043 1839 Dihedral : 29.642 179.660 4638 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.88 % Allowed : 26.33 % 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: 1.71 (0.26), residues: 1080 helix: 2.63 (0.21), residues: 644 sheet: 0.09 (0.58), residues: 59 loop : -1.50 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.007 0.001 TYR F 51 PHE 0.014 0.001 PHE K 499 TRP 0.009 0.001 TRP K 652 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (16116) covalent geometry : angle 0.59781 / 0.34 (23111) hydrogen bonds : bond 0.06355 / 7.00 ( 882) hydrogen bonds : angle 3.26956 / 4.41 ( 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 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9019 (OUTLIER) cc_final: 0.8412 (ptmt) REVERT: G 73 ASN cc_start: 0.8260 (t0) cc_final: 0.8039 (t0) REVERT: K 499 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.7212 (t80) REVERT: K 513 ILE cc_start: 0.8117 (pp) cc_final: 0.7160 (mp) outliers start: 27 outliers final: 17 residues processed: 153 average time/residue: 0.6576 time to fit residues: 108.9196 Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 76 GLN 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 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: 0.7980 chunk 42 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 29 optimal weight: 9.9990 chunk 110 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3932 r_free = 0.3932 target = 0.128322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.088273 restraints weight = 27601.120| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.96 r_work: 0.3023 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16116 Z= 0.150 Angle : 0.596 12.396 23111 Z= 0.341 Chirality : 0.042 0.299 2621 Planarity : 0.004 0.044 1839 Dihedral : 29.638 179.748 4636 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: 1.75 (0.26), residues: 1080 helix: 2.68 (0.21), residues: 644 sheet: 0.30 (0.60), residues: 57 loop : -1.53 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.007 0.001 TYR F 51 PHE 0.016 0.002 PHE K 600 TRP 0.009 0.001 TRP K 652 HIS 0.003 0.001 HIS K 746 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (16116) covalent geometry : angle 0.59581 / 0.34 (23111) hydrogen bonds : bond 0.06029 / 6.65 ( 882) hydrogen bonds : angle 3.23674 / 4.39 ( 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 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8399 (ptmt) REVERT: G 73 ASN cc_start: 0.8204 (t0) cc_final: 0.7961 (t0) outliers start: 27 outliers final: 19 residues processed: 152 average time/residue: 0.6732 time to fit residues: 110.5769 Evaluate side-chains 151 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 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 93 GLN 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 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 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: 10.0000 chunk 115 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 = 0.3903 r_free = 0.3903 target = 0.126515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.086079 restraints weight = 27401.784| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.00 r_work: 0.2974 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16116 Z= 0.187 Angle : 0.631 14.906 23111 Z= 0.357 Chirality : 0.044 0.295 2621 Planarity : 0.004 0.044 1839 Dihedral : 29.686 177.608 4634 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.77 % Allowed : 26.44 % 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: 1.56 (0.26), residues: 1080 helix: 2.54 (0.21), residues: 644 sheet: 0.31 (0.60), residues: 52 loop : -1.64 (0.27), residues: 384 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 0.014 0.002 PHE K 777 TRP 0.013 0.001 TRP K 652 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.19 (16116) covalent geometry : angle 0.63148 / 0.36 (23111) hydrogen bonds : bond 0.07019 / 7.74 ( 882) hydrogen bonds : angle 3.35517 / 4.52 ( 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 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9029 (OUTLIER) cc_final: 0.8456 (ptmt) REVERT: K 513 ILE cc_start: 0.8074 (pp) cc_final: 0.7123 (mp) outliers start: 26 outliers final: 20 residues processed: 154 average time/residue: 0.6587 time to fit residues: 109.4029 Evaluate side-chains 153 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.270 ------------------------------------------------------------------------------- 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 93 GLN 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 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 742 VAL Chi-restraints excluded: chain K residue 764 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 38 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 = 0.3910 r_free = 0.3910 target = 0.126923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.086838 restraints weight = 27498.620| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.99 r_work: 0.2988 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16116 Z= 0.173 Angle : 0.631 12.383 23111 Z= 0.356 Chirality : 0.045 0.296 2621 Planarity : 0.004 0.045 1839 Dihedral : 29.681 178.487 4634 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.45 % Allowed : 26.87 % Favored : 70.68 % 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: 1.57 (0.26), residues: 1080 helix: 2.55 (0.21), residues: 644 sheet: 0.12 (0.59), residues: 54 loop : -1.61 (0.27), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 30 TYR 0.009 0.001 TYR F 51 PHE 0.013 0.002 PHE K 499 TRP 0.013 0.001 TRP K 652 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (16116) covalent geometry : angle 0.63064 / 0.36 (23111) hydrogen bonds : bond 0.06773 / 7.46 ( 882) hydrogen bonds : angle 3.32055 / 4.48 ( 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 155 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8433 (ptmt) REVERT: K 513 ILE cc_start: 0.8075 (pp) cc_final: 0.7116 (mp) outliers start: 23 outliers final: 19 residues processed: 145 average time/residue: 0.7135 time to fit residues: 111.2583 Evaluate side-chains 152 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 93 GLN Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 56 LYS 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 545 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.0670 chunk 119 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 9.9990 chunk 109 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 55 optimal weight: 0.5980 chunk 114 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.127392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.086900 restraints weight = 27205.609| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.05 r_work: 0.3007 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 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 : 0.002 0.045 16116 Z= 0.147 Angle : 0.624 14.633 23111 Z= 0.353 Chirality : 0.044 0.297 2621 Planarity : 0.004 0.045 1839 Dihedral : 29.662 178.361 4634 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.35 % Allowed : 26.97 % Favored : 70.68 % 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: 1.64 (0.26), residues: 1080 helix: 2.61 (0.21), residues: 644 sheet: 0.07 (0.58), residues: 54 loop : -1.57 (0.27), residues: 382 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 0.013 0.002 PHE K 797 TRP 0.010 0.001 TRP K 652 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (16116) covalent geometry : angle 0.62392 / 0.35 (23111) hydrogen bonds : bond 0.06422 / 7.06 ( 882) hydrogen bonds : angle 3.29988 / 4.46 ( 2243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5307.73 seconds wall clock time: 90 minutes 44.59 seconds (5444.59 seconds total)