Starting phenix.real_space_refine on Fri May 16 21:44:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_44114.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_44114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_44114.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_44114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2t_44114/05_2025/9b2t_44114.cif" } resolution = 2.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.64, per 1000 atoms: 0.63 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: 3.41 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.20 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: 7.42 Time building geometry restraints manager: 4.07 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=" C3' DT I -65 " pdb=" O3' DT I -65 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.01e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.46e+00 bond pdb=" CB LYS K 527 " pdb=" CG LYS K 527 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.33e+00 bond pdb=" C3' DG I -52 " pdb=" O3' DG I -52 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CB ASP K 611 " pdb=" CG ASP K 611 " ideal model delta sigma weight residual 1.516 1.545 -0.029 2.50e-02 1.60e+03 1.30e+00 ... (remaining 16111 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 23052 3.18 - 6.37: 50 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=" CA LEU K 479 " pdb=" CB LEU K 479 " pdb=" CG LEU K 479 " ideal model delta sigma weight residual 116.30 129.25 -12.95 3.50e+00 8.16e-02 1.37e+01 angle pdb=" CA LYS K 527 " pdb=" CB LYS K 527 " pdb=" CG LYS K 527 " ideal model delta sigma weight residual 114.10 121.18 -7.08 2.00e+00 2.50e-01 1.25e+01 angle pdb=" CB MET E 90 " pdb=" CG MET E 90 " pdb=" SD MET E 90 " ideal model delta sigma weight residual 112.70 123.23 -10.53 3.00e+00 1.11e-01 1.23e+01 angle pdb=" C PHE K 499 " pdb=" CA PHE K 499 " pdb=" CB PHE K 499 " ideal model delta sigma weight residual 109.86 116.07 -6.21 1.80e+00 3.09e-01 1.19e+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 - 0.028: 1776 0.028 - 0.057: 603 0.057 - 0.085: 155 0.085 - 0.113: 69 0.113 - 0.142: 18 Chirality restraints: 2621 Sorted by residual: 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 chirality pdb=" CA ASN K 730 " pdb=" N ASN K 730 " pdb=" C ASN K 730 " pdb=" CB ASN K 730 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CG LEU K 573 " pdb=" CB LEU K 573 " pdb=" CD1 LEU K 573 " pdb=" CD2 LEU K 573 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 3.99e-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: 7.460 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: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 41.260 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.080 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: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16116 Z= 0.169 Angle : 0.583 15.917 23111 Z= 0.334 Chirality : 0.034 0.142 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP K 652 HIS 0.002 0.001 HIS K 630 PHE 0.033 0.002 PHE K 499 TYR 0.009 0.001 TYR F 51 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.12002 ( 882) hydrogen bonds : angle 4.08918 ( 2243) covalent geometry : bond 0.00365 (16116) covalent geometry : angle 0.58348 (23111) *********************** 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 : 1.298 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: 1.5644 time to fit residues: 277.1570 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 : 1.294 ------------------------------------------------------------------------------- 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 113 optimal weight: 0.9980 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3933 r_free = 0.3933 target = 0.128462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.089449 restraints weight = 27621.677| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.01 r_work: 0.3011 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16116 Z= 0.177 Angle : 0.548 10.771 23111 Z= 0.321 Chirality : 0.035 0.159 2621 Planarity : 0.004 0.042 1839 Dihedral : 29.091 178.747 4659 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.62 % Allowed : 25.91 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1080 helix: 2.62 (0.21), residues: 643 sheet: 0.09 (0.67), residues: 42 loop : -1.41 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 652 HIS 0.005 0.001 HIS K 630 PHE 0.015 0.001 PHE K 499 TYR 0.010 0.001 TYR F 51 ARG 0.007 0.000 ARG K 648 Details of bonding type rmsd hydrogen bonds : bond 0.05914 ( 882) hydrogen bonds : angle 3.27387 ( 2243) covalent geometry : bond 0.00383 (16116) covalent geometry : angle 0.54797 (23111) *********************** 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 182 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 148 time to evaluate : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.8033 (t0) cc_final: 0.7817 (t0) REVERT: K 499 PHE cc_start: 0.7888 (OUTLIER) cc_final: 0.7380 (t80) REVERT: K 513 ILE cc_start: 0.8415 (pp) cc_final: 0.7749 (mp) outliers start: 34 outliers final: 14 residues processed: 169 average time/residue: 1.5045 time to fit residues: 275.6751 Evaluate side-chains 154 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS 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 545 LEU 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 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 17 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 737 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.126222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.080945 restraints weight = 27285.420| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.00 r_work: 0.2996 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16116 Z= 0.229 Angle : 0.578 11.768 23111 Z= 0.338 Chirality : 0.038 0.157 2621 Planarity : 0.004 0.043 1839 Dihedral : 29.272 176.823 4639 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.16 % Allowed : 25.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1080 helix: 2.56 (0.21), residues: 643 sheet: 0.23 (0.65), residues: 42 loop : -1.53 (0.26), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 652 HIS 0.006 0.001 HIS K 794 PHE 0.018 0.002 PHE K 556 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG K 648 Details of bonding type rmsd hydrogen bonds : bond 0.07048 ( 882) hydrogen bonds : angle 3.35766 ( 2243) covalent geometry : bond 0.00517 (16116) covalent geometry : angle 0.57835 (23111) *********************** 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: 39 poor density : 134 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: K 499 PHE cc_start: 0.7859 (OUTLIER) cc_final: 0.7437 (t80) outliers start: 39 outliers final: 19 residues processed: 160 average time/residue: 1.5707 time to fit residues: 271.6392 Evaluate side-chains 156 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 76 THR 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 80 THR Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 93 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 35 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 121 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 598 GLN K 746 HIS K 778 HIS K 783 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.126050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.086064 restraints weight = 27280.324| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.09 r_work: 0.2939 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16116 Z= 0.225 Angle : 0.580 11.244 23111 Z= 0.338 Chirality : 0.037 0.142 2621 Planarity : 0.004 0.044 1839 Dihedral : 29.269 177.080 4639 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.94 % Allowed : 24.41 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1080 helix: 2.45 (0.21), residues: 645 sheet: 0.30 (0.66), residues: 47 loop : -1.63 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 652 HIS 0.006 0.001 HIS K 630 PHE 0.014 0.002 PHE K 499 TYR 0.010 0.001 TYR F 51 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.06889 ( 882) hydrogen bonds : angle 3.32153 ( 2243) covalent geometry : bond 0.00507 (16116) covalent geometry : angle 0.57982 (23111) *********************** 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 175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 138 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 73 ASN cc_start: 0.8414 (t0) cc_final: 0.8204 (t0) REVERT: K 499 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7232 (t80) REVERT: K 513 ILE cc_start: 0.8178 (pp) cc_final: 0.7333 (mp) outliers start: 37 outliers final: 21 residues processed: 167 average time/residue: 1.6343 time to fit residues: 294.7283 Evaluate side-chains 159 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR 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 E residue 80 THR 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 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 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 116 optimal weight: 8.9990 chunk 114 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 chunk 124 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 125 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 778 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.126058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.084966 restraints weight = 27607.735| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.93 r_work: 0.2967 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 16116 Z= 0.213 Angle : 0.578 13.140 23111 Z= 0.336 Chirality : 0.037 0.186 2621 Planarity : 0.004 0.046 1839 Dihedral : 29.273 176.715 4636 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.84 % Allowed : 24.95 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.26), residues: 1080 helix: 2.49 (0.21), residues: 645 sheet: 0.53 (0.65), residues: 47 loop : -1.63 (0.27), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 652 HIS 0.005 0.001 HIS K 630 PHE 0.013 0.002 PHE K 499 TYR 0.008 0.001 TYR C 50 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.06690 ( 882) hydrogen bonds : angle 3.29956 ( 2243) covalent geometry : bond 0.00478 (16116) covalent geometry : angle 0.57756 (23111) *********************** 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 184 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 122 LYS cc_start: 0.9014 (OUTLIER) cc_final: 0.8392 (ptmt) REVERT: G 73 ASN cc_start: 0.8346 (t0) cc_final: 0.8115 (t0) REVERT: K 513 ILE cc_start: 0.8224 (pp) cc_final: 0.7424 (mp) outliers start: 36 outliers final: 23 residues processed: 174 average time/residue: 1.4738 time to fit residues: 277.8238 Evaluate side-chains 168 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 59 LYS 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 76 GLN Chi-restraints excluded: chain E residue 80 THR 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 K residue 499 PHE Chi-restraints excluded: chain K residue 545 LEU 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 764 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 1 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.123670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.083731 restraints weight = 27246.244| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.93 r_work: 0.2881 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16116 Z= 0.277 Angle : 0.621 11.849 23111 Z= 0.362 Chirality : 0.040 0.166 2621 Planarity : 0.005 0.052 1839 Dihedral : 29.396 176.173 4636 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.16 % Allowed : 24.31 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.26), residues: 1080 helix: 2.38 (0.21), residues: 645 sheet: 0.39 (0.67), residues: 42 loop : -1.71 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 652 HIS 0.006 0.001 HIS E 113 PHE 0.015 0.002 PHE K 797 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.07902 ( 882) hydrogen bonds : angle 3.43503 ( 2243) covalent geometry : bond 0.00635 (16116) covalent geometry : angle 0.62130 (23111) *********************** 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 189 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 150 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9187 (OUTLIER) cc_final: 0.8606 (mmt90) REVERT: A 122 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8512 (ptmt) REVERT: H 96 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8625 (ttp-170) outliers start: 39 outliers final: 23 residues processed: 177 average time/residue: 1.6160 time to fit residues: 307.8529 Evaluate side-chains 175 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR 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 80 THR 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 96 ARG Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 498 VAL 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 650 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 65 optimal weight: 2.9990 chunk 104 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 119 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.126861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.086153 restraints weight = 26913.066| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.84 r_work: 0.2998 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16116 Z= 0.316 Angle : 0.655 11.302 23111 Z= 0.381 Chirality : 0.041 0.163 2621 Planarity : 0.005 0.047 1839 Dihedral : 29.487 175.679 4635 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.62 % Allowed : 25.59 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.25), residues: 1080 helix: 2.27 (0.21), residues: 639 sheet: -0.06 (0.67), residues: 42 loop : -1.74 (0.26), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 652 HIS 0.005 0.001 HIS K 794 PHE 0.017 0.002 PHE K 797 TYR 0.018 0.002 TYR K 736 ARG 0.006 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.08355 ( 882) hydrogen bonds : angle 3.53884 ( 2243) covalent geometry : bond 0.00729 (16116) covalent geometry : angle 0.65537 (23111) *********************** 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 190 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8651 (mmt90) REVERT: A 122 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8505 (ptmt) REVERT: E 59 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8369 (pm20) REVERT: H 96 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8550 (ttp-170) outliers start: 34 outliers final: 23 residues processed: 177 average time/residue: 1.6718 time to fit residues: 319.1599 Evaluate side-chains 178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ARG 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 73 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR 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 96 ARG 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 650 LEU Chi-restraints excluded: chain K residue 655 VAL Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 725 MET Chi-restraints excluded: chain K residue 742 VAL 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 6 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 76 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 0.4980 chunk 19 optimal weight: 3.9990 chunk 132 optimal weight: 0.0370 chunk 55 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.135527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.089631 restraints weight = 28866.829| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.82 r_work: 0.3115 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16116 Z= 0.162 Angle : 0.602 11.848 23111 Z= 0.349 Chirality : 0.037 0.192 2621 Planarity : 0.004 0.043 1839 Dihedral : 29.360 176.404 4635 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.88 % Allowed : 26.76 % Favored : 70.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1080 helix: 2.48 (0.21), residues: 643 sheet: 0.15 (0.59), residues: 52 loop : -1.67 (0.27), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 652 HIS 0.006 0.001 HIS K 630 PHE 0.014 0.002 PHE K 499 TYR 0.014 0.001 TYR K 736 ARG 0.007 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.06433 ( 882) hydrogen bonds : angle 3.30237 ( 2243) covalent geometry : bond 0.00335 (16116) covalent geometry : angle 0.60187 (23111) *********************** 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 193 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8208 (tt0) REVERT: K 708 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8353 (mm-30) REVERT: K 779 ARG cc_start: 0.6783 (tmm-80) cc_final: 0.6298 (ptp90) REVERT: K 781 MET cc_start: 0.7888 (ptm) cc_final: 0.7660 (ptt) outliers start: 27 outliers final: 15 residues processed: 181 average time/residue: 1.6470 time to fit residues: 320.5901 Evaluate side-chains 178 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 1.149 ------------------------------------------------------------------------------- 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 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 49 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 603 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 705 SER Chi-restraints excluded: chain K residue 708 GLU Chi-restraints excluded: chain K residue 742 VAL 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 90 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 110 optimal weight: 0.0050 chunk 30 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 116 optimal weight: 8.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 783 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.134961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.090136 restraints weight = 28823.480| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.84 r_work: 0.3134 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16116 Z= 0.190 Angle : 0.588 11.625 23111 Z= 0.341 Chirality : 0.036 0.171 2621 Planarity : 0.004 0.044 1839 Dihedral : 29.299 174.206 4635 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.81 % Allowed : 27.93 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1080 helix: 2.60 (0.21), residues: 639 sheet: 0.22 (0.57), residues: 57 loop : -1.56 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 652 HIS 0.004 0.001 HIS K 630 PHE 0.014 0.002 PHE K 495 TYR 0.012 0.001 TYR K 736 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06126 ( 882) hydrogen bonds : angle 3.23393 ( 2243) covalent geometry : bond 0.00419 (16116) covalent geometry : angle 0.58850 (23111) *********************** 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 165 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8298 (tt0) REVERT: K 725 MET cc_start: 0.4706 (ptp) cc_final: 0.3969 (ptm) REVERT: K 779 ARG cc_start: 0.6743 (tmm-80) cc_final: 0.6287 (ptp90) outliers start: 17 outliers final: 12 residues processed: 157 average time/residue: 1.7784 time to fit residues: 298.5135 Evaluate side-chains 161 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL Chi-restraints excluded: chain K residue 612 LEU Chi-restraints excluded: chain K residue 683 VAL Chi-restraints excluded: chain K residue 685 ILE Chi-restraints excluded: chain K residue 705 SER 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 50 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 127 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 133 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.135508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.090036 restraints weight = 29239.210| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.81 r_work: 0.3130 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16116 Z= 0.190 Angle : 0.590 11.616 23111 Z= 0.339 Chirality : 0.036 0.181 2621 Planarity : 0.004 0.045 1839 Dihedral : 29.290 174.463 4634 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.60 % Allowed : 28.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.26), residues: 1080 helix: 2.62 (0.21), residues: 639 sheet: 0.19 (0.58), residues: 52 loop : -1.63 (0.27), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 652 HIS 0.005 0.001 HIS K 630 PHE 0.016 0.002 PHE K 797 TYR 0.011 0.001 TYR K 736 ARG 0.008 0.000 ARG H 30 Details of bonding type rmsd hydrogen bonds : bond 0.06180 ( 882) hydrogen bonds : angle 3.24249 ( 2243) covalent geometry : bond 0.00422 (16116) covalent geometry : angle 0.59028 (23111) ********************** 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 162 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 93 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8254 (tt0) REVERT: K 616 ARG cc_start: 0.7154 (ptt90) cc_final: 0.6882 (ptt90) REVERT: K 695 ARG cc_start: 0.7550 (tmt170) cc_final: 0.7214 (tmm160) REVERT: K 725 MET cc_start: 0.4830 (ptp) cc_final: 0.4100 (ptm) REVERT: K 777 PHE cc_start: 0.6279 (t80) cc_final: 0.5809 (t80) REVERT: K 779 ARG cc_start: 0.6885 (tmm-80) cc_final: 0.6403 (ptm160) outliers start: 15 outliers final: 13 residues processed: 157 average time/residue: 1.8068 time to fit residues: 303.6218 Evaluate side-chains 160 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain K residue 499 PHE Chi-restraints excluded: chain K residue 602 VAL 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 705 SER 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 35 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 115 optimal weight: 0.0170 chunk 48 optimal weight: 0.5980 overall best weight: 1.2422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.135042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.090218 restraints weight = 28993.478| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.80 r_work: 0.3137 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16116 Z= 0.193 Angle : 0.590 11.306 23111 Z= 0.340 Chirality : 0.036 0.183 2621 Planarity : 0.004 0.045 1839 Dihedral : 29.283 174.837 4634 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.60 % Allowed : 28.14 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1080 helix: 2.62 (0.21), residues: 640 sheet: 0.21 (0.57), residues: 52 loop : -1.62 (0.28), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 652 HIS 0.004 0.001 HIS K 794 PHE 0.012 0.001 PHE K 499 TYR 0.011 0.001 TYR K 736 ARG 0.007 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.06191 ( 882) hydrogen bonds : angle 3.22051 ( 2243) covalent geometry : bond 0.00428 (16116) covalent geometry : angle 0.59046 (23111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12832.62 seconds wall clock time: 220 minutes 39.13 seconds (13239.13 seconds total)