Starting phenix.real_space_refine on Thu May 15 04:39:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.map" model { file = "/net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txx_41708/05_2025/8txx_41708.cif" } resolution = 3.7 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= 0.002 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 294 5.49 5 S 15 5.16 5 C 7227 2.51 5 N 2431 2.21 5 O 3002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12969 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 251 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain breaks: 1 Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 Time building chain proxies: 7.31, per 1000 atoms: 0.56 Number of scatterers: 12969 At special positions: 0 Unit cell: (99.6, 124.832, 123.504, 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 15 16.00 P 294 15.00 O 3002 8.00 N 2431 7.00 C 7227 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=1, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 988.0 milliseconds 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1632 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 12 sheets defined 67.9% alpha, 3.7% beta 135 base pairs and 242 stacking pairs defined. Time for finding SS restraints: 5.28 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.169A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.647A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.668A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.687A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 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: 4.121A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.506A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 447 through 461 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.745A pdb=" N ARG M 74 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY M 75 " --> pdb=" O ARG M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 71 through 75' Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.608A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.681A 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 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.477A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.297A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB3, first strand: chain 'M' and resid 44 through 45 435 hydrogen bonds defined for protein. 1267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 4.42 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2733 1.33 - 1.45: 4234 1.45 - 1.57: 6212 1.57 - 1.69: 586 1.69 - 1.81: 26 Bond restraints: 13791 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CG GLN A 125 " pdb=" CD GLN A 125 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.03e+00 bond pdb=" CB CYS A 96 " pdb=" SG CYS A 96 " ideal model delta sigma weight residual 1.808 1.776 0.032 3.30e-02 9.18e+02 9.25e-01 bond pdb=" CD LYS B 79 " pdb=" CE LYS B 79 " ideal model delta sigma weight residual 1.520 1.491 0.029 3.00e-02 1.11e+03 9.13e-01 bond pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.99e-01 ... (remaining 13786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 19232 1.39 - 2.77: 579 2.77 - 4.16: 41 4.16 - 5.54: 16 5.54 - 6.93: 4 Bond angle restraints: 19872 Sorted by residual: angle pdb=" C ILE A 124 " pdb=" N GLN A 125 " pdb=" CA GLN A 125 " ideal model delta sigma weight residual 120.72 115.00 5.72 1.67e+00 3.59e-01 1.17e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.23e+00 angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 110.77 116.37 -5.60 1.93e+00 2.68e-01 8.43e+00 angle pdb=" N GLN A 125 " pdb=" CA GLN A 125 " pdb=" CB GLN A 125 " ideal model delta sigma weight residual 110.39 114.91 -4.52 1.66e+00 3.63e-01 7.40e+00 angle pdb=" CA GLN A 76 " pdb=" CB GLN A 76 " pdb=" CG GLN A 76 " ideal model delta sigma weight residual 114.10 119.51 -5.41 2.00e+00 2.50e-01 7.31e+00 ... (remaining 19867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.52: 6039 31.52 - 63.04: 1499 63.04 - 94.56: 43 94.56 - 126.09: 1 126.09 - 157.61: 2 Dihedral angle restraints: 7584 sinusoidal: 5052 harmonic: 2532 Sorted by residual: dihedral pdb=" CA TYR K 474 " pdb=" C TYR K 474 " pdb=" N HIS K 475 " pdb=" CA HIS K 475 " ideal model delta harmonic sigma weight residual 180.00 156.78 23.22 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 62.39 157.61 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 78.91 141.09 1 3.50e+01 8.16e-04 1.39e+01 ... (remaining 7581 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1640 0.031 - 0.061: 464 0.061 - 0.092: 109 0.092 - 0.123: 40 0.123 - 0.154: 8 Chirality restraints: 2261 Sorted by residual: chirality pdb=" CA ASN C 38 " pdb=" N ASN C 38 " pdb=" C ASN C 38 " pdb=" CB ASN C 38 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.13e-01 chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.48e-01 ... (remaining 2258 not shown) Planarity restraints: 1502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 83 " -0.010 2.00e-02 2.50e+03 1.17e-02 2.74e+00 pdb=" CG TYR D 83 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 83 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR D 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR D 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR D 83 " -0.009 2.00e-02 2.50e+03 pdb=" CZ TYR D 83 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 83 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.022 2.00e-02 2.50e+03 8.95e-03 2.40e+00 pdb=" N9 DG I 47 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.007 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.021 2.00e-02 2.50e+03 8.94e-03 2.20e+00 pdb=" N9 DA I -35 " -0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.002 2.00e-02 2.50e+03 ... (remaining 1499 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 146 2.64 - 3.20: 10939 3.20 - 3.77: 23313 3.77 - 4.33: 29611 4.33 - 4.90: 43114 Nonbonded interactions: 107123 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.074 3.040 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG J 48 " model vdw 2.102 3.040 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.140 2.496 nonbonded pdb=" NZ LYS B 79 " pdb=" OP1 DG J 27 " model vdw 2.215 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.250 3.040 ... (remaining 107118 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' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.45 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 31.840 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 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 0.063 13794 Z= 0.173 Angle : 0.551 6.929 19878 Z= 0.327 Chirality : 0.033 0.154 2261 Planarity : 0.003 0.036 1500 Dihedral : 26.694 157.607 5946 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 2.62 (0.29), residues: 853 helix: 2.67 (0.22), residues: 560 sheet: 1.12 (1.38), residues: 17 loop : -0.21 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS H 109 PHE 0.010 0.001 PHE E 104 TYR 0.028 0.002 TYR D 83 ARG 0.005 0.000 ARG C 29 Details of bonding type rmsd link_TRANS : bond 0.00047 ( 2) link_TRANS : angle 0.46968 ( 6) hydrogen bonds : bond 0.11674 ( 783) hydrogen bonds : angle 3.83172 ( 1959) covalent geometry : bond 0.00357 (13791) covalent geometry : angle 0.55138 (19872) Misc. bond : bond 0.06282 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8504 (mmm) cc_final: 0.8053 (tpp) REVERT: A 123 ASP cc_start: 0.8817 (m-30) cc_final: 0.8567 (m-30) REVERT: B 27 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8914 (mp10) REVERT: B 88 TYR cc_start: 0.8607 (m-80) cc_final: 0.8082 (m-10) REVERT: D 51 ASP cc_start: 0.8750 (p0) cc_final: 0.8199 (p0) REVERT: D 57 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8580 (mmtp) REVERT: D 86 ARG cc_start: 0.9070 (mmt-90) cc_final: 0.8801 (mtt-85) REVERT: E 59 GLU cc_start: 0.8380 (pm20) cc_final: 0.7987 (pm20) REVERT: E 76 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8467 (tm-30) REVERT: F 88 TYR cc_start: 0.8759 (m-80) cc_final: 0.8445 (m-80) REVERT: H 33 ARG cc_start: 0.8429 (mtp85) cc_final: 0.7809 (mtp-110) REVERT: H 42 TYR cc_start: 0.8941 (t80) cc_final: 0.8680 (t80) REVERT: H 79 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8798 (ttm-80) REVERT: C 64 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8446 (tm-30) REVERT: C 95 LYS cc_start: 0.9398 (ttmt) cc_final: 0.9191 (ttmt) REVERT: C 110 ASN cc_start: 0.8949 (t0) cc_final: 0.8344 (p0) REVERT: G 74 LYS cc_start: 0.9412 (mttp) cc_final: 0.9152 (mmtp) REVERT: G 76 THR cc_start: 0.9096 (p) cc_final: 0.8667 (t) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.3107 time to fit residues: 90.1015 Evaluate side-chains 161 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.6980 chunk 83 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 0.0000 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN H 109 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.060894 restraints weight = 44602.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.063121 restraints weight = 20990.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064652 restraints weight = 13919.383| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13794 Z= 0.207 Angle : 0.574 5.804 19878 Z= 0.339 Chirality : 0.035 0.156 2261 Planarity : 0.004 0.039 1500 Dihedral : 29.712 158.669 4186 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.58 % Allowed : 11.55 % Favored : 85.87 % 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: 2.71 (0.30), residues: 853 helix: 2.69 (0.22), residues: 575 sheet: 1.17 (1.37), residues: 17 loop : -0.23 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS H 109 PHE 0.007 0.001 PHE E 67 TYR 0.028 0.002 TYR H 40 ARG 0.004 0.000 ARG D 99 Details of bonding type rmsd link_TRANS : bond 0.00043 ( 2) link_TRANS : angle 0.60958 ( 6) hydrogen bonds : bond 0.05033 ( 783) hydrogen bonds : angle 3.05811 ( 1959) covalent geometry : bond 0.00467 (13791) covalent geometry : angle 0.57363 (19872) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 177 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8682 (mmm) cc_final: 0.8147 (tpp) REVERT: B 27 GLN cc_start: 0.9230 (mm-40) cc_final: 0.8949 (mp10) REVERT: B 85 ASP cc_start: 0.8868 (m-30) cc_final: 0.8657 (m-30) REVERT: D 47 GLN cc_start: 0.8638 (mt0) cc_final: 0.8336 (mt0) REVERT: D 51 ASP cc_start: 0.8315 (p0) cc_final: 0.7843 (p0) REVERT: D 57 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8415 (mmtp) REVERT: D 86 ARG cc_start: 0.8992 (mmt-90) cc_final: 0.8765 (mtt-85) REVERT: F 24 ASP cc_start: 0.8012 (t0) cc_final: 0.7749 (t0) REVERT: F 88 TYR cc_start: 0.8757 (m-80) cc_final: 0.8428 (m-80) REVERT: H 33 ARG cc_start: 0.8665 (mtp85) cc_final: 0.8044 (mtp-110) REVERT: C 56 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 110 ASN cc_start: 0.8939 (t0) cc_final: 0.8356 (p0) REVERT: G 76 THR cc_start: 0.9140 (p) cc_final: 0.8637 (t) outliers start: 19 outliers final: 15 residues processed: 190 average time/residue: 0.2712 time to fit residues: 71.2534 Evaluate side-chains 181 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 89 optimal weight: 0.1980 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.0030 chunk 35 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.064274 restraints weight = 36185.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.066182 restraints weight = 19421.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.067573 restraints weight = 13843.157| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2832 r_free = 0.2832 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13794 Z= 0.149 Angle : 0.528 5.864 19878 Z= 0.317 Chirality : 0.033 0.145 2261 Planarity : 0.003 0.041 1500 Dihedral : 29.547 158.022 4186 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.77 % Allowed : 13.99 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.82 (0.30), residues: 853 helix: 2.84 (0.22), residues: 575 sheet: 1.33 (1.39), residues: 17 loop : -0.40 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.007 0.001 PHE E 67 TYR 0.015 0.001 TYR H 40 ARG 0.003 0.000 ARG D 99 Details of bonding type rmsd link_TRANS : bond 0.00082 ( 2) link_TRANS : angle 0.32815 ( 6) hydrogen bonds : bond 0.04176 ( 783) hydrogen bonds : angle 2.70640 ( 1959) covalent geometry : bond 0.00318 (13791) covalent geometry : angle 0.52773 (19872) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8098 (tt0) cc_final: 0.7866 (tt0) REVERT: B 85 ASP cc_start: 0.8695 (m-30) cc_final: 0.8424 (m-30) REVERT: D 42 TYR cc_start: 0.8102 (t80) cc_final: 0.7335 (t80) REVERT: D 46 LYS cc_start: 0.9317 (mmtt) cc_final: 0.8875 (mmtp) REVERT: D 47 GLN cc_start: 0.8403 (mt0) cc_final: 0.8146 (mt0) REVERT: D 51 ASP cc_start: 0.8170 (p0) cc_final: 0.7673 (p0) REVERT: D 57 LYS cc_start: 0.8811 (mmmm) cc_final: 0.8451 (mmtp) REVERT: D 86 ARG cc_start: 0.8922 (mmt-90) cc_final: 0.8676 (mtt-85) REVERT: D 105 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8001 (mm-30) REVERT: E 76 GLN cc_start: 0.8724 (tm-30) cc_final: 0.8491 (tm-30) REVERT: E 105 GLU cc_start: 0.7888 (tt0) cc_final: 0.7643 (tt0) REVERT: F 24 ASP cc_start: 0.7793 (t0) cc_final: 0.7529 (t0) REVERT: H 33 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8033 (mtp-110) REVERT: H 120 LYS cc_start: 0.9068 (tptm) cc_final: 0.8757 (tptm) REVERT: C 110 ASN cc_start: 0.8863 (t0) cc_final: 0.8420 (p0) REVERT: G 64 GLU cc_start: 0.9263 (tm-30) cc_final: 0.8965 (tm-30) REVERT: G 76 THR cc_start: 0.9099 (p) cc_final: 0.8578 (t) outliers start: 13 outliers final: 9 residues processed: 189 average time/residue: 0.2804 time to fit residues: 72.9013 Evaluate side-chains 175 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 87 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 94 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN D 95 GLN H 84 ASN C 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.098202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.061968 restraints weight = 41778.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.063954 restraints weight = 21342.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.065442 restraints weight = 14724.957| |-----------------------------------------------------------------------------| r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13794 Z= 0.182 Angle : 0.553 9.183 19878 Z= 0.326 Chirality : 0.034 0.164 2261 Planarity : 0.004 0.037 1500 Dihedral : 29.705 158.794 4186 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.26 % Allowed : 15.22 % Favored : 81.52 % 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: 2.77 (0.29), residues: 853 helix: 2.82 (0.21), residues: 576 sheet: 1.22 (1.36), residues: 17 loop : -0.46 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.015 0.001 TYR D 40 ARG 0.003 0.000 ARG C 29 Details of bonding type rmsd link_TRANS : bond 0.00029 ( 2) link_TRANS : angle 0.35414 ( 6) hydrogen bonds : bond 0.04627 ( 783) hydrogen bonds : angle 2.82024 ( 1959) covalent geometry : bond 0.00405 (13791) covalent geometry : angle 0.55258 (19872) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 172 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8053 (tt0) cc_final: 0.7824 (tt0) REVERT: A 90 MET cc_start: 0.8660 (mmm) cc_final: 0.8155 (tpp) REVERT: B 85 ASP cc_start: 0.8808 (m-30) cc_final: 0.8513 (m-30) REVERT: D 42 TYR cc_start: 0.8138 (t80) cc_final: 0.7354 (t80) REVERT: D 46 LYS cc_start: 0.9330 (mmtt) cc_final: 0.8893 (mmtp) REVERT: D 47 GLN cc_start: 0.8517 (mt0) cc_final: 0.8217 (mt0) REVERT: D 51 ASP cc_start: 0.8211 (p0) cc_final: 0.7546 (p0) REVERT: D 85 LYS cc_start: 0.9244 (OUTLIER) cc_final: 0.8995 (mtmm) REVERT: D 86 ARG cc_start: 0.8918 (mmt-90) cc_final: 0.8681 (mtt-85) REVERT: F 24 ASP cc_start: 0.7779 (t0) cc_final: 0.7561 (t0) REVERT: F 88 TYR cc_start: 0.8777 (m-80) cc_final: 0.8332 (m-80) REVERT: H 33 ARG cc_start: 0.8632 (mtp85) cc_final: 0.8028 (mtp-110) REVERT: H 120 LYS cc_start: 0.9118 (tptm) cc_final: 0.8806 (tptm) REVERT: C 56 GLU cc_start: 0.8759 (tm-30) cc_final: 0.8159 (tm-30) REVERT: C 110 ASN cc_start: 0.8872 (t0) cc_final: 0.8403 (p0) REVERT: G 76 THR cc_start: 0.9142 (p) cc_final: 0.8612 (t) REVERT: G 91 GLU cc_start: 0.8134 (tp30) cc_final: 0.7697 (tp30) outliers start: 24 outliers final: 16 residues processed: 185 average time/residue: 0.2848 time to fit residues: 72.3960 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 109 optimal weight: 0.0970 chunk 103 optimal weight: 0.0050 chunk 47 optimal weight: 2.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.100496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.066521 restraints weight = 47171.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.067968 restraints weight = 23529.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.068901 restraints weight = 14756.030| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2865 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2865 r_free = 0.2865 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2865 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13794 Z= 0.145 Angle : 0.530 7.603 19878 Z= 0.316 Chirality : 0.032 0.144 2261 Planarity : 0.003 0.037 1500 Dihedral : 29.523 158.227 4186 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.17 % Allowed : 16.58 % Favored : 81.25 % 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: 2.92 (0.29), residues: 853 helix: 2.97 (0.21), residues: 575 sheet: 1.17 (1.34), residues: 17 loop : -0.48 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 109 PHE 0.007 0.001 PHE A 67 TYR 0.015 0.001 TYR H 40 ARG 0.006 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00087 ( 2) link_TRANS : angle 0.32618 ( 6) hydrogen bonds : bond 0.04002 ( 783) hydrogen bonds : angle 2.61155 ( 1959) covalent geometry : bond 0.00306 (13791) covalent geometry : angle 0.52985 (19872) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 85 ASP cc_start: 0.8769 (m-30) cc_final: 0.8482 (m-30) REVERT: D 42 TYR cc_start: 0.8034 (t80) cc_final: 0.7117 (t80) REVERT: D 47 GLN cc_start: 0.8268 (mt0) cc_final: 0.7910 (mt0) REVERT: D 51 ASP cc_start: 0.8114 (p0) cc_final: 0.7496 (p0) REVERT: D 59 MET cc_start: 0.9146 (tpp) cc_final: 0.8843 (tpp) REVERT: D 85 LYS cc_start: 0.9253 (OUTLIER) cc_final: 0.9032 (mtmm) REVERT: E 59 GLU cc_start: 0.8642 (pm20) cc_final: 0.8345 (pm20) REVERT: F 24 ASP cc_start: 0.7920 (t0) cc_final: 0.7704 (t0) REVERT: H 33 ARG cc_start: 0.8608 (mtp85) cc_final: 0.7995 (mtp-110) REVERT: H 59 MET cc_start: 0.9252 (tpp) cc_final: 0.8965 (tpp) REVERT: H 120 LYS cc_start: 0.9116 (tptm) cc_final: 0.8557 (ttpp) REVERT: C 110 ASN cc_start: 0.8821 (t0) cc_final: 0.8421 (p0) REVERT: G 24 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8676 (mm-40) REVERT: G 64 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9019 (tm-30) REVERT: G 76 THR cc_start: 0.9160 (p) cc_final: 0.8640 (t) outliers start: 16 outliers final: 12 residues processed: 188 average time/residue: 0.2890 time to fit residues: 75.0097 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 7.9990 chunk 23 optimal weight: 0.7980 chunk 90 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS D 95 GLN H 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.095653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.058599 restraints weight = 46970.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.060890 restraints weight = 21455.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.062378 restraints weight = 14011.509| |-----------------------------------------------------------------------------| r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 13794 Z= 0.263 Angle : 0.613 9.363 19878 Z= 0.357 Chirality : 0.037 0.170 2261 Planarity : 0.004 0.042 1500 Dihedral : 29.954 160.088 4186 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.40 % Allowed : 15.76 % Favored : 80.84 % 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: 2.63 (0.29), residues: 853 helix: 2.76 (0.21), residues: 577 sheet: 1.02 (1.33), residues: 17 loop : -0.66 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE H 70 TYR 0.023 0.002 TYR H 40 ARG 0.005 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00162 ( 2) link_TRANS : angle 0.47521 ( 6) hydrogen bonds : bond 0.05420 ( 783) hydrogen bonds : angle 3.09434 ( 1959) covalent geometry : bond 0.00606 (13791) covalent geometry : angle 0.61342 (19872) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8807 (mmm) cc_final: 0.8178 (tpp) REVERT: B 50 ILE cc_start: 0.9456 (OUTLIER) cc_final: 0.9157 (tp) REVERT: B 85 ASP cc_start: 0.8901 (m-30) cc_final: 0.8595 (m-30) REVERT: D 42 TYR cc_start: 0.8259 (t80) cc_final: 0.7512 (t80) REVERT: D 46 LYS cc_start: 0.9322 (mmtt) cc_final: 0.9061 (mmtp) REVERT: D 47 GLN cc_start: 0.8547 (mt0) cc_final: 0.8170 (mt0) REVERT: D 51 ASP cc_start: 0.8412 (p0) cc_final: 0.7877 (p0) REVERT: D 85 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9082 (mtmm) REVERT: E 59 GLU cc_start: 0.8761 (pm20) cc_final: 0.8545 (pm20) REVERT: H 33 ARG cc_start: 0.8709 (mtp85) cc_final: 0.7998 (mtp-110) REVERT: H 71 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8334 (tm-30) REVERT: H 120 LYS cc_start: 0.9116 (tptm) cc_final: 0.8537 (ttpp) REVERT: C 56 GLU cc_start: 0.8925 (tm-30) cc_final: 0.8551 (tm-30) REVERT: C 110 ASN cc_start: 0.8986 (t0) cc_final: 0.8403 (p0) REVERT: G 76 THR cc_start: 0.9200 (p) cc_final: 0.8801 (t) REVERT: G 91 GLU cc_start: 0.8248 (tp30) cc_final: 0.7734 (tp30) outliers start: 25 outliers final: 19 residues processed: 177 average time/residue: 0.2774 time to fit residues: 67.2133 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 27 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.095671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.058935 restraints weight = 46709.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.061219 restraints weight = 21124.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.062731 restraints weight = 13761.509| |-----------------------------------------------------------------------------| r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13794 Z= 0.239 Angle : 0.602 8.449 19878 Z= 0.353 Chirality : 0.036 0.159 2261 Planarity : 0.004 0.044 1500 Dihedral : 29.902 161.469 4186 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.12 % Allowed : 16.98 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.56 (0.29), residues: 853 helix: 2.74 (0.21), residues: 575 sheet: 0.98 (1.31), residues: 17 loop : -0.74 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 31 PHE 0.007 0.001 PHE G 25 TYR 0.013 0.002 TYR H 40 ARG 0.003 0.000 ARG F 67 Details of bonding type rmsd link_TRANS : bond 0.00093 ( 2) link_TRANS : angle 0.51238 ( 6) hydrogen bonds : bond 0.05103 ( 783) hydrogen bonds : angle 3.01340 ( 1959) covalent geometry : bond 0.00549 (13791) covalent geometry : angle 0.60178 (19872) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.8810 (mmm) cc_final: 0.8180 (tpp) REVERT: B 50 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9135 (tp) REVERT: B 85 ASP cc_start: 0.8907 (m-30) cc_final: 0.8588 (m-30) REVERT: D 47 GLN cc_start: 0.8535 (mt0) cc_final: 0.8160 (mt0) REVERT: D 51 ASP cc_start: 0.8391 (p0) cc_final: 0.7849 (p0) REVERT: D 57 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8764 (mmmt) REVERT: D 85 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.9082 (mtmm) REVERT: D 86 ARG cc_start: 0.8965 (mmt-90) cc_final: 0.8711 (mtt-85) REVERT: E 59 GLU cc_start: 0.8728 (pm20) cc_final: 0.8419 (pm20) REVERT: H 33 ARG cc_start: 0.8729 (mtp85) cc_final: 0.8022 (mtp-110) REVERT: H 71 GLU cc_start: 0.8551 (tm-30) cc_final: 0.8326 (tm-30) REVERT: H 120 LYS cc_start: 0.9143 (tptm) cc_final: 0.8722 (ttmm) REVERT: C 56 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8356 (tm-30) REVERT: C 110 ASN cc_start: 0.8981 (t0) cc_final: 0.8400 (p0) REVERT: G 56 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8431 (tm-30) REVERT: G 64 GLU cc_start: 0.9351 (tm-30) cc_final: 0.9066 (tm-30) REVERT: G 91 GLU cc_start: 0.8346 (tp30) cc_final: 0.7997 (tp30) outliers start: 23 outliers final: 18 residues processed: 183 average time/residue: 0.2897 time to fit residues: 73.3184 Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 27 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.097962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.062053 restraints weight = 40194.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.064231 restraints weight = 19596.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.065676 restraints weight = 13224.478| |-----------------------------------------------------------------------------| r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2807 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2807 r_free = 0.2807 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2807 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13794 Z= 0.160 Angle : 0.554 8.084 19878 Z= 0.329 Chirality : 0.033 0.161 2261 Planarity : 0.003 0.040 1500 Dihedral : 29.743 161.713 4186 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.45 % Allowed : 17.93 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.77 (0.29), residues: 853 helix: 2.92 (0.22), residues: 574 sheet: 1.03 (1.32), residues: 17 loop : -0.69 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE H 70 TYR 0.016 0.001 TYR H 40 ARG 0.004 0.000 ARG C 99 Details of bonding type rmsd link_TRANS : bond 0.00034 ( 2) link_TRANS : angle 0.35962 ( 6) hydrogen bonds : bond 0.04287 ( 783) hydrogen bonds : angle 2.71805 ( 1959) covalent geometry : bond 0.00351 (13791) covalent geometry : angle 0.55405 (19872) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8651 (tpt90) cc_final: 0.8119 (tpt90) REVERT: B 85 ASP cc_start: 0.8815 (m-30) cc_final: 0.8521 (m-30) REVERT: D 47 GLN cc_start: 0.8402 (mt0) cc_final: 0.8136 (mt0) REVERT: D 51 ASP cc_start: 0.8184 (p0) cc_final: 0.7586 (p0) REVERT: D 85 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.9032 (mtmm) REVERT: D 86 ARG cc_start: 0.8893 (mmt-90) cc_final: 0.8611 (mtt-85) REVERT: H 33 ARG cc_start: 0.8664 (mtp85) cc_final: 0.8000 (mtp-110) REVERT: H 59 MET cc_start: 0.9289 (tpp) cc_final: 0.8985 (tpp) REVERT: H 120 LYS cc_start: 0.9107 (tptm) cc_final: 0.8727 (tptm) REVERT: C 56 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8170 (tm-30) REVERT: C 110 ASN cc_start: 0.8890 (t0) cc_final: 0.8458 (p0) REVERT: G 56 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8402 (tm-30) REVERT: G 64 GLU cc_start: 0.9287 (tm-30) cc_final: 0.8989 (tm-30) REVERT: G 91 GLU cc_start: 0.8229 (tp30) cc_final: 0.7776 (tp30) outliers start: 18 outliers final: 13 residues processed: 185 average time/residue: 0.2819 time to fit residues: 71.1633 Evaluate side-chains 185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 75 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.061198 restraints weight = 51906.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.063552 restraints weight = 22640.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.065139 restraints weight = 14386.278| |-----------------------------------------------------------------------------| r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13794 Z= 0.168 Angle : 0.570 9.052 19878 Z= 0.335 Chirality : 0.033 0.153 2261 Planarity : 0.004 0.036 1500 Dihedral : 29.758 161.964 4186 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.45 % Allowed : 18.21 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.74 (0.29), residues: 853 helix: 2.88 (0.21), residues: 575 sheet: 1.07 (1.33), residues: 17 loop : -0.68 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.024 0.001 TYR D 40 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd link_TRANS : bond 0.00007 ( 2) link_TRANS : angle 0.32057 ( 6) hydrogen bonds : bond 0.04355 ( 783) hydrogen bonds : angle 2.74009 ( 1959) covalent geometry : bond 0.00371 (13791) covalent geometry : angle 0.57048 (19872) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8671 (tpt90) cc_final: 0.8130 (tpt90) REVERT: B 85 ASP cc_start: 0.8826 (m-30) cc_final: 0.8528 (m-30) REVERT: D 47 GLN cc_start: 0.8390 (mt0) cc_final: 0.8134 (mt0) REVERT: D 51 ASP cc_start: 0.8200 (p0) cc_final: 0.7609 (p0) REVERT: D 57 LYS cc_start: 0.8905 (mmmt) cc_final: 0.8350 (mmtp) REVERT: D 86 ARG cc_start: 0.8898 (mmt-90) cc_final: 0.8616 (mtt-85) REVERT: F 35 ARG cc_start: 0.8918 (mtp85) cc_final: 0.8459 (mtt-85) REVERT: H 33 ARG cc_start: 0.8674 (mtp85) cc_final: 0.7997 (mtp-110) REVERT: H 59 MET cc_start: 0.9299 (tpp) cc_final: 0.8947 (tpp) REVERT: H 120 LYS cc_start: 0.9093 (tptm) cc_final: 0.8725 (ttmm) REVERT: C 56 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 110 ASN cc_start: 0.8926 (t0) cc_final: 0.8457 (p0) REVERT: G 56 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8394 (tm-30) REVERT: G 91 GLU cc_start: 0.8233 (tp30) cc_final: 0.7759 (tp30) outliers start: 18 outliers final: 13 residues processed: 181 average time/residue: 0.2824 time to fit residues: 70.4777 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 91 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 0.0470 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.097914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.061367 restraints weight = 51828.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.063732 restraints weight = 22496.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.065295 restraints weight = 14271.524| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2789 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2789 r_free = 0.2789 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2789 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 13794 Z= 0.187 Angle : 0.793 59.200 19878 Z= 0.492 Chirality : 0.034 0.350 2261 Planarity : 0.004 0.044 1500 Dihedral : 29.759 161.969 4186 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.77 % Allowed : 19.02 % Favored : 79.21 % Cbeta Deviations : 0.12 % 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: 2.72 (0.29), residues: 853 helix: 2.86 (0.21), residues: 575 sheet: 1.07 (1.32), residues: 17 loop : -0.68 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.022 0.001 TYR D 40 ARG 0.006 0.000 ARG C 29 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 2) link_TRANS : angle 0.32104 ( 6) hydrogen bonds : bond 0.04370 ( 783) hydrogen bonds : angle 2.76707 ( 1959) covalent geometry : bond 0.00399 (13791) covalent geometry : angle 0.79356 (19872) Misc. bond : bond 0.00024 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8683 (tpt90) cc_final: 0.8130 (tpt90) REVERT: B 85 ASP cc_start: 0.8840 (m-30) cc_final: 0.8538 (m-30) REVERT: D 47 GLN cc_start: 0.8403 (mt0) cc_final: 0.8143 (mt0) REVERT: D 51 ASP cc_start: 0.8233 (p0) cc_final: 0.7643 (p0) REVERT: D 57 LYS cc_start: 0.8912 (mmmt) cc_final: 0.8358 (mmtp) REVERT: D 86 ARG cc_start: 0.8894 (mmt-90) cc_final: 0.8607 (mtt-85) REVERT: F 35 ARG cc_start: 0.8921 (mtp85) cc_final: 0.8450 (mtt-85) REVERT: H 33 ARG cc_start: 0.8685 (mtp85) cc_final: 0.7985 (mtp-110) REVERT: H 59 MET cc_start: 0.9300 (tpp) cc_final: 0.8950 (tpp) REVERT: H 84 ASN cc_start: 0.8900 (t0) cc_final: 0.7783 (t0) REVERT: H 120 LYS cc_start: 0.9095 (tptm) cc_final: 0.8714 (ttmm) REVERT: C 56 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8184 (tm-30) REVERT: C 110 ASN cc_start: 0.8942 (t0) cc_final: 0.8461 (p0) REVERT: G 56 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8405 (tm-30) REVERT: G 64 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8988 (tm-30) REVERT: G 91 GLU cc_start: 0.8244 (tp30) cc_final: 0.7763 (tp30) outliers start: 13 outliers final: 13 residues processed: 176 average time/residue: 0.2867 time to fit residues: 69.2678 Evaluate side-chains 183 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 170 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 28 optimal weight: 0.0770 chunk 93 optimal weight: 0.2980 chunk 47 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.097878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.061963 restraints weight = 41494.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.064140 restraints weight = 19951.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.065574 restraints weight = 13384.503| |-----------------------------------------------------------------------------| r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 13794 Z= 0.187 Angle : 0.793 59.200 19878 Z= 0.492 Chirality : 0.034 0.350 2261 Planarity : 0.004 0.044 1500 Dihedral : 29.759 161.969 4186 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.77 % Allowed : 19.02 % Favored : 79.21 % Cbeta Deviations : 0.12 % 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: 2.72 (0.29), residues: 853 helix: 2.86 (0.21), residues: 575 sheet: 1.07 (1.32), residues: 17 loop : -0.68 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.022 0.001 TYR D 40 ARG 0.006 0.000 ARG C 29 Details of bonding type rmsd link_TRANS : bond 0.00010 ( 2) link_TRANS : angle 0.32104 ( 6) hydrogen bonds : bond 0.04370 ( 783) hydrogen bonds : angle 2.76707 ( 1959) covalent geometry : bond 0.00399 (13791) covalent geometry : angle 0.79356 (19872) Misc. bond : bond 0.00024 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4535.80 seconds wall clock time: 79 minutes 31.87 seconds (4771.87 seconds total)