Starting phenix.real_space_refine on Wed Jul 30 19:46:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txx_41708/07_2025/8txx_41708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txx_41708/07_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_41708/07_2025/8txx_41708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2025/8txx_41708.map" model { file = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_2025/8txx_41708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txx_41708/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 9.02, per 1000 atoms: 0.70 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: 3.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.72 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: 5.31 Time building geometry restraints manager: 4.11 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: 1.240 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: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 38.800 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.040 ------------------------------------------------------------------------------- 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 : 1.156 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: 0.4036 time to fit residues: 117.3221 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 : 1.126 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.097853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.060894 restraints weight = 44605.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.063125 restraints weight = 20982.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064644 restraints weight = 13918.144| |-----------------------------------------------------------------------------| r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 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 = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8680 (mmm) cc_final: 0.8143 (tpp) REVERT: B 27 GLN cc_start: 0.9229 (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: 0.8637 (mt0) cc_final: 0.8335 (mt0) REVERT: D 51 ASP cc_start: 0.8313 (p0) cc_final: 0.7840 (p0) REVERT: D 57 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8413 (mmtp) REVERT: D 86 ARG cc_start: 0.8990 (mmt-90) cc_final: 0.8763 (mtt-85) REVERT: F 24 ASP cc_start: 0.8012 (t0) cc_final: 0.7750 (t0) REVERT: F 88 TYR cc_start: 0.8757 (m-80) cc_final: 0.8429 (m-80) REVERT: H 33 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8045 (mtp-110) REVERT: C 56 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8303 (tm-30) REVERT: C 110 ASN cc_start: 0.8939 (t0) cc_final: 0.8355 (p0) REVERT: G 76 THR cc_start: 0.9141 (p) cc_final: 0.8638 (t) outliers start: 19 outliers final: 15 residues processed: 190 average time/residue: 0.2982 time to fit residues: 78.6432 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 : 0.973 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 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 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 = 0.3442 r_free = 0.3442 target = 0.098904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.062911 restraints weight = 36149.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.064906 restraints weight = 18484.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066377 restraints weight = 12890.702| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.165 Angle : 0.539 5.962 19878 Z= 0.322 Chirality : 0.033 0.144 2261 Planarity : 0.004 0.042 1500 Dihedral : 29.622 158.466 4186 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.17 % Allowed : 14.13 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.30), residues: 853 helix: 2.84 (0.22), residues: 574 sheet: 1.27 (1.38), residues: 17 loop : -0.42 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 82 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 0.00068 ( 2) link_TRANS : angle 0.38419 ( 6) hydrogen bonds : bond 0.04436 ( 783) hydrogen bonds : angle 2.79930 ( 1959) covalent geometry : bond 0.00361 (13791) covalent geometry : angle 0.53857 (19872) Misc. bond : bond 0.00005 ( 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 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8103 (tt0) cc_final: 0.7884 (tt0) REVERT: A 90 MET cc_start: 0.8654 (mmm) cc_final: 0.8124 (tpp) REVERT: B 85 ASP cc_start: 0.8793 (m-30) cc_final: 0.8507 (m-30) REVERT: D 42 TYR cc_start: 0.8135 (t80) cc_final: 0.7354 (t80) REVERT: D 46 LYS cc_start: 0.9318 (mmtt) cc_final: 0.8910 (mmtp) REVERT: D 47 GLN cc_start: 0.8463 (mt0) cc_final: 0.8148 (mt0) REVERT: D 51 ASP cc_start: 0.8257 (p0) cc_final: 0.7763 (p0) REVERT: D 57 LYS cc_start: 0.8891 (mmmm) cc_final: 0.8521 (mmtp) REVERT: D 85 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8964 (mtmm) REVERT: D 86 ARG cc_start: 0.8945 (mmt-90) cc_final: 0.8677 (mtt-85) REVERT: D 105 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8082 (mm-30) REVERT: E 76 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8538 (tm-30) REVERT: F 24 ASP cc_start: 0.7860 (t0) cc_final: 0.7591 (t0) REVERT: F 88 TYR cc_start: 0.8730 (m-80) cc_final: 0.8380 (m-80) REVERT: H 33 ARG cc_start: 0.8623 (mtp85) cc_final: 0.8011 (mtp-110) REVERT: H 120 LYS cc_start: 0.9073 (tptm) cc_final: 0.8736 (tptm) REVERT: C 56 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8174 (tm-30) REVERT: C 110 ASN cc_start: 0.8892 (t0) cc_final: 0.8364 (p0) REVERT: G 64 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 76 THR cc_start: 0.9119 (p) cc_final: 0.8592 (t) outliers start: 16 outliers final: 12 residues processed: 185 average time/residue: 0.3221 time to fit residues: 81.7782 Evaluate side-chains 179 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.028 ------------------------------------------------------------------------------- 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 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 F residue 63 GLU Chi-restraints excluded: chain H residue 84 ASN 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: 3.9990 chunk 84 optimal weight: 30.0000 chunk 31 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 107 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 82 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** H 84 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.098809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.062598 restraints weight = 41872.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.064673 restraints weight = 21309.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.065936 restraints weight = 14660.945| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2817 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2817 r_free = 0.2817 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2817 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.162 Angle : 0.538 8.502 19878 Z= 0.321 Chirality : 0.033 0.152 2261 Planarity : 0.003 0.040 1500 Dihedral : 29.628 158.636 4186 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.53 % Allowed : 14.54 % Favored : 81.93 % 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: 2.79 (0.30), residues: 853 helix: 2.85 (0.22), residues: 575 sheet: 1.24 (1.37), residues: 17 loop : -0.48 (0.39), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE A 67 TYR 0.017 0.001 TYR H 40 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00017 ( 2) link_TRANS : angle 0.29746 ( 6) hydrogen bonds : bond 0.04370 ( 783) hydrogen bonds : angle 2.74190 ( 1959) covalent geometry : bond 0.00355 (13791) covalent geometry : angle 0.53845 (19872) Misc. bond : bond 0.00004 ( 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 203 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8040 (tt0) cc_final: 0.7809 (tt0) REVERT: B 85 ASP cc_start: 0.8793 (m-30) cc_final: 0.8497 (m-30) REVERT: D 35 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8328 (tp30) REVERT: D 42 TYR cc_start: 0.8116 (t80) cc_final: 0.7332 (t80) REVERT: D 46 LYS cc_start: 0.9324 (mmtt) cc_final: 0.8877 (mmtp) REVERT: D 47 GLN cc_start: 0.8422 (mt0) cc_final: 0.8114 (mt0) REVERT: D 51 ASP cc_start: 0.8225 (p0) cc_final: 0.7765 (p0) REVERT: D 85 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8974 (mtmm) REVERT: D 86 ARG cc_start: 0.8921 (mmt-90) cc_final: 0.8683 (mtt-85) REVERT: E 105 GLU cc_start: 0.7915 (tt0) cc_final: 0.7687 (tt0) REVERT: F 24 ASP cc_start: 0.7841 (t0) cc_final: 0.7592 (t0) REVERT: F 88 TYR cc_start: 0.8692 (m-80) cc_final: 0.8326 (m-80) REVERT: H 33 ARG cc_start: 0.8625 (mtp85) cc_final: 0.8036 (mtp-110) REVERT: H 120 LYS cc_start: 0.9143 (tptm) cc_final: 0.8809 (tptm) REVERT: C 110 ASN cc_start: 0.8871 (t0) cc_final: 0.8409 (p0) REVERT: G 76 THR cc_start: 0.9142 (p) cc_final: 0.8611 (t) REVERT: G 91 GLU cc_start: 0.8128 (tp30) cc_final: 0.7720 (tp30) outliers start: 26 outliers final: 21 residues processed: 192 average time/residue: 0.2982 time to fit residues: 79.2083 Evaluate side-chains 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 165 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 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 112 ILE Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 84 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 45 optimal weight: 0.0000 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: 0.7980 chunk 109 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 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 = 0.3440 r_free = 0.3440 target = 0.098678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.064335 restraints weight = 47319.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.065797 restraints weight = 23800.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.066532 restraints weight = 15469.527| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2816 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2816 r_free = 0.2816 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2816 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.166 Angle : 0.544 7.479 19878 Z= 0.322 Chirality : 0.033 0.157 2261 Planarity : 0.003 0.038 1500 Dihedral : 29.636 158.830 4186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.26 % Allowed : 14.95 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.82 (0.29), residues: 853 helix: 2.90 (0.21), residues: 575 sheet: 1.12 (1.34), residues: 17 loop : -0.54 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 82 PHE 0.006 0.001 PHE H 70 TYR 0.016 0.001 TYR D 40 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00015 ( 2) link_TRANS : angle 0.28232 ( 6) hydrogen bonds : bond 0.04392 ( 783) hydrogen bonds : angle 2.76140 ( 1959) covalent geometry : bond 0.00366 (13791) covalent geometry : angle 0.54369 (19872) Misc. bond : bond 0.00000 ( 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 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8091 (tt0) cc_final: 0.7855 (tt0) REVERT: A 90 MET cc_start: 0.8633 (mmm) cc_final: 0.8127 (tpp) REVERT: A 108 ASN cc_start: 0.9396 (t0) cc_final: 0.9190 (t0) REVERT: B 85 ASP cc_start: 0.8801 (m-30) cc_final: 0.8498 (m-30) REVERT: D 42 TYR cc_start: 0.8097 (t80) cc_final: 0.7182 (t80) REVERT: D 47 GLN cc_start: 0.8415 (mt0) cc_final: 0.8085 (mt0) REVERT: D 51 ASP cc_start: 0.8141 (p0) cc_final: 0.7699 (p0) REVERT: D 85 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.9005 (mtmm) REVERT: D 86 ARG cc_start: 0.8917 (mmt-90) cc_final: 0.8689 (mtt-85) REVERT: E 59 GLU cc_start: 0.8646 (pm20) cc_final: 0.8342 (pm20) REVERT: E 105 GLU cc_start: 0.7905 (tt0) cc_final: 0.7661 (tt0) REVERT: F 24 ASP cc_start: 0.7854 (t0) cc_final: 0.7627 (t0) REVERT: H 33 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8016 (mtp-110) REVERT: H 120 LYS cc_start: 0.9114 (tptm) cc_final: 0.8804 (tptm) REVERT: C 110 ASN cc_start: 0.8871 (t0) cc_final: 0.8398 (p0) REVERT: G 64 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9026 (tm-30) REVERT: G 76 THR cc_start: 0.9182 (p) cc_final: 0.8653 (t) REVERT: G 91 GLU cc_start: 0.8177 (tp30) cc_final: 0.7746 (tp30) outliers start: 24 outliers final: 20 residues processed: 186 average time/residue: 0.2997 time to fit residues: 76.4267 Evaluate side-chains 184 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 163 time to evaluate : 1.012 ------------------------------------------------------------------------------- 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 110 CYS 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 F residue 63 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 85 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 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 = 0.3445 r_free = 0.3445 target = 0.098988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.064755 restraints weight = 46749.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.066091 restraints weight = 23813.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.067170 restraints weight = 15040.465| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2821 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2821 r_free = 0.2821 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2821 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.164 Angle : 0.543 8.971 19878 Z= 0.322 Chirality : 0.033 0.165 2261 Planarity : 0.003 0.039 1500 Dihedral : 29.627 158.883 4186 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.26 % Allowed : 14.95 % Favored : 81.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.85 (0.30), residues: 853 helix: 2.94 (0.21), residues: 575 sheet: 1.05 (1.33), residues: 17 loop : -0.57 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE C 25 TYR 0.020 0.001 TYR H 40 ARG 0.005 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00019 ( 2) link_TRANS : angle 0.30199 ( 6) hydrogen bonds : bond 0.04344 ( 783) hydrogen bonds : angle 2.73604 ( 1959) covalent geometry : bond 0.00359 (13791) covalent geometry : angle 0.54338 (19872) Misc. bond : bond 0.00002 ( 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 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8099 (tt0) cc_final: 0.7867 (tt0) REVERT: A 125 GLN cc_start: 0.8439 (mt0) cc_final: 0.8224 (mt0) REVERT: A 129 ARG cc_start: 0.8548 (tpt90) cc_final: 0.8080 (tpt90) REVERT: B 85 ASP cc_start: 0.8792 (m-30) cc_final: 0.8479 (m-30) REVERT: D 42 TYR cc_start: 0.8136 (t80) cc_final: 0.7385 (t80) REVERT: D 46 LYS cc_start: 0.9312 (mmtt) cc_final: 0.9040 (mmtp) REVERT: D 47 GLN cc_start: 0.8489 (mt0) cc_final: 0.8174 (mt0) REVERT: D 51 ASP cc_start: 0.8097 (p0) cc_final: 0.7467 (p0) REVERT: D 85 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.9051 (mtmm) REVERT: D 86 ARG cc_start: 0.8913 (mmt-90) cc_final: 0.8672 (mtt-85) REVERT: H 33 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8016 (mtp-110) REVERT: H 120 LYS cc_start: 0.9103 (tptm) cc_final: 0.8560 (ttpp) REVERT: C 110 ASN cc_start: 0.8888 (t0) cc_final: 0.8380 (p0) REVERT: G 24 GLN cc_start: 0.9005 (mm-40) cc_final: 0.8792 (mm-40) REVERT: G 76 THR cc_start: 0.9200 (p) cc_final: 0.8676 (t) REVERT: G 91 GLU cc_start: 0.8098 (tp30) cc_final: 0.7665 (tp30) outliers start: 24 outliers final: 18 residues processed: 186 average time/residue: 0.2936 time to fit residues: 74.8768 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 169 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS 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 F residue 63 GLU 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 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: 0.8980 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.0980 chunk 16 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.099467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.065321 restraints weight = 46619.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.066823 restraints weight = 23248.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067641 restraints weight = 14964.878| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1813 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= 0.157 Angle : 0.541 9.155 19878 Z= 0.321 Chirality : 0.033 0.162 2261 Planarity : 0.003 0.038 1500 Dihedral : 29.608 158.825 4186 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.26 % Allowed : 15.35 % Favored : 81.39 % 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: 2.89 (0.30), residues: 853 helix: 2.98 (0.21), residues: 575 sheet: 1.07 (1.33), residues: 17 loop : -0.56 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE H 70 TYR 0.016 0.001 TYR H 40 ARG 0.003 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00037 ( 2) link_TRANS : angle 0.29506 ( 6) hydrogen bonds : bond 0.04249 ( 783) hydrogen bonds : angle 2.68008 ( 1959) covalent geometry : bond 0.00341 (13791) covalent geometry : angle 0.54151 (19872) Misc. bond : bond 0.00006 ( 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 200 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 1.112 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8094 (tt0) cc_final: 0.7868 (tt0) REVERT: A 107 THR cc_start: 0.9560 (OUTLIER) cc_final: 0.9336 (t) REVERT: A 125 GLN cc_start: 0.8444 (mt0) cc_final: 0.8191 (mt0) REVERT: A 129 ARG cc_start: 0.8545 (tpt90) cc_final: 0.8079 (tpt90) REVERT: B 85 ASP cc_start: 0.8759 (m-30) cc_final: 0.8388 (m-30) REVERT: D 42 TYR cc_start: 0.8115 (t80) cc_final: 0.7351 (t80) REVERT: D 46 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8933 (mmtp) REVERT: D 47 GLN cc_start: 0.8458 (mt0) cc_final: 0.8159 (mt0) REVERT: D 51 ASP cc_start: 0.8137 (p0) cc_final: 0.7667 (p0) REVERT: D 85 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9056 (mtmm) REVERT: D 86 ARG cc_start: 0.8894 (mmt-90) cc_final: 0.8663 (mtt-85) REVERT: H 33 ARG cc_start: 0.8600 (mtp85) cc_final: 0.7993 (mtp-110) REVERT: H 59 MET cc_start: 0.9267 (tpp) cc_final: 0.8968 (tpp) REVERT: H 120 LYS cc_start: 0.9102 (tptm) cc_final: 0.8566 (ttpp) REVERT: C 110 ASN cc_start: 0.8882 (t0) cc_final: 0.8380 (p0) REVERT: G 63 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9213 (mm) REVERT: G 64 GLU cc_start: 0.9257 (tm-30) cc_final: 0.9009 (tm-30) REVERT: G 76 THR cc_start: 0.9183 (p) cc_final: 0.8661 (t) REVERT: G 91 GLU cc_start: 0.8167 (tp30) cc_final: 0.7718 (tp30) outliers start: 24 outliers final: 18 residues processed: 191 average time/residue: 0.2927 time to fit residues: 77.2605 Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 26 ILE 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 H residue 101 LEU Chi-restraints excluded: chain K residue 449 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 Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 27 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- 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 = 0.3471 r_free = 0.3471 target = 0.100588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.064828 restraints weight = 40203.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.066745 restraints weight = 20651.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.068040 restraints weight = 14332.442| |-----------------------------------------------------------------------------| r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2851 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1952 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= 0.146 Angle : 0.540 9.673 19878 Z= 0.320 Chirality : 0.032 0.159 2261 Planarity : 0.003 0.038 1500 Dihedral : 29.547 158.592 4186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.85 % Allowed : 16.58 % Favored : 80.57 % 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: 2.94 (0.30), residues: 853 helix: 3.00 (0.21), residues: 575 sheet: 1.09 (1.33), residues: 17 loop : -0.52 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 75 PHE 0.006 0.001 PHE E 67 TYR 0.014 0.001 TYR H 40 ARG 0.004 0.000 ARG A 116 Details of bonding type rmsd link_TRANS : bond 0.00069 ( 2) link_TRANS : angle 0.32500 ( 6) hydrogen bonds : bond 0.04020 ( 783) hydrogen bonds : angle 2.61176 ( 1959) covalent geometry : bond 0.00312 (13791) covalent geometry : angle 0.53974 (19872) Misc. bond : bond 0.00012 ( 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 198 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 177 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9542 (OUTLIER) cc_final: 0.9310 (t) REVERT: A 125 GLN cc_start: 0.8384 (mt0) cc_final: 0.8096 (mt0) REVERT: A 129 ARG cc_start: 0.8400 (tpt90) cc_final: 0.7941 (tpt90) REVERT: B 25 ASN cc_start: 0.8750 (t0) cc_final: 0.8543 (t0) REVERT: B 85 ASP cc_start: 0.8755 (m-30) cc_final: 0.8398 (m-30) REVERT: D 42 TYR cc_start: 0.8055 (t80) cc_final: 0.7275 (t80) REVERT: D 46 LYS cc_start: 0.9314 (mmtt) cc_final: 0.8921 (mmtp) REVERT: D 47 GLN cc_start: 0.8420 (mt0) cc_final: 0.8157 (mt0) REVERT: D 51 ASP cc_start: 0.8133 (p0) cc_final: 0.7540 (p0) REVERT: D 85 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9032 (mtmm) REVERT: D 86 ARG cc_start: 0.8869 (mmt-90) cc_final: 0.8636 (mtt-85) REVERT: H 33 ARG cc_start: 0.8610 (mtp85) cc_final: 0.7993 (mtp-110) REVERT: H 120 LYS cc_start: 0.9105 (tptm) cc_final: 0.8564 (ttpp) REVERT: C 110 ASN cc_start: 0.8860 (t0) cc_final: 0.8400 (p0) REVERT: G 64 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9000 (tm-30) REVERT: G 76 THR cc_start: 0.9146 (p) cc_final: 0.8623 (t) REVERT: G 91 GLU cc_start: 0.8149 (tp30) cc_final: 0.7700 (tp30) outliers start: 21 outliers final: 16 residues processed: 188 average time/residue: 0.2864 time to fit residues: 74.3078 Evaluate side-chains 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS 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 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 57 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain K residue 449 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 Chi-restraints excluded: chain G residue 15 LYS 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: 0.9990 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 27 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 C 24 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.099917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.066021 restraints weight = 51753.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.068409 restraints weight = 25370.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.069432 restraints weight = 13842.201| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13794 Z= 0.160 Angle : 0.550 9.270 19878 Z= 0.324 Chirality : 0.033 0.155 2261 Planarity : 0.003 0.037 1500 Dihedral : 29.603 158.925 4186 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.85 % Allowed : 16.44 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.89 (0.29), residues: 853 helix: 2.98 (0.21), residues: 575 sheet: 1.09 (1.33), residues: 17 loop : -0.57 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE H 70 TYR 0.014 0.001 TYR H 40 ARG 0.004 0.000 ARG F 67 Details of bonding type rmsd link_TRANS : bond 0.00027 ( 2) link_TRANS : angle 0.28121 ( 6) hydrogen bonds : bond 0.04212 ( 783) hydrogen bonds : angle 2.66748 ( 1959) covalent geometry : bond 0.00350 (13791) covalent geometry : angle 0.54992 (19872) Misc. bond : bond 0.00010 ( 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 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 173 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 THR cc_start: 0.9564 (OUTLIER) cc_final: 0.9350 (t) REVERT: A 125 GLN cc_start: 0.8337 (mt0) cc_final: 0.8095 (mt0) REVERT: A 129 ARG cc_start: 0.8523 (tpt90) cc_final: 0.8003 (tpt90) REVERT: B 85 ASP cc_start: 0.8784 (m-30) cc_final: 0.8478 (m-30) REVERT: D 42 TYR cc_start: 0.8101 (t80) cc_final: 0.7312 (t80) REVERT: D 46 LYS cc_start: 0.9321 (mmtt) cc_final: 0.8923 (mmtp) REVERT: D 47 GLN cc_start: 0.8486 (mt0) cc_final: 0.8231 (mt0) REVERT: D 51 ASP cc_start: 0.8100 (p0) cc_final: 0.7481 (p0) REVERT: D 85 LYS cc_start: 0.9268 (OUTLIER) cc_final: 0.9065 (mtmm) REVERT: D 86 ARG cc_start: 0.8901 (mmt-90) cc_final: 0.8671 (mtt-85) REVERT: E 76 GLN cc_start: 0.8779 (tm-30) cc_final: 0.8544 (tm-30) REVERT: E 120 MET cc_start: 0.8065 (tpp) cc_final: 0.7431 (mmt) REVERT: H 33 ARG cc_start: 0.8599 (mtp85) cc_final: 0.7988 (mtp-110) REVERT: H 59 MET cc_start: 0.9276 (tpp) cc_final: 0.8967 (tpp) REVERT: H 120 LYS cc_start: 0.9114 (tptm) cc_final: 0.8783 (tptm) REVERT: C 110 ASN cc_start: 0.8828 (t0) cc_final: 0.8367 (p0) REVERT: G 64 GLU cc_start: 0.9311 (tm-30) cc_final: 0.9053 (tm-30) REVERT: G 76 THR cc_start: 0.9186 (p) cc_final: 0.8657 (t) REVERT: G 91 GLU cc_start: 0.8141 (tp30) cc_final: 0.7699 (tp30) outliers start: 21 outliers final: 17 residues processed: 184 average time/residue: 0.3631 time to fit residues: 92.9595 Evaluate side-chains 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.340 ------------------------------------------------------------------------------- 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 107 THR Chi-restraints excluded: chain A residue 110 CYS 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 K residue 449 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 Chi-restraints excluded: chain G residue 15 LYS 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 91 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 84 optimal weight: 0.0050 chunk 46 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.098331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.064044 restraints weight = 51929.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.065321 restraints weight = 24815.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.066258 restraints weight = 16263.811| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 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 = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13794 Z= 0.189 Angle : 0.576 9.346 19878 Z= 0.337 Chirality : 0.034 0.146 2261 Planarity : 0.004 0.037 1500 Dihedral : 29.717 159.379 4186 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.58 % Allowed : 16.98 % Favored : 80.43 % 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: 2.79 (0.29), residues: 853 helix: 2.90 (0.22), residues: 575 sheet: 1.05 (1.31), residues: 17 loop : -0.62 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.012 0.001 PHE C 25 TYR 0.028 0.001 TYR D 40 ARG 0.006 0.000 ARG C 29 Details of bonding type rmsd link_TRANS : bond 0.00043 ( 2) link_TRANS : angle 0.30508 ( 6) hydrogen bonds : bond 0.04609 ( 783) hydrogen bonds : angle 2.80762 ( 1959) covalent geometry : bond 0.00428 (13791) covalent geometry : angle 0.57639 (19872) Misc. bond : bond 0.00006 ( 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 187 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8353 (mt0) cc_final: 0.8038 (mt0) REVERT: A 129 ARG cc_start: 0.8668 (tpt90) cc_final: 0.8131 (tpt90) REVERT: B 85 ASP cc_start: 0.8799 (m-30) cc_final: 0.8494 (m-30) REVERT: D 42 TYR cc_start: 0.8160 (t80) cc_final: 0.7188 (t80) REVERT: D 47 GLN cc_start: 0.8342 (mt0) cc_final: 0.7994 (mt0) REVERT: D 51 ASP cc_start: 0.8127 (p0) cc_final: 0.7521 (p0) REVERT: D 85 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.9046 (mtmm) REVERT: D 86 ARG cc_start: 0.8910 (mmt-90) cc_final: 0.8674 (mtt-85) REVERT: E 57 SER cc_start: 0.9120 (t) cc_final: 0.8911 (p) REVERT: E 120 MET cc_start: 0.8201 (tpp) cc_final: 0.7634 (mmt) REVERT: H 33 ARG cc_start: 0.8637 (mtp85) cc_final: 0.8040 (mtp-110) REVERT: H 120 LYS cc_start: 0.9109 (tptm) cc_final: 0.8753 (tptm) REVERT: C 56 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8175 (tm-30) REVERT: C 110 ASN cc_start: 0.8886 (t0) cc_final: 0.8354 (p0) REVERT: G 24 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8331 (mm-40) REVERT: G 56 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8350 (tm-30) REVERT: G 76 THR cc_start: 0.9233 (p) cc_final: 0.8799 (t) REVERT: G 91 GLU cc_start: 0.8174 (tp30) cc_final: 0.7876 (tp30) outliers start: 19 outliers final: 14 residues processed: 178 average time/residue: 0.2952 time to fit residues: 72.1475 Evaluate side-chains 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 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 90 MET Chi-restraints excluded: chain K residue 449 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 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: 0.9990 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 8 optimal weight: 0.0370 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 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 = 0.3460 r_free = 0.3460 target = 0.099842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.064090 restraints weight = 41392.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066170 restraints weight = 21016.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.067396 restraints weight = 14435.226| |-----------------------------------------------------------------------------| r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2830 r_free = 0.2830 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13794 Z= 0.153 Angle : 0.554 9.571 19878 Z= 0.326 Chirality : 0.033 0.144 2261 Planarity : 0.003 0.038 1500 Dihedral : 29.596 158.991 4186 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.90 % Allowed : 17.93 % Favored : 80.16 % 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: 2.83 (0.29), residues: 853 helix: 2.93 (0.21), residues: 575 sheet: 1.18 (1.33), residues: 17 loop : -0.60 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.006 0.001 PHE C 25 TYR 0.013 0.001 TYR D 40 ARG 0.005 0.000 ARG F 67 Details of bonding type rmsd link_TRANS : bond 0.00054 ( 2) link_TRANS : angle 0.31910 ( 6) hydrogen bonds : bond 0.04131 ( 783) hydrogen bonds : angle 2.64920 ( 1959) covalent geometry : bond 0.00334 (13791) covalent geometry : angle 0.55415 (19872) Misc. bond : bond 0.00057 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4718.98 seconds wall clock time: 84 minutes 34.00 seconds (5074.00 seconds total)