Starting phenix.real_space_refine on Mon Dec 30 08:52:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txx_41708/12_2024/8txx_41708.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txx_41708/12_2024/8txx_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_41708/12_2024/8txx_41708.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txx_41708/12_2024/8txx_41708.map" model { file = "/net/cci-nas-00/data/ceres_data/8txx_41708/12_2024/8txx_41708.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txx_41708/12_2024/8txx_41708.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 15 5.16 5 C 7227 2.51 5 N 2431 2.21 5 O 3002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 8.21, per 1000 atoms: 0.63 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: 3.20 Conformation dependent library (CDL) restraints added in 1.1 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: 5.57 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.724A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 4.169A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.090A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.647A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.668A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.581A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.687A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.538A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.121A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.506A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 447 through 461 Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 56 through 60 Processing helix chain 'M' and resid 71 through 75 removed outlier: 3.745A pdb=" N ARG M 74 " --> pdb=" O LEU M 71 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY M 75 " --> pdb=" O ARG M 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 71 through 75' Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.521A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 38 removed outlier: 3.608A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.681A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.477A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.597A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.297A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 Processing sheet with id=AB3, first strand: chain 'M' and resid 44 through 45 435 hydrogen bonds defined for protein. 1267 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 692 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 242 stacking parallelities Total time for adding SS restraints: 4.85 Time building geometry restraints manager: 3.77 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.140 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.880 ------------------------------------------------------------------------------- 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 0.041 13791 Z= 0.196 Angle : 0.551 6.929 19872 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 *********************** 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 : 1.003 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: 0.3242 time to fit residues: 94.4382 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 : 1.011 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 13791 Z= 0.266 Angle : 0.574 5.804 19872 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 *********************** 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 : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8726 (mmm) cc_final: 0.8185 (tpp) REVERT: B 27 GLN cc_start: 0.9265 (mm-40) cc_final: 0.8995 (mp10) REVERT: B 85 ASP cc_start: 0.8909 (m-30) cc_final: 0.8693 (m-30) REVERT: D 47 GLN cc_start: 0.8690 (mt0) cc_final: 0.8391 (mt0) REVERT: D 51 ASP cc_start: 0.8515 (p0) cc_final: 0.8076 (p0) REVERT: D 57 LYS cc_start: 0.8900 (mmmm) cc_final: 0.8415 (mmtp) REVERT: D 86 ARG cc_start: 0.9056 (mmt-90) cc_final: 0.8806 (mtt-85) REVERT: F 24 ASP cc_start: 0.8191 (t0) cc_final: 0.7917 (t0) REVERT: F 88 TYR cc_start: 0.8709 (m-80) cc_final: 0.8342 (m-80) REVERT: H 33 ARG cc_start: 0.8698 (mtp85) cc_final: 0.8000 (mtp-110) REVERT: C 56 GLU cc_start: 0.8948 (tm-30) cc_final: 0.8365 (tm-30) REVERT: C 110 ASN cc_start: 0.9011 (t0) cc_final: 0.8380 (p0) REVERT: G 76 THR cc_start: 0.9112 (p) cc_final: 0.8619 (t) outliers start: 19 outliers final: 15 residues processed: 190 average time/residue: 0.2909 time to fit residues: 76.1633 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 : 1.192 ------------------------------------------------------------------------------- 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 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 108 optimal weight: 0.5980 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13791 Z= 0.315 Angle : 0.593 7.052 19872 Z= 0.349 Chirality : 0.036 0.163 2261 Planarity : 0.004 0.045 1500 Dihedral : 29.870 159.698 4186 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.40 % Allowed : 13.32 % Favored : 83.29 % 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: 2.59 (0.29), residues: 853 helix: 2.65 (0.21), residues: 576 sheet: 1.13 (1.36), residues: 17 loop : -0.44 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE H 70 TYR 0.017 0.002 TYR H 40 ARG 0.003 0.000 ARG D 31 *********************** 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 195 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9020 (mt) cc_final: 0.8742 (mt) REVERT: A 73 GLU cc_start: 0.8117 (tt0) cc_final: 0.7838 (tt0) REVERT: A 90 MET cc_start: 0.8836 (mmm) cc_final: 0.8408 (tpp) REVERT: B 43 VAL cc_start: 0.9654 (t) cc_final: 0.9390 (p) REVERT: B 85 ASP cc_start: 0.8876 (m-30) cc_final: 0.8593 (m-30) REVERT: D 47 GLN cc_start: 0.8632 (mt0) cc_final: 0.8310 (mt0) REVERT: D 51 ASP cc_start: 0.8564 (p0) cc_final: 0.8142 (p0) REVERT: D 57 LYS cc_start: 0.8936 (mmmm) cc_final: 0.8495 (mmtp) REVERT: D 85 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.9037 (mtmm) REVERT: D 86 ARG cc_start: 0.9045 (mmt-90) cc_final: 0.8756 (mtt-85) REVERT: D 105 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8331 (mm-30) REVERT: E 105 GLU cc_start: 0.8071 (tt0) cc_final: 0.7831 (tt0) REVERT: F 88 TYR cc_start: 0.8659 (m-80) cc_final: 0.8157 (m-80) REVERT: H 33 ARG cc_start: 0.8719 (mtp85) cc_final: 0.7978 (mtp-110) REVERT: H 120 LYS cc_start: 0.9099 (tptm) cc_final: 0.8506 (ttpp) REVERT: C 56 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 110 ASN cc_start: 0.9006 (t0) cc_final: 0.8387 (p0) REVERT: G 76 THR cc_start: 0.9153 (p) cc_final: 0.8748 (t) REVERT: G 91 GLU cc_start: 0.8367 (tp30) cc_final: 0.8024 (tp30) outliers start: 25 outliers final: 21 residues processed: 184 average time/residue: 0.3123 time to fit residues: 79.0632 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain H residue 84 ASN Chi-restraints excluded: chain H residue 101 LEU 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 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 0.3980 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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** B 93 GLN D 49 HIS D 95 GLN H 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13791 Z= 0.206 Angle : 0.546 6.422 19872 Z= 0.326 Chirality : 0.034 0.150 2261 Planarity : 0.003 0.039 1500 Dihedral : 29.711 159.635 4186 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.85 % Allowed : 15.62 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.30), residues: 853 helix: 2.80 (0.22), residues: 574 sheet: 0.99 (1.32), residues: 17 loop : -0.55 (0.38), residues: 262 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 0.018 0.001 TYR H 40 ARG 0.002 0.000 ARG D 99 *********************** 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 197 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8969 (mt) cc_final: 0.8747 (mt) REVERT: A 90 MET cc_start: 0.8764 (mmm) cc_final: 0.8258 (tpp) REVERT: B 85 ASP cc_start: 0.8860 (m-30) cc_final: 0.8549 (m-30) REVERT: D 46 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8699 (mmtm) REVERT: D 47 GLN cc_start: 0.8570 (mt0) cc_final: 0.8247 (mt0) REVERT: D 51 ASP cc_start: 0.8513 (p0) cc_final: 0.8133 (p0) REVERT: D 85 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9107 (mtmm) REVERT: D 86 ARG cc_start: 0.8986 (mmt-90) cc_final: 0.8709 (mtt-85) REVERT: E 59 GLU cc_start: 0.8777 (pm20) cc_final: 0.8571 (pm20) REVERT: E 105 GLU cc_start: 0.8072 (tt0) cc_final: 0.7812 (tt0) REVERT: H 33 ARG cc_start: 0.8706 (mtp85) cc_final: 0.7981 (mtp-110) REVERT: H 120 LYS cc_start: 0.9092 (tptm) cc_final: 0.8473 (ttpp) REVERT: C 56 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8265 (tm-30) REVERT: C 110 ASN cc_start: 0.9034 (t0) cc_final: 0.8435 (p0) REVERT: G 36 LYS cc_start: 0.8995 (tppt) cc_final: 0.8707 (tppt) REVERT: G 64 GLU cc_start: 0.9338 (tm-30) cc_final: 0.9024 (tm-30) REVERT: G 76 THR cc_start: 0.9140 (p) cc_final: 0.8713 (t) REVERT: G 91 GLU cc_start: 0.8243 (tp30) cc_final: 0.7771 (tp30) outliers start: 21 outliers final: 15 residues processed: 186 average time/residue: 0.3053 time to fit residues: 79.0226 Evaluate side-chains 180 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 84 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13791 Z= 0.416 Angle : 0.643 9.369 19872 Z= 0.374 Chirality : 0.038 0.159 2261 Planarity : 0.004 0.047 1500 Dihedral : 30.056 161.660 4186 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.80 % Allowed : 15.22 % Favored : 80.98 % 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: 2.37 (0.29), residues: 853 helix: 2.56 (0.21), residues: 577 sheet: 0.71 (1.29), residues: 17 loop : -0.73 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 49 PHE 0.007 0.001 PHE H 70 TYR 0.018 0.002 TYR H 40 ARG 0.003 0.000 ARG D 31 *********************** 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 191 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8916 (mmm) cc_final: 0.8492 (tpp) REVERT: B 85 ASP cc_start: 0.8902 (m-30) cc_final: 0.8587 (m-30) REVERT: D 46 LYS cc_start: 0.9226 (mmtt) cc_final: 0.8796 (mmtm) REVERT: D 47 GLN cc_start: 0.8726 (mt0) cc_final: 0.8325 (mt0) REVERT: D 51 ASP cc_start: 0.8552 (p0) cc_final: 0.8013 (p0) REVERT: D 85 LYS cc_start: 0.9351 (OUTLIER) cc_final: 0.9138 (mtmm) REVERT: E 59 GLU cc_start: 0.8791 (pm20) cc_final: 0.8514 (pm20) REVERT: E 105 GLU cc_start: 0.8176 (tt0) cc_final: 0.7922 (tt0) REVERT: H 33 ARG cc_start: 0.8755 (mtp85) cc_final: 0.7985 (mtp-110) REVERT: H 71 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8324 (tm-30) REVERT: H 120 LYS cc_start: 0.9142 (tptm) cc_final: 0.8704 (ttmm) REVERT: C 56 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 110 ASN cc_start: 0.8970 (t0) cc_final: 0.8341 (p0) REVERT: G 76 THR cc_start: 0.9213 (p) cc_final: 0.8794 (t) REVERT: G 91 GLU cc_start: 0.8373 (tp30) cc_final: 0.8023 (tp30) outliers start: 28 outliers final: 20 residues processed: 181 average time/residue: 0.3076 time to fit residues: 76.3030 Evaluate side-chains 182 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 161 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 B residue 30 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 85 LYS Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13791 Z= 0.210 Angle : 0.558 8.216 19872 Z= 0.332 Chirality : 0.033 0.155 2261 Planarity : 0.004 0.042 1500 Dihedral : 29.817 161.554 4186 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.12 % Allowed : 16.03 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.62 (0.30), residues: 853 helix: 2.79 (0.22), residues: 575 sheet: 0.73 (1.28), residues: 17 loop : -0.70 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.019 0.001 TYR H 40 ARG 0.003 0.000 ARG A 116 *********************** 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 201 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8979 (mt) cc_final: 0.8773 (mt) REVERT: A 90 MET cc_start: 0.8773 (mmm) cc_final: 0.8343 (tpp) REVERT: A 125 GLN cc_start: 0.8686 (mt0) cc_final: 0.8385 (mt0) REVERT: B 85 ASP cc_start: 0.8852 (m-30) cc_final: 0.8546 (m-30) REVERT: D 42 TYR cc_start: 0.8133 (t80) cc_final: 0.7321 (t80) REVERT: D 46 LYS cc_start: 0.9227 (mmtt) cc_final: 0.8825 (mmtp) REVERT: D 47 GLN cc_start: 0.8565 (mt0) cc_final: 0.8176 (mt0) REVERT: D 51 ASP cc_start: 0.8393 (p0) cc_final: 0.7837 (p0) REVERT: D 57 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8312 (mmtp) REVERT: D 86 ARG cc_start: 0.8974 (mmt-90) cc_final: 0.8691 (mtt-85) REVERT: E 59 GLU cc_start: 0.8775 (pm20) cc_final: 0.8260 (pm20) REVERT: E 76 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8621 (tm-30) REVERT: E 105 GLU cc_start: 0.8063 (tt0) cc_final: 0.7784 (tt0) REVERT: H 33 ARG cc_start: 0.8728 (mtp85) cc_final: 0.7954 (mtp-110) REVERT: H 59 MET cc_start: 0.9337 (tpp) cc_final: 0.9024 (tpp) REVERT: H 120 LYS cc_start: 0.9104 (tptm) cc_final: 0.8509 (ttpp) REVERT: C 56 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8320 (tm-30) REVERT: C 110 ASN cc_start: 0.8962 (t0) cc_final: 0.8351 (p0) REVERT: G 64 GLU cc_start: 0.9344 (tm-30) cc_final: 0.9016 (tm-30) REVERT: G 91 GLU cc_start: 0.8334 (tp30) cc_final: 0.7928 (tp30) outliers start: 23 outliers final: 19 residues processed: 192 average time/residue: 0.3029 time to fit residues: 79.6517 Evaluate side-chains 185 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL 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 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.0050 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.7400 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13791 Z= 0.328 Angle : 0.607 7.920 19872 Z= 0.356 Chirality : 0.036 0.153 2261 Planarity : 0.004 0.044 1500 Dihedral : 29.986 162.933 4186 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.40 % Allowed : 16.58 % Favored : 80.03 % 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: 2.51 (0.29), residues: 853 helix: 2.70 (0.21), residues: 577 sheet: 0.81 (1.30), residues: 17 loop : -0.77 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 82 PHE 0.007 0.001 PHE H 70 TYR 0.021 0.002 TYR H 40 ARG 0.004 0.000 ARG A 116 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1706 Ramachandran restraints generated. 853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8890 (mmm) cc_final: 0.8392 (tpp) REVERT: B 85 ASP cc_start: 0.8895 (m-30) cc_final: 0.8594 (m-30) REVERT: D 46 LYS cc_start: 0.9241 (mmtt) cc_final: 0.9035 (mmtt) REVERT: D 47 GLN cc_start: 0.8619 (mt0) cc_final: 0.8213 (mt0) REVERT: D 51 ASP cc_start: 0.8466 (p0) cc_final: 0.7946 (p0) REVERT: D 57 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8359 (mmtp) REVERT: D 86 ARG cc_start: 0.8998 (mmt-90) cc_final: 0.8711 (mtt-85) REVERT: E 59 GLU cc_start: 0.8808 (pm20) cc_final: 0.8482 (pm20) REVERT: E 76 GLN cc_start: 0.8964 (tm-30) cc_final: 0.8760 (tm-30) REVERT: E 105 GLU cc_start: 0.8029 (tt0) cc_final: 0.7790 (tt0) REVERT: F 88 TYR cc_start: 0.8396 (m-80) cc_final: 0.8136 (m-80) REVERT: H 33 ARG cc_start: 0.8846 (mtp85) cc_final: 0.8025 (mtp-110) REVERT: H 120 LYS cc_start: 0.9141 (tptm) cc_final: 0.8509 (ttpp) REVERT: C 56 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8592 (tm-30) REVERT: C 110 ASN cc_start: 0.8973 (t0) cc_final: 0.8341 (p0) REVERT: G 56 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8478 (tm-30) REVERT: G 91 GLU cc_start: 0.8387 (tp30) cc_final: 0.8021 (tp30) outliers start: 25 outliers final: 22 residues processed: 185 average time/residue: 0.2952 time to fit residues: 75.0341 Evaluate side-chains 186 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU 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 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL 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 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU 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 15 LYS Chi-restraints excluded: chain G residue 18 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13791 Z= 0.263 Angle : 0.583 7.446 19872 Z= 0.344 Chirality : 0.035 0.163 2261 Planarity : 0.004 0.043 1500 Dihedral : 29.916 163.397 4186 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.26 % Allowed : 16.98 % Favored : 79.76 % 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: 2.55 (0.29), residues: 853 helix: 2.75 (0.21), residues: 575 sheet: 0.84 (1.31), residues: 17 loop : -0.79 (0.38), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.007 0.001 PHE G 25 TYR 0.020 0.001 TYR H 40 ARG 0.005 0.000 ARG A 116 *********************** 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: 24 poor density : 174 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8842 (mmm) cc_final: 0.8340 (tpp) REVERT: A 129 ARG cc_start: 0.8748 (tpt90) cc_final: 0.8068 (tpt90) REVERT: B 85 ASP cc_start: 0.8877 (m-30) cc_final: 0.8580 (m-30) REVERT: D 46 LYS cc_start: 0.9255 (mmtt) cc_final: 0.9044 (mmtt) REVERT: D 47 GLN cc_start: 0.8568 (mt0) cc_final: 0.8281 (mt0) REVERT: D 51 ASP cc_start: 0.8414 (p0) cc_final: 0.8011 (p0) REVERT: D 57 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8391 (mmtp) REVERT: D 86 ARG cc_start: 0.8971 (mmt-90) cc_final: 0.8691 (mtt-85) REVERT: E 59 GLU cc_start: 0.8792 (pm20) cc_final: 0.8116 (pm20) REVERT: E 76 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8722 (tm-30) REVERT: E 105 GLU cc_start: 0.8034 (tt0) cc_final: 0.7741 (tt0) REVERT: H 33 ARG cc_start: 0.8840 (mtp85) cc_final: 0.8019 (mtp-110) REVERT: H 120 LYS cc_start: 0.9135 (tptm) cc_final: 0.8504 (ttpp) REVERT: C 56 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8339 (tm-30) REVERT: C 110 ASN cc_start: 0.8968 (t0) cc_final: 0.8361 (p0) REVERT: G 56 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8462 (tm-30) REVERT: G 63 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9138 (mm) REVERT: G 91 GLU cc_start: 0.8349 (tp30) cc_final: 0.7977 (tp30) outliers start: 24 outliers final: 21 residues processed: 188 average time/residue: 0.2947 time to fit residues: 76.5587 Evaluate side-chains 188 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 166 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL 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 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain M residue 7 THR 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 Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13791 Z= 0.298 Angle : 0.599 7.247 19872 Z= 0.351 Chirality : 0.035 0.160 2261 Planarity : 0.004 0.044 1500 Dihedral : 29.933 163.728 4186 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.26 % Allowed : 17.12 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.29), residues: 853 helix: 2.72 (0.21), residues: 576 sheet: 0.84 (1.32), residues: 17 loop : -0.80 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 82 PHE 0.007 0.001 PHE H 70 TYR 0.020 0.002 TYR H 40 ARG 0.004 0.000 ARG C 99 *********************** 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: 24 poor density : 170 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8856 (mmm) cc_final: 0.8350 (tpp) REVERT: A 129 ARG cc_start: 0.8756 (tpt90) cc_final: 0.8070 (tpt90) REVERT: B 85 ASP cc_start: 0.8887 (m-30) cc_final: 0.8590 (m-30) REVERT: D 46 LYS cc_start: 0.9242 (mmtt) cc_final: 0.9020 (mmtt) REVERT: D 47 GLN cc_start: 0.8591 (mt0) cc_final: 0.8196 (mt0) REVERT: D 51 ASP cc_start: 0.8424 (p0) cc_final: 0.7892 (p0) REVERT: D 57 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8384 (mmtp) REVERT: D 86 ARG cc_start: 0.8979 (mmt-90) cc_final: 0.8701 (mtt-85) REVERT: E 59 GLU cc_start: 0.8778 (pm20) cc_final: 0.8435 (pm20) REVERT: E 76 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 105 GLU cc_start: 0.8047 (tt0) cc_final: 0.7751 (tt0) REVERT: F 88 TYR cc_start: 0.8346 (m-80) cc_final: 0.8099 (m-80) REVERT: H 33 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8022 (mtp-110) REVERT: H 120 LYS cc_start: 0.9137 (tptm) cc_final: 0.8509 (ttpp) REVERT: C 56 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8570 (tm-30) REVERT: C 110 ASN cc_start: 0.8967 (t0) cc_final: 0.8361 (p0) REVERT: G 56 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8467 (tm-30) REVERT: G 63 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9121 (mm) REVERT: G 91 GLU cc_start: 0.8367 (tp30) cc_final: 0.7994 (tp30) outliers start: 24 outliers final: 23 residues processed: 183 average time/residue: 0.3179 time to fit residues: 79.8756 Evaluate side-chains 192 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain K residue 449 LEU Chi-restraints excluded: chain M residue 7 THR 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 Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 9 optimal weight: 0.0570 chunk 67 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.4106 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 13791 Z= 0.432 Angle : 0.669 7.642 19872 Z= 0.388 Chirality : 0.039 0.171 2261 Planarity : 0.004 0.050 1500 Dihedral : 30.239 165.764 4186 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.40 % Allowed : 17.12 % Favored : 79.48 % 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: 2.23 (0.29), residues: 853 helix: 2.53 (0.21), residues: 576 sheet: 0.67 (1.33), residues: 17 loop : -0.97 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 31 PHE 0.008 0.001 PHE A 78 TYR 0.029 0.002 TYR H 40 ARG 0.005 0.001 ARG C 29 ********************** 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 189 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.8911 (mmm) cc_final: 0.8261 (tpp) REVERT: B 85 ASP cc_start: 0.8924 (m-30) cc_final: 0.8623 (m-30) REVERT: D 47 GLN cc_start: 0.8698 (mt0) cc_final: 0.8436 (mt0) REVERT: D 51 ASP cc_start: 0.8468 (p0) cc_final: 0.7940 (p0) REVERT: D 57 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8431 (mmtp) REVERT: E 59 GLU cc_start: 0.8782 (pm20) cc_final: 0.8432 (pm20) REVERT: E 76 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8747 (tm-30) REVERT: E 105 GLU cc_start: 0.8199 (tt0) cc_final: 0.7916 (tt0) REVERT: F 88 TYR cc_start: 0.8403 (m-80) cc_final: 0.8166 (m-80) REVERT: H 33 ARG cc_start: 0.8876 (mtp85) cc_final: 0.8055 (mtp-110) REVERT: H 40 TYR cc_start: 0.8724 (m-10) cc_final: 0.8502 (m-10) REVERT: H 120 LYS cc_start: 0.9135 (tptm) cc_final: 0.8527 (ttpp) REVERT: C 56 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8667 (tm-30) REVERT: C 110 ASN cc_start: 0.9018 (t0) cc_final: 0.8337 (p0) REVERT: G 63 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9224 (mm) REVERT: G 91 GLU cc_start: 0.8474 (tp30) cc_final: 0.8097 (tp30) outliers start: 25 outliers final: 20 residues processed: 178 average time/residue: 0.2975 time to fit residues: 72.7448 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 : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 48 VAL 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 50 ILE Chi-restraints excluded: chain H residue 80 LEU 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 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 63 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** E 125 GLN H 84 ASN K 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.062809 restraints weight = 49558.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.064402 restraints weight = 23552.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.065051 restraints weight = 15886.527| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2787 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2787 r_free = 0.2787 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2787 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13791 Z= 0.195 Angle : 0.577 9.536 19872 Z= 0.339 Chirality : 0.034 0.146 2261 Planarity : 0.004 0.042 1500 Dihedral : 29.910 166.061 4186 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.72 % Allowed : 18.61 % Favored : 78.67 % 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: 2.54 (0.30), residues: 853 helix: 2.79 (0.22), residues: 574 sheet: 0.54 (1.27), residues: 17 loop : -0.88 (0.38), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.015 0.001 TYR H 40 ARG 0.004 0.000 ARG C 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2347.92 seconds wall clock time: 44 minutes 11.71 seconds (2651.71 seconds total)