Starting phenix.real_space_refine on Fri Mar 15 15:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/03_2024/7tan_25777.pdb" } resolution = 3.0 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 12 5.16 5 C 6691 2.51 5 N 2284 2.21 5 O 2838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 51": "OD1" <-> "OD2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 61": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12119 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 725 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3033 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2994 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "L" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 35 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Time building chain proxies: 6.93, per 1000 atoms: 0.57 Number of scatterers: 12119 At special positions: 0 Unit cell: (77.35, 122.85, 126.49, 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 12 16.00 P 294 15.00 O 2838 8.00 N 2284 7.00 C 6691 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.79 Conformation dependent library (CDL) restraints added in 1.3 seconds 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1436 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 9 sheets defined 69.4% alpha, 2.9% beta 60 base pairs and 258 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 4.064A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.653A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.582A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.586A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.962A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.223A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.720A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 4.024A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.825A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.587A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.840A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.503A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.698A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.539A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.588A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.615A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.018A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.761A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.968A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 37 through 49 removed outlier: 3.759A pdb=" N GLN H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL H 48 " --> pdb=" O VAL H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.651A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.933A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.828A 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 96 through 98 removed outlier: 6.798A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.490A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.890A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.455A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 369 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 147 hydrogen bonds 294 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 258 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2205 1.33 - 1.45: 4172 1.45 - 1.57: 5945 1.57 - 1.69: 586 1.69 - 1.80: 22 Bond restraints: 12930 Sorted by residual: bond pdb=" C GLU G 61 " pdb=" O GLU G 61 " ideal model delta sigma weight residual 1.236 1.248 -0.011 1.15e-02 7.56e+03 9.21e-01 bond pdb=" CB ARG B 92 " pdb=" CG ARG B 92 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.19e-01 bond pdb=" C ASN B 64 " pdb=" O ASN B 64 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.16e-01 bond pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.80e-01 bond pdb=" C GLY A 102 " pdb=" O GLY A 102 " ideal model delta sigma weight residual 1.234 1.243 -0.009 1.20e-02 6.94e+03 5.97e-01 ... (remaining 12925 not shown) Histogram of bond angle deviations from ideal: 99.87 - 106.38: 1990 106.38 - 112.89: 6743 112.89 - 119.41: 3538 119.41 - 125.92: 5478 125.92 - 132.43: 967 Bond angle restraints: 18716 Sorted by residual: angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.92 -6.38 1.91e+00 2.74e-01 1.12e+01 angle pdb=" C SER L 388 " pdb=" N ARG L 389 " pdb=" CA ARG L 389 " ideal model delta sigma weight residual 121.56 124.96 -3.40 1.56e+00 4.11e-01 4.74e+00 angle pdb=" N ARG L 389 " pdb=" CA ARG L 389 " pdb=" C ARG L 389 " ideal model delta sigma weight residual 110.42 113.42 -3.00 1.46e+00 4.69e-01 4.23e+00 angle pdb=" CA ASP B 24 " pdb=" CB ASP B 24 " pdb=" CG ASP B 24 " ideal model delta sigma weight residual 112.60 114.44 -1.84 1.00e+00 1.00e+00 3.38e+00 angle pdb=" C SER K 388 " pdb=" N ARG K 389 " pdb=" CA ARG K 389 " ideal model delta sigma weight residual 122.82 125.37 -2.55 1.42e+00 4.96e-01 3.22e+00 ... (remaining 18711 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 4575 17.03 - 34.07: 1014 34.07 - 51.10: 1023 51.10 - 68.13: 379 68.13 - 85.16: 25 Dihedral angle restraints: 7016 sinusoidal: 4792 harmonic: 2224 Sorted by residual: dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -136.48 -43.52 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CB GLU G 41 " pdb=" CG GLU G 41 " pdb=" CD GLU G 41 " pdb=" OE1 GLU G 41 " ideal model delta sinusoidal sigma weight residual 0.00 -85.16 85.16 1 3.00e+01 1.11e-03 9.77e+00 dihedral pdb=" CG ARG C 71 " pdb=" CD ARG C 71 " pdb=" NE ARG C 71 " pdb=" CZ ARG C 71 " ideal model delta sinusoidal sigma weight residual -90.00 -132.16 42.16 2 1.50e+01 4.44e-03 9.61e+00 ... (remaining 7013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1793 0.040 - 0.081: 285 0.081 - 0.121: 49 0.121 - 0.161: 4 0.161 - 0.202: 1 Chirality restraints: 2132 Sorted by residual: chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE G 111 " pdb=" N ILE G 111 " pdb=" C ILE G 111 " pdb=" CB ILE G 111 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.87e-01 ... (remaining 2129 not shown) Planarity restraints: 1347 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.024 5.00e-02 4.00e+02 3.62e-02 2.09e+00 pdb=" N PRO C 80 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 105 " 0.007 2.00e-02 2.50e+03 1.35e-02 1.82e+00 pdb=" CD GLU H 105 " -0.023 2.00e-02 2.50e+03 pdb=" OE1 GLU H 105 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU H 105 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 32 " 0.018 2.00e-02 2.50e+03 7.59e-03 1.73e+00 pdb=" N9 DG I 32 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 32 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I 32 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 32 " 0.002 2.00e-02 2.50e+03 pdb=" O6 DG I 32 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DG I 32 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 32 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 32 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG I 32 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 32 " -0.002 2.00e-02 2.50e+03 ... (remaining 1344 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3496 2.86 - 3.37: 10080 3.37 - 3.88: 21084 3.88 - 4.39: 25540 4.39 - 4.90: 36647 Nonbonded interactions: 96847 Sorted by model distance: nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.351 2.440 nonbonded pdb=" N2 DG I 74 " pdb=" O2 DC J -73 " model vdw 2.381 2.520 nonbonded pdb=" O GLN E 125 " pdb=" NH2 ARG E 134 " model vdw 2.427 2.520 nonbonded pdb=" NZ LYS B 59 " pdb=" OE2 GLU B 63 " model vdw 2.487 2.520 nonbonded pdb=" O2 DT I 69 " pdb=" N2 DG J -68 " model vdw 2.503 2.520 ... (remaining 96842 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 21 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 8.010 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 37.350 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 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 : 0.003 0.030 12930 Z= 0.196 Angle : 0.469 6.382 18716 Z= 0.283 Chirality : 0.031 0.202 2132 Planarity : 0.003 0.036 1347 Dihedral : 27.155 85.162 5580 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.18 (0.32), residues: 748 helix: 2.89 (0.24), residues: 503 sheet: None (None), residues: 0 loop : -1.88 (0.33), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 31 PHE 0.008 0.001 PHE B 61 TYR 0.008 0.001 TYR B 51 ARG 0.005 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.862 Fit side-chains REVERT: C 104 GLN cc_start: 0.8357 (mm-40) cc_final: 0.8096 (mm-40) REVERT: D 51 ASP cc_start: 0.7542 (p0) cc_final: 0.7295 (p0) REVERT: H 34 LYS cc_start: 0.7917 (mptt) cc_final: 0.7653 (mmtp) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.9847 time to fit residues: 256.8700 Evaluate side-chains 100 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN F 25 ASN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12930 Z= 0.189 Angle : 0.475 4.905 18716 Z= 0.290 Chirality : 0.031 0.140 2132 Planarity : 0.004 0.038 1347 Dihedral : 29.707 80.627 4058 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.72 % Allowed : 9.69 % Favored : 88.59 % 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: 2.42 (0.32), residues: 748 helix: 2.99 (0.24), residues: 511 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.008 0.001 PHE B 61 TYR 0.008 0.001 TYR D 121 ARG 0.005 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 1.052 Fit side-chains REVERT: A 120 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: A 129 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7714 (tpt-90) REVERT: C 24 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8063 (mp10) REVERT: C 104 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8081 (mm-40) REVERT: D 51 ASP cc_start: 0.7618 (p0) cc_final: 0.7287 (p0) REVERT: H 34 LYS cc_start: 0.7941 (mptt) cc_final: 0.7677 (mmtp) outliers start: 11 outliers final: 6 residues processed: 105 average time/residue: 1.9290 time to fit residues: 213.8419 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 84 ASN D 95 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12930 Z= 0.288 Angle : 0.521 5.107 18716 Z= 0.313 Chirality : 0.034 0.149 2132 Planarity : 0.004 0.039 1347 Dihedral : 29.851 84.489 4058 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.34 % Allowed : 11.72 % Favored : 85.94 % 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: 2.18 (0.32), residues: 748 helix: 2.80 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.78 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.010 0.002 PHE B 61 TYR 0.011 0.002 TYR D 121 ARG 0.006 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 105 time to evaluate : 0.977 Fit side-chains REVERT: A 129 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7700 (tpt-90) REVERT: C 24 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.7870 (mp10) REVERT: C 104 GLN cc_start: 0.8435 (mm-40) cc_final: 0.8148 (mm-40) REVERT: D 51 ASP cc_start: 0.7636 (p0) cc_final: 0.7316 (p0) REVERT: H 93 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7335 (mp0) outliers start: 15 outliers final: 8 residues processed: 111 average time/residue: 1.8803 time to fit residues: 220.2896 Evaluate side-chains 113 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12930 Z= 0.208 Angle : 0.497 5.390 18716 Z= 0.303 Chirality : 0.032 0.175 2132 Planarity : 0.004 0.040 1347 Dihedral : 29.826 84.490 4058 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.34 % Allowed : 13.59 % Favored : 84.06 % 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: 2.28 (0.32), residues: 748 helix: 2.88 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.010 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.007 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 98 time to evaluate : 0.900 Fit side-chains REVERT: A 42 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.8245 (mmm-85) REVERT: A 129 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7742 (tpt-90) REVERT: C 24 GLN cc_start: 0.8658 (OUTLIER) cc_final: 0.7857 (mp10) REVERT: C 104 GLN cc_start: 0.8418 (mm-40) cc_final: 0.8131 (mm-40) REVERT: D 51 ASP cc_start: 0.7626 (p0) cc_final: 0.7316 (p0) REVERT: D 93 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.6682 (mp0) REVERT: H 93 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7336 (mp0) outliers start: 15 outliers final: 8 residues processed: 104 average time/residue: 1.8842 time to fit residues: 207.6665 Evaluate side-chains 110 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12930 Z= 0.214 Angle : 0.493 6.156 18716 Z= 0.299 Chirality : 0.032 0.170 2132 Planarity : 0.004 0.040 1347 Dihedral : 29.786 84.511 4058 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 13.44 % Favored : 84.06 % 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: 2.32 (0.32), residues: 748 helix: 2.92 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.010 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.009 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.109 Fit side-chains REVERT: A 42 ARG cc_start: 0.8397 (mmm-85) cc_final: 0.8189 (mmm-85) REVERT: A 120 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8214 (mtt) REVERT: A 129 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7730 (tpt-90) REVERT: C 24 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: C 104 GLN cc_start: 0.8409 (mm-40) cc_final: 0.8118 (mm-40) REVERT: D 51 ASP cc_start: 0.7626 (p0) cc_final: 0.7308 (p0) REVERT: D 93 GLU cc_start: 0.8037 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: H 93 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7230 (mp0) outliers start: 16 outliers final: 9 residues processed: 109 average time/residue: 1.8776 time to fit residues: 216.0017 Evaluate side-chains 114 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.1980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12930 Z= 0.181 Angle : 0.483 4.959 18716 Z= 0.295 Chirality : 0.031 0.187 2132 Planarity : 0.003 0.039 1347 Dihedral : 29.777 84.500 4058 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.19 % Allowed : 14.06 % Favored : 83.75 % 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: 2.36 (0.32), residues: 748 helix: 2.96 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.75 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR D 121 ARG 0.003 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.992 Fit side-chains REVERT: A 42 ARG cc_start: 0.8391 (mmm-85) cc_final: 0.8185 (mmm-85) REVERT: A 129 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7727 (tpt-90) REVERT: C 24 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: C 104 GLN cc_start: 0.8399 (mm-40) cc_final: 0.8105 (mm-40) REVERT: D 51 ASP cc_start: 0.7623 (p0) cc_final: 0.7305 (p0) REVERT: D 93 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.6621 (mp0) REVERT: H 93 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7224 (mp0) outliers start: 14 outliers final: 9 residues processed: 107 average time/residue: 1.8242 time to fit residues: 206.4063 Evaluate side-chains 111 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.0570 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12930 Z= 0.183 Angle : 0.478 5.535 18716 Z= 0.293 Chirality : 0.031 0.189 2132 Planarity : 0.003 0.039 1347 Dihedral : 29.754 84.469 4058 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.03 % Allowed : 14.06 % Favored : 83.91 % 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: 2.40 (0.32), residues: 748 helix: 3.00 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.74 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.009 0.001 PHE B 61 TYR 0.008 0.001 TYR D 121 ARG 0.001 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.965 Fit side-chains REVERT: A 42 ARG cc_start: 0.8383 (mmm-85) cc_final: 0.8183 (mmm-85) REVERT: A 129 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7679 (tpt-90) REVERT: C 24 GLN cc_start: 0.8667 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: C 104 GLN cc_start: 0.8397 (mm-40) cc_final: 0.8103 (mm-40) REVERT: D 51 ASP cc_start: 0.7622 (p0) cc_final: 0.7301 (p0) REVERT: D 93 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.6607 (mp0) REVERT: H 93 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7152 (mp0) outliers start: 13 outliers final: 9 residues processed: 106 average time/residue: 1.8234 time to fit residues: 204.2562 Evaluate side-chains 111 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12930 Z= 0.313 Angle : 0.539 5.083 18716 Z= 0.323 Chirality : 0.035 0.177 2132 Planarity : 0.004 0.041 1347 Dihedral : 29.875 86.759 4058 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.81 % Allowed : 13.91 % Favored : 83.28 % 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: 2.04 (0.32), residues: 748 helix: 2.73 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.89 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.012 0.002 PHE B 61 TYR 0.012 0.002 TYR D 121 ARG 0.003 0.000 ARG E 131 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.921 Fit side-chains REVERT: A 40 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.7917 (tpt90) REVERT: A 42 ARG cc_start: 0.8396 (mmm-85) cc_final: 0.8188 (mmm-85) REVERT: A 129 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7669 (tpt-90) REVERT: C 24 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.7847 (mp10) REVERT: C 104 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8151 (mm-40) REVERT: D 51 ASP cc_start: 0.7655 (p0) cc_final: 0.7314 (p0) REVERT: F 63 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7588 (tt0) REVERT: H 93 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7313 (mp0) outliers start: 18 outliers final: 8 residues processed: 109 average time/residue: 1.9481 time to fit residues: 223.7923 Evaluate side-chains 115 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12930 Z= 0.179 Angle : 0.510 5.568 18716 Z= 0.311 Chirality : 0.032 0.207 2132 Planarity : 0.004 0.040 1347 Dihedral : 29.871 86.651 4058 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 15.16 % Favored : 82.81 % 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: 2.15 (0.32), residues: 748 helix: 2.82 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.85 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 109 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.003 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 101 time to evaluate : 1.004 Fit side-chains REVERT: A 40 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7782 (tpt90) REVERT: A 42 ARG cc_start: 0.8368 (mmm-85) cc_final: 0.8157 (mmm-85) REVERT: A 129 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7738 (tpt-90) REVERT: C 24 GLN cc_start: 0.8686 (OUTLIER) cc_final: 0.7839 (mp10) REVERT: C 104 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8143 (mm-40) REVERT: D 51 ASP cc_start: 0.7654 (p0) cc_final: 0.7327 (p0) REVERT: F 63 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7552 (tt0) REVERT: H 93 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7387 (mp0) outliers start: 13 outliers final: 7 residues processed: 107 average time/residue: 1.9116 time to fit residues: 216.1036 Evaluate side-chains 113 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.1980 chunk 61 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12930 Z= 0.201 Angle : 0.507 8.006 18716 Z= 0.309 Chirality : 0.033 0.189 2132 Planarity : 0.004 0.040 1347 Dihedral : 29.848 86.561 4058 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 15.62 % Favored : 82.34 % 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: 2.19 (0.32), residues: 748 helix: 2.84 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.84 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 113 PHE 0.010 0.001 PHE B 61 TYR 0.010 0.001 TYR D 121 ARG 0.003 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1496 Ramachandran restraints generated. 748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.927 Fit side-chains REVERT: A 40 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7733 (tpt90) REVERT: A 42 ARG cc_start: 0.8367 (mmm-85) cc_final: 0.8155 (mmm-85) REVERT: A 129 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7733 (tpt-90) REVERT: C 24 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.7858 (mp10) REVERT: C 92 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7520 (mt-10) REVERT: C 104 GLN cc_start: 0.8419 (mm-40) cc_final: 0.8141 (mm-40) REVERT: D 51 ASP cc_start: 0.7642 (p0) cc_final: 0.7311 (p0) REVERT: F 63 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: H 93 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7306 (mp0) outliers start: 13 outliers final: 6 residues processed: 107 average time/residue: 1.8923 time to fit residues: 213.5309 Evaluate side-chains 112 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ARG Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 24 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 57 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.144143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093985 restraints weight = 15347.029| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 1.23 r_work: 0.2838 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12930 Z= 0.186 Angle : 0.502 7.390 18716 Z= 0.307 Chirality : 0.032 0.189 2132 Planarity : 0.004 0.040 1347 Dihedral : 29.840 86.525 4058 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.03 % Allowed : 15.62 % Favored : 82.34 % 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: 2.21 (0.32), residues: 748 helix: 2.86 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.83 (0.35), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 113 PHE 0.010 0.001 PHE B 61 TYR 0.009 0.001 TYR D 121 ARG 0.003 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3984.01 seconds wall clock time: 70 minutes 52.92 seconds (4252.92 seconds total)