Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 10:02:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/04_2023/7tan_25777.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/04_2023/7tan_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_25777/04_2023/7tan_25777.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/04_2023/7tan_25777.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/04_2023/7tan_25777.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tan_25777/04_2023/7tan_25777.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 6.47, per 1000 atoms: 0.53 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: 5.89 Conformation dependent library (CDL) restraints added in 1.1 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: 4.68 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: 4.01 Time building geometry restraints manager: 6.28 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: 4485 17.03 - 34.07: 866 34.07 - 51.10: 1013 51.10 - 68.13: 379 68.13 - 85.16: 25 Dihedral angle restraints: 6768 sinusoidal: 4544 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 6765 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: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 8.190 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 37.410 Find NCS groups from input model: 0.440 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.440 ------------------------------------------------------------------------------- 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 : 27.320 85.162 5332 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 % 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 *********************** 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 : 1.135 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 2.0909 time to fit residues: 270.6792 Evaluate side-chains 100 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 100 time to evaluate : 0.968 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1758 ------------------------------------------------------------------------------- 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: 0.8172 moved from start: 0.1209 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 4.732 18716 Z= 0.290 Chirality : 0.031 0.140 2132 Planarity : 0.003 0.036 1347 Dihedral : 30.208 80.453 3810 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.88 % 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: 2.41 (0.32), residues: 748 helix: 2.98 (0.23), residues: 511 sheet: None (None), residues: 0 loop : -1.73 (0.34), residues: 237 *********************** 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: 12 poor density : 98 time to evaluate : 0.982 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 104 average time/residue: 1.9616 time to fit residues: 215.0677 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 97 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.1491 time to fit residues: 2.0558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0570 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: 1.5504 ------------------------------------------------------------------------------- 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: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 12930 Z= 0.279 Angle : 0.523 5.155 18716 Z= 0.314 Chirality : 0.034 0.156 2132 Planarity : 0.004 0.039 1347 Dihedral : 30.339 85.058 3810 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.88 % 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 (0.31), residues: 748 helix: 2.80 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.76 (0.35), residues: 239 *********************** 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 116 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 1.060 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 109 average time/residue: 1.9539 time to fit residues: 224.6257 Evaluate side-chains 109 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 101 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 3 residues processed: 5 average time/residue: 0.4989 time to fit residues: 4.1337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 54 optimal weight: 0.0060 overall best weight: 0.7808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 24 GLN D 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 12930 Z= 0.182 Angle : 0.490 5.471 18716 Z= 0.300 Chirality : 0.032 0.169 2132 Planarity : 0.004 0.040 1347 Dihedral : 30.308 84.938 3810 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.56 % 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: 2.33 (0.32), residues: 748 helix: 2.93 (0.23), residues: 508 sheet: None (None), residues: 0 loop : -1.73 (0.35), residues: 240 *********************** 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 109 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 99 time to evaluate : 1.017 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 102 average time/residue: 1.9126 time to fit residues: 206.0380 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.1009 time to fit residues: 1.6783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 12930 Z= 0.212 Angle : 0.481 5.035 18716 Z= 0.293 Chirality : 0.031 0.142 2132 Planarity : 0.004 0.040 1347 Dihedral : 30.209 85.152 3810 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 1.72 % 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: 2.38 (0.32), residues: 748 helix: 2.96 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.71 (0.36), residues: 239 *********************** 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 113 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.031 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 1.9179 time to fit residues: 216.7144 Evaluate side-chains 107 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.963 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 3 residues processed: 4 average time/residue: 0.4959 time to fit residues: 3.4509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0020 chunk 23 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 0.0770 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN ** 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: 0.8188 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12930 Z= 0.157 Angle : 0.469 4.988 18716 Z= 0.289 Chirality : 0.031 0.187 2132 Planarity : 0.003 0.038 1347 Dihedral : 30.217 85.074 3810 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.78 % 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 (0.32), residues: 748 helix: 3.06 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 239 *********************** 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 103 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 98 time to evaluate : 0.983 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 101 average time/residue: 1.8385 time to fit residues: 196.4452 Evaluate side-chains 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.996 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1039 time to fit residues: 1.3783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 0.1980 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN ** 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: 0.8189 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 12930 Z= 0.183 Angle : 0.470 5.001 18716 Z= 0.288 Chirality : 0.031 0.175 2132 Planarity : 0.003 0.039 1347 Dihedral : 30.191 85.037 3810 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.62 % 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 (0.32), residues: 748 helix: 3.07 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.65 (0.35), residues: 239 *********************** 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 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.007 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 100 average time/residue: 1.8622 time to fit residues: 197.0388 Evaluate side-chains 99 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 96 time to evaluate : 1.009 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.1164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN D 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 12930 Z= 0.266 Angle : 0.511 5.057 18716 Z= 0.308 Chirality : 0.033 0.173 2132 Planarity : 0.004 0.040 1347 Dihedral : 30.280 86.370 3810 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.32), residues: 748 helix: 2.88 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.78 (0.35), residues: 239 *********************** 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 107 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 0.848 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 102 average time/residue: 1.9579 time to fit residues: 211.4025 Evaluate side-chains 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.6690 time to fit residues: 3.3508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12930 Z= 0.250 Angle : 0.509 5.128 18716 Z= 0.307 Chirality : 0.033 0.192 2132 Planarity : 0.004 0.040 1347 Dihedral : 30.279 86.385 3810 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer Outliers : 0.94 % 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: 2.25 (0.32), residues: 748 helix: 2.87 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.79 (0.35), residues: 239 *********************** 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 104 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.988 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 2.0672 time to fit residues: 222.9537 Evaluate side-chains 101 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.1069 time to fit residues: 1.3606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.0670 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 63 optimal weight: 0.0040 chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.4330 ------------------------------------------------------------------------------- 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: 0.8210 moved from start: 0.1859 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= 0.164 Angle : 0.494 7.275 18716 Z= 0.301 Chirality : 0.031 0.216 2132 Planarity : 0.004 0.039 1347 Dihedral : 30.287 86.276 3810 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.32), residues: 748 helix: 2.98 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.72 (0.35), residues: 239 ********************** 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 102 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.995 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 102 average time/residue: 1.8430 time to fit residues: 199.0494 Evaluate side-chains 102 residues out of total 640 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 99 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 1.1398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 79 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.144588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094657 restraints weight = 15359.751| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.23 r_work: 0.2853 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 12930 Z= 0.244 Angle : 0.501 5.294 18716 Z= 0.303 Chirality : 0.033 0.181 2132 Planarity : 0.004 0.040 1347 Dihedral : 30.266 86.610 3810 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer Outliers : 0.78 % 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: 2.33 (0.32), residues: 748 helix: 2.92 (0.23), residues: 509 sheet: None (None), residues: 0 loop : -1.73 (0.36), residues: 239 =============================================================================== Job complete usr+sys time: 3801.89 seconds wall clock time: 67 minutes 56.09 seconds (4076.09 seconds total)