Starting phenix.real_space_refine on Fri Aug 2 18:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9eme_19818/08_2024/9eme_19818.cif" } resolution = 2.92 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2562 2.51 5 N 714 2.21 5 O 852 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4140 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Chain: "C" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Chain: "D" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Chain: "E" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Chain: "F" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 690 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Time building chain proxies: 3.14, per 1000 atoms: 0.76 Number of scatterers: 4140 At special positions: 0 Unit cell: (79.04, 92.56, 52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 852 8.00 N 714 7.00 C 2562 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.02 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.02 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.02 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.02 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.02 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.02 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: 1.45 Conformation dependent library (CDL) restraints added in 779.5 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 23 removed outlier: 6.582A pdb=" N GLN A 16 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG B 19 " --> pdb=" O GLN A 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 18 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR B 21 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE A 20 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN B 23 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS A 22 " --> pdb=" O GLN B 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN B 16 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG C 19 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL B 18 " --> pdb=" O ARG C 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 21 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE B 20 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN C 23 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS B 22 " --> pdb=" O GLN C 23 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLN C 16 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG D 19 " --> pdb=" O GLN C 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 18 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR D 21 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE C 20 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN D 23 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N CYS C 22 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN D 16 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N ARG E 19 " --> pdb=" O GLN D 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL D 18 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 21 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 20 " --> pdb=" O THR E 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN E 23 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS D 22 " --> pdb=" O GLN E 23 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLN E 16 " --> pdb=" O THR F 17 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG F 19 " --> pdb=" O GLN E 16 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL E 18 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N THR F 21 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE E 20 " --> pdb=" O THR F 21 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N GLN F 23 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N CYS E 22 " --> pdb=" O GLN F 23 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 30 Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 47 removed outlier: 6.844A pdb=" N LEU A 45 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU B 45 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU C 45 " --> pdb=" O VAL D 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU D 45 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU E 45 " --> pdb=" O VAL F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'A' and resid 71 through 78 removed outlier: 6.757A pdb=" N ALA B 77 " --> pdb=" O GLY A 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN A 78 " --> pdb=" O ALA B 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA C 77 " --> pdb=" O GLY B 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN B 78 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA D 77 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN C 78 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA E 77 " --> pdb=" O GLY D 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN D 78 " --> pdb=" O ALA E 77 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ALA F 77 " --> pdb=" O GLY E 76 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLN E 78 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 81 through 83 removed outlier: 8.450A pdb=" N ASP A 81 " --> pdb=" O GLU B 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP B 81 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP C 81 " --> pdb=" O GLU D 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP D 81 " --> pdb=" O GLU E 82 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ASP E 81 " --> pdb=" O GLU F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 103 through 106 80 hydrogen bonds defined for protein. 240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.96 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 690 1.30 - 1.43: 1224 1.43 - 1.55: 2286 1.55 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 4212 Sorted by residual: bond pdb=" C VAL A 46 " pdb=" O VAL A 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.47e+01 bond pdb=" C VAL F 46 " pdb=" O VAL F 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL E 46 " pdb=" O VAL E 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.46e+01 bond pdb=" C VAL D 46 " pdb=" O VAL D 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 bond pdb=" C VAL B 46 " pdb=" O VAL B 46 " ideal model delta sigma weight residual 1.238 1.173 0.065 1.10e-02 8.26e+03 3.45e+01 ... (remaining 4207 not shown) Histogram of bond angle deviations from ideal: 103.29 - 109.54: 744 109.54 - 115.78: 1770 115.78 - 122.03: 2194 122.03 - 128.28: 979 128.28 - 134.52: 25 Bond angle restraints: 5712 Sorted by residual: angle pdb=" N SER F 64 " pdb=" CA SER F 64 " pdb=" C SER F 64 " ideal model delta sigma weight residual 110.97 120.58 -9.61 1.09e+00 8.42e-01 7.77e+01 angle pdb=" N SER C 64 " pdb=" CA SER C 64 " pdb=" C SER C 64 " ideal model delta sigma weight residual 110.97 120.56 -9.59 1.09e+00 8.42e-01 7.75e+01 angle pdb=" N SER D 64 " pdb=" CA SER D 64 " pdb=" C SER D 64 " ideal model delta sigma weight residual 110.97 120.54 -9.57 1.09e+00 8.42e-01 7.71e+01 angle pdb=" N SER E 64 " pdb=" CA SER E 64 " pdb=" C SER E 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.70e+01 angle pdb=" N SER A 64 " pdb=" CA SER A 64 " pdb=" C SER A 64 " ideal model delta sigma weight residual 110.97 120.53 -9.56 1.09e+00 8.42e-01 7.69e+01 ... (remaining 5707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 2160 14.03 - 28.06: 156 28.06 - 42.09: 84 42.09 - 56.12: 24 56.12 - 70.15: 6 Dihedral angle restraints: 2430 sinusoidal: 864 harmonic: 1566 Sorted by residual: dihedral pdb=" C HIS E 95 " pdb=" N HIS E 95 " pdb=" CA HIS E 95 " pdb=" CB HIS E 95 " ideal model delta harmonic sigma weight residual -122.60 -131.87 9.27 0 2.50e+00 1.60e-01 1.38e+01 dihedral pdb=" C HIS F 95 " pdb=" N HIS F 95 " pdb=" CA HIS F 95 " pdb=" CB HIS F 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 dihedral pdb=" C HIS C 95 " pdb=" N HIS C 95 " pdb=" CA HIS C 95 " pdb=" CB HIS C 95 " ideal model delta harmonic sigma weight residual -122.60 -131.86 9.26 0 2.50e+00 1.60e-01 1.37e+01 ... (remaining 2427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 228 0.062 - 0.124: 186 0.124 - 0.186: 142 0.186 - 0.248: 62 0.248 - 0.310: 18 Chirality restraints: 636 Sorted by residual: chirality pdb=" CA HIS B 95 " pdb=" N HIS B 95 " pdb=" C HIS B 95 " pdb=" CB HIS B 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA HIS A 95 " pdb=" N HIS A 95 " pdb=" C HIS A 95 " pdb=" CB HIS A 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA HIS D 95 " pdb=" N HIS D 95 " pdb=" C HIS D 95 " pdb=" CB HIS D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 633 not shown) Planarity restraints: 738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY E 100 " 0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C GLY E 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY E 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY E 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY B 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY B 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY B 101 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 100 " 0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C GLY C 100 " -0.072 2.00e-02 2.50e+03 pdb=" O GLY C 100 " 0.026 2.00e-02 2.50e+03 pdb=" N GLY C 101 " 0.025 2.00e-02 2.50e+03 ... (remaining 735 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 2442 3.03 - 3.50: 3840 3.50 - 3.96: 6802 3.96 - 4.43: 7884 4.43 - 4.90: 15157 Nonbonded interactions: 36125 Sorted by model distance: nonbonded pdb=" N GLY B 100 " pdb=" O GLY B 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY A 100 " pdb=" O GLY A 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY C 100 " pdb=" O GLY C 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY F 100 " pdb=" O GLY F 100 " model vdw 2.562 2.496 nonbonded pdb=" N GLY E 100 " pdb=" O GLY E 100 " model vdw 2.562 2.496 ... (remaining 36120 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5839 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 : 0.015 0.065 4212 Z= 0.988 Angle : 2.116 9.606 5712 Z= 1.591 Chirality : 0.121 0.310 636 Planarity : 0.012 0.042 738 Dihedral : 14.206 70.153 1428 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % 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: -4.40 (0.21), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.16), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.005 TRP C 34 HIS 0.007 0.003 HIS B 95 PHE 0.006 0.002 PHE C 61 TYR 0.014 0.002 TYR B 30 ARG 0.007 0.002 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.581 Fit side-chains REVERT: A 23 GLN cc_start: 0.7914 (tt0) cc_final: 0.6979 (tm-30) REVERT: A 89 SER cc_start: 0.6068 (t) cc_final: 0.5827 (t) REVERT: B 23 GLN cc_start: 0.6604 (tt0) cc_final: 0.5670 (tm-30) REVERT: C 19 ARG cc_start: 0.5982 (ttm170) cc_final: 0.5702 (ttm170) REVERT: C 23 GLN cc_start: 0.6797 (tt0) cc_final: 0.5708 (tm-30) REVERT: C 27 LEU cc_start: 0.6638 (tt) cc_final: 0.6275 (mp) REVERT: D 23 GLN cc_start: 0.7023 (tt0) cc_final: 0.5726 (tm-30) REVERT: D 33 SER cc_start: 0.7831 (p) cc_final: 0.7617 (p) REVERT: D 38 LYS cc_start: 0.7392 (mttt) cc_final: 0.7167 (mtpp) REVERT: D 78 GLN cc_start: 0.7055 (mt0) cc_final: 0.6721 (mt0) REVERT: F 23 GLN cc_start: 0.6897 (tt0) cc_final: 0.6431 (tm-30) REVERT: F 78 GLN cc_start: 0.7283 (mt0) cc_final: 0.6979 (mt0) REVERT: F 80 GLU cc_start: 0.6813 (mt-10) cc_final: 0.6218 (tt0) REVERT: F 90 ARG cc_start: 0.6815 (ttt180) cc_final: 0.6035 (tpm170) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 1.0107 time to fit residues: 125.9858 Evaluate side-chains 61 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN ** A 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 ASN A 78 GLN B 52 ASN B 68 ASN B 78 GLN C 68 ASN C 78 GLN D 68 ASN E 16 GLN E 68 ASN ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 ASN F 68 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4212 Z= 0.173 Angle : 0.555 6.719 5712 Z= 0.311 Chirality : 0.043 0.119 636 Planarity : 0.002 0.034 738 Dihedral : 4.997 18.169 600 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.38 % Allowed : 15.77 % Favored : 80.86 % 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: -3.47 (0.27), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.64 (0.20), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 34 HIS 0.002 0.001 HIS E 95 PHE 0.002 0.001 PHE A 99 TYR 0.011 0.002 TYR A 31 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 52 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7827 (mttt) REVERT: A 81 ASP cc_start: 0.6672 (m-30) cc_final: 0.6373 (m-30) REVERT: B 31 TYR cc_start: 0.7975 (m-80) cc_final: 0.7676 (m-80) REVERT: D 23 GLN cc_start: 0.6966 (tt0) cc_final: 0.6069 (tm-30) REVERT: D 68 ASN cc_start: 0.6135 (OUTLIER) cc_final: 0.5856 (m110) REVERT: D 78 GLN cc_start: 0.6611 (mt0) cc_final: 0.6371 (mt0) REVERT: E 90 ARG cc_start: 0.6428 (ttp80) cc_final: 0.5937 (ttm-80) REVERT: F 19 ARG cc_start: 0.6514 (ttp80) cc_final: 0.6027 (ttp-110) REVERT: F 23 GLN cc_start: 0.7232 (tt0) cc_final: 0.6694 (tm-30) REVERT: F 78 GLN cc_start: 0.7068 (mt0) cc_final: 0.6800 (mt0) REVERT: F 80 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6474 (tt0) REVERT: F 90 ARG cc_start: 0.6504 (ttt180) cc_final: 0.5520 (tpm170) outliers start: 15 outliers final: 9 residues processed: 65 average time/residue: 1.1315 time to fit residues: 76.4536 Evaluate side-chains 57 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 46 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 CYS Chi-restraints excluded: chain A residue 38 LYS Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain D residue 22 CYS Chi-restraints excluded: chain D residue 68 ASN Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 49 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN B 51 ASN B 68 ASN D 51 ASN D 68 ASN F 68 ASN F 88 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6001 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 4212 Z= 0.501 Angle : 0.687 6.925 5712 Z= 0.384 Chirality : 0.046 0.114 636 Planarity : 0.003 0.023 738 Dihedral : 5.728 19.019 600 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.35 % Allowed : 19.14 % Favored : 79.50 % 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: -3.11 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 34 HIS 0.011 0.003 HIS D 95 PHE 0.010 0.002 PHE B 99 TYR 0.021 0.003 TYR A 30 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.462 Fit side-chains REVERT: A 82 GLU cc_start: 0.7533 (mt-10) cc_final: 0.7179 (mt-10) REVERT: A 90 ARG cc_start: 0.6867 (ttp80) cc_final: 0.6661 (ttp80) REVERT: B 31 TYR cc_start: 0.8032 (m-80) cc_final: 0.7704 (m-80) REVERT: C 82 GLU cc_start: 0.6767 (mt-10) cc_final: 0.5991 (mt-10) REVERT: D 68 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.6010 (m110) REVERT: E 82 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6475 (mt-10) REVERT: F 80 GLU cc_start: 0.7011 (mt-10) cc_final: 0.6408 (tt0) REVERT: F 90 ARG cc_start: 0.6053 (ttt180) cc_final: 0.5184 (tpm170) outliers start: 6 outliers final: 2 residues processed: 44 average time/residue: 1.3788 time to fit residues: 62.8618 Evaluate side-chains 41 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain D residue 68 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 ASN D 68 ASN D 78 GLN F 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 4212 Z= 0.438 Angle : 0.637 6.293 5712 Z= 0.355 Chirality : 0.045 0.113 636 Planarity : 0.003 0.018 738 Dihedral : 5.634 19.151 600 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.35 % Allowed : 21.40 % Favored : 77.25 % 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: -3.10 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 34 HIS 0.009 0.003 HIS D 95 PHE 0.008 0.001 PHE B 99 TYR 0.019 0.003 TYR A 30 ARG 0.002 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.492 Fit side-chains REVERT: A 82 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 31 TYR cc_start: 0.8064 (m-80) cc_final: 0.7702 (m-80) REVERT: C 82 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6007 (mt-10) REVERT: E 38 LYS cc_start: 0.7955 (mtmm) cc_final: 0.7738 (mttm) REVERT: E 82 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6482 (mt-10) REVERT: F 80 GLU cc_start: 0.7002 (mt-10) cc_final: 0.6392 (tt0) REVERT: F 90 ARG cc_start: 0.6290 (ttt180) cc_final: 0.5029 (tpm170) outliers start: 6 outliers final: 3 residues processed: 41 average time/residue: 1.3418 time to fit residues: 57.1775 Evaluate side-chains 40 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain E residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4212 Z= 0.171 Angle : 0.504 5.016 5712 Z= 0.278 Chirality : 0.043 0.112 636 Planarity : 0.002 0.014 738 Dihedral : 4.756 17.921 600 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.58 % Allowed : 21.62 % Favored : 76.80 % 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: -3.10 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.002 0.001 HIS A 95 PHE 0.004 0.001 PHE E 61 TYR 0.010 0.001 TYR F 86 ARG 0.001 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7691 (mt-10) cc_final: 0.7328 (mt-10) REVERT: A 90 ARG cc_start: 0.6778 (ttp80) cc_final: 0.6462 (ttp80) REVERT: B 31 TYR cc_start: 0.7999 (m-80) cc_final: 0.7699 (m-80) REVERT: C 82 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6168 (mt-10) REVERT: D 38 LYS cc_start: 0.8058 (mttm) cc_final: 0.7293 (mptt) REVERT: E 38 LYS cc_start: 0.7944 (mtmm) cc_final: 0.7720 (mttm) REVERT: F 19 ARG cc_start: 0.6384 (ttp80) cc_final: 0.6166 (ttp-110) REVERT: F 80 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6406 (tt0) REVERT: F 90 ARG cc_start: 0.6330 (ttt180) cc_final: 0.5017 (ttm170) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.9528 time to fit residues: 48.4943 Evaluate side-chains 48 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5989 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 4212 Z= 0.295 Angle : 0.558 5.537 5712 Z= 0.308 Chirality : 0.043 0.112 636 Planarity : 0.002 0.020 738 Dihedral : 5.042 17.946 600 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.80 % Allowed : 22.30 % Favored : 75.90 % 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: -3.08 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.005 0.002 HIS D 95 PHE 0.005 0.001 PHE B 99 TYR 0.013 0.002 TYR A 30 ARG 0.003 0.000 ARG E 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7207 (mt-10) REVERT: A 90 ARG cc_start: 0.6736 (ttp80) cc_final: 0.6396 (ttp80) REVERT: B 31 TYR cc_start: 0.8060 (m-80) cc_final: 0.7728 (m-80) REVERT: C 82 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6119 (mt-10) REVERT: E 38 LYS cc_start: 0.7919 (mtmm) cc_final: 0.7668 (mttm) REVERT: E 82 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6672 (mt-10) REVERT: E 90 ARG cc_start: 0.6560 (ttp80) cc_final: 0.5905 (ptm160) REVERT: F 80 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6395 (tt0) REVERT: F 90 ARG cc_start: 0.6300 (ttt180) cc_final: 0.5146 (ttm170) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 1.3199 time to fit residues: 65.5993 Evaluate side-chains 45 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 40 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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: 0.5980 moved from start: 0.3608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4212 Z= 0.222 Angle : 0.530 6.493 5712 Z= 0.290 Chirality : 0.043 0.112 636 Planarity : 0.002 0.021 738 Dihedral : 4.820 17.734 600 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.58 % Allowed : 22.97 % Favored : 75.45 % 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: -3.07 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.33 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 PHE 0.004 0.001 PHE A 99 TYR 0.013 0.001 TYR B 86 ARG 0.003 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7322 (mt-10) REVERT: B 31 TYR cc_start: 0.8025 (m-80) cc_final: 0.7705 (m-80) REVERT: C 82 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6043 (mt-10) REVERT: D 38 LYS cc_start: 0.8090 (mttm) cc_final: 0.7359 (mptt) REVERT: E 38 LYS cc_start: 0.7898 (mtmm) cc_final: 0.7634 (mttm) REVERT: E 90 ARG cc_start: 0.6552 (ttp80) cc_final: 0.5884 (ptm160) REVERT: F 80 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6412 (tt0) REVERT: F 90 ARG cc_start: 0.6266 (ttt180) cc_final: 0.5131 (ttm170) outliers start: 7 outliers final: 7 residues processed: 47 average time/residue: 1.1934 time to fit residues: 58.3748 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 40 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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: 0.5993 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4212 Z= 0.281 Angle : 0.559 7.000 5712 Z= 0.306 Chirality : 0.044 0.113 636 Planarity : 0.002 0.027 738 Dihedral : 4.983 17.840 600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.35 % Allowed : 23.87 % Favored : 74.77 % 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: -3.04 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 34 HIS 0.005 0.002 HIS D 95 PHE 0.005 0.001 PHE B 99 TYR 0.015 0.002 TYR B 86 ARG 0.004 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 90 ARG cc_start: 0.6631 (ttp80) cc_final: 0.6307 (ttp80) REVERT: B 31 TYR cc_start: 0.8018 (m-80) cc_final: 0.7678 (m-80) REVERT: C 82 GLU cc_start: 0.6783 (mt-10) cc_final: 0.6005 (mt-10) REVERT: D 90 ARG cc_start: 0.6697 (ttp80) cc_final: 0.6448 (ttp80) REVERT: E 38 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7665 (mttm) REVERT: E 82 GLU cc_start: 0.7025 (mt-10) cc_final: 0.6753 (mt-10) REVERT: E 90 ARG cc_start: 0.6579 (ttp80) cc_final: 0.5864 (ptm160) REVERT: F 80 GLU cc_start: 0.6924 (mt-10) cc_final: 0.6627 (mt-10) REVERT: F 90 ARG cc_start: 0.6264 (ttt180) cc_final: 0.5104 (ttm170) outliers start: 6 outliers final: 6 residues processed: 48 average time/residue: 1.2625 time to fit residues: 62.8442 Evaluate side-chains 48 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain B residue 38 LYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 53 optimal weight: 0.0030 chunk 49 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4212 Z= 0.145 Angle : 0.503 7.148 5712 Z= 0.274 Chirality : 0.043 0.114 636 Planarity : 0.002 0.018 738 Dihedral : 4.484 16.874 600 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.58 % Allowed : 23.42 % Favored : 75.00 % 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: -3.01 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.21), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 34 HIS 0.002 0.001 HIS D 95 PHE 0.004 0.001 PHE E 61 TYR 0.018 0.001 TYR B 86 ARG 0.003 0.000 ARG C 90 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7191 (mt-10) REVERT: A 90 ARG cc_start: 0.6730 (ttp80) cc_final: 0.6429 (ttp80) REVERT: B 31 TYR cc_start: 0.8017 (m-80) cc_final: 0.7705 (m-80) REVERT: C 82 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6102 (mt-10) REVERT: D 90 ARG cc_start: 0.6771 (ttp80) cc_final: 0.6521 (ttp80) REVERT: E 38 LYS cc_start: 0.7901 (mtmm) cc_final: 0.7657 (mttm) REVERT: E 90 ARG cc_start: 0.6522 (ttp80) cc_final: 0.5807 (ptm160) REVERT: F 19 ARG cc_start: 0.6414 (ttp80) cc_final: 0.6188 (ttp-110) REVERT: F 80 GLU cc_start: 0.6935 (mt-10) cc_final: 0.6461 (tt0) REVERT: F 90 ARG cc_start: 0.6387 (ttt180) cc_final: 0.5251 (ttm170) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 1.1651 time to fit residues: 59.4393 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 78 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5970 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4212 Z= 0.212 Angle : 0.530 7.014 5712 Z= 0.289 Chirality : 0.043 0.124 636 Planarity : 0.002 0.013 738 Dihedral : 4.657 17.041 600 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.35 % Allowed : 23.65 % Favored : 75.00 % 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: -2.99 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 PHE 0.003 0.001 PHE B 99 TYR 0.015 0.002 TYR D 86 ARG 0.002 0.000 ARG B 90 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7253 (mt-10) REVERT: A 90 ARG cc_start: 0.6731 (ttp80) cc_final: 0.6477 (ttp80) REVERT: B 31 TYR cc_start: 0.8007 (m-80) cc_final: 0.7677 (m-80) REVERT: C 82 GLU cc_start: 0.6907 (mt-10) cc_final: 0.6138 (mt-10) REVERT: D 38 LYS cc_start: 0.7975 (mttp) cc_final: 0.7677 (mptt) REVERT: D 90 ARG cc_start: 0.6676 (ttp80) cc_final: 0.6458 (ttp80) REVERT: E 38 LYS cc_start: 0.7921 (mtmm) cc_final: 0.7654 (mttm) REVERT: E 90 ARG cc_start: 0.6456 (ttp80) cc_final: 0.5722 (ptm160) REVERT: F 19 ARG cc_start: 0.6398 (ttp80) cc_final: 0.6179 (ttp-110) REVERT: F 80 GLU cc_start: 0.6917 (mt-10) cc_final: 0.6436 (tt0) REVERT: F 90 ARG cc_start: 0.6344 (ttt180) cc_final: 0.5231 (ttm170) outliers start: 6 outliers final: 6 residues processed: 46 average time/residue: 1.1935 time to fit residues: 57.0879 Evaluate side-chains 47 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain C residue 22 CYS Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain F residue 22 CYS Chi-restraints excluded: chain F residue 38 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 7 optimal weight: 0.1980 chunk 37 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.115660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.104974 restraints weight = 5866.117| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.00 r_work: 0.3758 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3655 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4212 Z= 0.184 Angle : 0.519 7.040 5712 Z= 0.282 Chirality : 0.043 0.128 636 Planarity : 0.002 0.014 738 Dihedral : 4.564 16.910 600 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.58 % Allowed : 23.42 % Favored : 75.00 % 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: -2.99 (0.28), residues: 528 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 34 HIS 0.003 0.001 HIS D 95 PHE 0.004 0.001 PHE E 61 TYR 0.015 0.001 TYR F 86 ARG 0.001 0.000 ARG B 90 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.62 seconds wall clock time: 36 minutes 43.29 seconds (2203.29 seconds total)