Starting phenix.real_space_refine on Sat Mar 16 22:46:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d9m_27266/03_2024/8d9m_27266_updated.pdb" } resolution = 4.2 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 ------------------------------------------------------------------------------- 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= 0.010 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 Fe 56 7.16 5 S 126 5.16 5 C 10276 2.51 5 N 2660 2.21 5 O 2849 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15967 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER B 284 " pdbres="HEC B 601 " Not linked: pdbres="HEC B 601 " pdbres="HEC B 602 " Not linked: pdbres="HEC B 602 " pdbres="HEC B 603 " Not linked: pdbres="HEC B 603 " pdbres="HEC B 604 " Not linked: pdbres="HEC B 604 " pdbres="HEC B 605 " ... (remaining 3 not shown) Chain: "C" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER C 284 " pdbres="HEC C 601 " Not linked: pdbres="HEC C 601 " pdbres="HEC C 602 " Not linked: pdbres="HEC C 602 " pdbres="HEC C 603 " Not linked: pdbres="HEC C 603 " pdbres="HEC C 604 " Not linked: pdbres="HEC C 604 " pdbres="HEC C 605 " ... (remaining 3 not shown) Chain: "D" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER D 284 " pdbres="HEC D 601 " Not linked: pdbres="HEC D 601 " pdbres="HEC D 602 " Not linked: pdbres="HEC D 602 " pdbres="HEC D 603 " Not linked: pdbres="HEC D 603 " pdbres="HEC D 604 " Not linked: pdbres="HEC D 604 " pdbres="HEC D 605 " ... (remaining 3 not shown) Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER A 284 " pdbres="HEC A 601 " Not linked: pdbres="HEC A 601 " pdbres="HEC A 602 " Not linked: pdbres="HEC A 602 " pdbres="HEC A 603 " Not linked: pdbres="HEC A 603 " pdbres="HEC A 604 " Not linked: pdbres="HEC A 604 " pdbres="HEC A 605 " ... (remaining 3 not shown) Chain: "E" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER E 284 " pdbres="HEC E 601 " Not linked: pdbres="HEC E 601 " pdbres="HEC E 602 " Not linked: pdbres="HEC E 602 " pdbres="HEC E 603 " Not linked: pdbres="HEC E 603 " pdbres="HEC E 604 " Not linked: pdbres="HEC E 604 " pdbres="HEC E 605 " ... (remaining 3 not shown) Chain: "F" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER F 284 " pdbres="HEC F 601 " Not linked: pdbres="HEC F 601 " pdbres="HEC F 602 " Not linked: pdbres="HEC F 602 " pdbres="HEC F 603 " Not linked: pdbres="HEC F 603 " pdbres="HEC F 604 " Not linked: pdbres="HEC F 604 " pdbres="HEC F 605 " ... (remaining 3 not shown) Chain: "G" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2281 Unusual residues: {'HEC': 8} Classifications: {'peptide': 258, 'undetermined': 8} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 236, None: 8} Not linked: pdbres="SER G 284 " pdbres="HEC G 601 " Not linked: pdbres="HEC G 601 " pdbres="HEC G 602 " Not linked: pdbres="HEC G 602 " pdbres="HEC G 603 " Not linked: pdbres="HEC G 603 " pdbres="HEC G 604 " Not linked: pdbres="HEC G 604 " pdbres="HEC G 605 " ... (remaining 3 not shown) Time building chain proxies: 8.12, per 1000 atoms: 0.51 Number of scatterers: 15967 At special positions: 0 Unit cell: (81, 81, 438.48, 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) Fe 56 26.01 S 126 16.00 O 2849 8.00 N 2660 7.00 C 10276 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=180, symmetry=0 Number of additional bonds: simple=180, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.26 Conformation dependent library (CDL) restraints added in 2.6 seconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3318 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 14 sheets defined 15.9% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.53 Creating SS restraints... Processing helix chain 'B' and resid 58 through 65 Processing helix chain 'B' and resid 67 through 70 Processing helix chain 'B' and resid 124 through 127 No H-bonds generated for 'chain 'B' and resid 124 through 127' Processing helix chain 'B' and resid 202 through 205 No H-bonds generated for 'chain 'B' and resid 202 through 205' Processing helix chain 'B' and resid 225 through 231 removed outlier: 3.942A pdb=" N VAL B 231 " --> pdb=" O ARG B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 240 removed outlier: 3.846A pdb=" N ASN B 240 " --> pdb=" O ASN B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 removed outlier: 3.597A pdb=" N CYS B 275 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 65 Processing helix chain 'C' and resid 67 through 70 Processing helix chain 'C' and resid 124 through 127 No H-bonds generated for 'chain 'C' and resid 124 through 127' Processing helix chain 'C' and resid 202 through 205 No H-bonds generated for 'chain 'C' and resid 202 through 205' Processing helix chain 'C' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL C 231 " --> pdb=" O ARG C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 240 removed outlier: 3.847A pdb=" N ASN C 240 " --> pdb=" O ASN C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 276 removed outlier: 3.598A pdb=" N CYS C 275 " --> pdb=" O ASP C 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 65 Processing helix chain 'D' and resid 67 through 70 Processing helix chain 'D' and resid 124 through 127 No H-bonds generated for 'chain 'D' and resid 124 through 127' Processing helix chain 'D' and resid 202 through 205 No H-bonds generated for 'chain 'D' and resid 202 through 205' Processing helix chain 'D' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 240 removed outlier: 3.847A pdb=" N ASN D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 276 removed outlier: 3.598A pdb=" N CYS D 275 " --> pdb=" O ASP D 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 65 Processing helix chain 'A' and resid 67 through 70 Processing helix chain 'A' and resid 124 through 127 No H-bonds generated for 'chain 'A' and resid 124 through 127' Processing helix chain 'A' and resid 202 through 205 No H-bonds generated for 'chain 'A' and resid 202 through 205' Processing helix chain 'A' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 240 removed outlier: 3.846A pdb=" N ASN A 240 " --> pdb=" O ASN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 removed outlier: 3.598A pdb=" N CYS A 275 " --> pdb=" O ASP A 271 " (cutoff:3.500A) Processing helix chain 'E' and resid 58 through 65 Processing helix chain 'E' and resid 67 through 70 Processing helix chain 'E' and resid 124 through 127 No H-bonds generated for 'chain 'E' and resid 124 through 127' Processing helix chain 'E' and resid 202 through 205 No H-bonds generated for 'chain 'E' and resid 202 through 205' Processing helix chain 'E' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL E 231 " --> pdb=" O ARG E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 240 removed outlier: 3.846A pdb=" N ASN E 240 " --> pdb=" O ASN E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 276 removed outlier: 3.598A pdb=" N CYS E 275 " --> pdb=" O ASP E 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 65 Processing helix chain 'F' and resid 67 through 70 Processing helix chain 'F' and resid 124 through 127 No H-bonds generated for 'chain 'F' and resid 124 through 127' Processing helix chain 'F' and resid 202 through 205 No H-bonds generated for 'chain 'F' and resid 202 through 205' Processing helix chain 'F' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL F 231 " --> pdb=" O ARG F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 240 removed outlier: 3.847A pdb=" N ASN F 240 " --> pdb=" O ASN F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 276 removed outlier: 3.597A pdb=" N CYS F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 65 Processing helix chain 'G' and resid 67 through 70 Processing helix chain 'G' and resid 124 through 127 No H-bonds generated for 'chain 'G' and resid 124 through 127' Processing helix chain 'G' and resid 202 through 205 No H-bonds generated for 'chain 'G' and resid 202 through 205' Processing helix chain 'G' and resid 225 through 231 removed outlier: 3.941A pdb=" N VAL G 231 " --> pdb=" O ARG G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 240 removed outlier: 3.847A pdb=" N ASN G 240 " --> pdb=" O ASN G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 276 removed outlier: 3.598A pdb=" N CYS G 275 " --> pdb=" O ASP G 271 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 95 through 97 Processing sheet with id= B, first strand: chain 'B' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR B 195 " --> pdb=" O ASP B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 95 through 97 Processing sheet with id= D, first strand: chain 'C' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR C 195 " --> pdb=" O ASP C 190 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 95 through 97 Processing sheet with id= F, first strand: chain 'D' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR D 195 " --> pdb=" O ASP D 190 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 95 through 97 Processing sheet with id= H, first strand: chain 'A' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR A 195 " --> pdb=" O ASP A 190 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 95 through 97 Processing sheet with id= J, first strand: chain 'E' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR E 195 " --> pdb=" O ASP E 190 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 95 through 97 Processing sheet with id= L, first strand: chain 'F' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR F 195 " --> pdb=" O ASP F 190 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 95 through 97 Processing sheet with id= N, first strand: chain 'G' and resid 188 through 190 removed outlier: 3.909A pdb=" N THR G 195 " --> pdb=" O ASP G 190 " (cutoff:3.500A) 112 hydrogen bonds defined for protein. 294 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: 3.57 Time building geometry restraints manager: 8.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 6902 1.39 - 1.56: 9499 1.56 - 1.73: 7 1.73 - 1.90: 140 1.90 - 2.08: 224 Bond restraints: 16772 Sorted by residual: bond pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 1.524 1.484 0.040 1.48e-02 4.57e+03 7.33e+00 bond pdb=" CA ALA C 89 " pdb=" C ALA C 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.27e+00 bond pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.22e+00 bond pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.17e+00 bond pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.48e-02 4.57e+03 7.14e+00 ... (remaining 16767 not shown) Histogram of bond angle deviations from ideal: 86.87 - 105.34: 788 105.34 - 123.81: 20093 123.81 - 142.27: 2772 142.27 - 160.74: 0 160.74 - 179.21: 112 Bond angle restraints: 23765 Sorted by residual: angle pdb=" N ALA D 89 " pdb=" CA ALA D 89 " pdb=" C ALA D 89 " ideal model delta sigma weight residual 112.72 107.01 5.71 1.14e+00 7.69e-01 2.51e+01 angle pdb=" N ALA A 89 " pdb=" CA ALA A 89 " pdb=" C ALA A 89 " ideal model delta sigma weight residual 112.72 107.02 5.70 1.14e+00 7.69e-01 2.50e+01 angle pdb=" N ALA B 89 " pdb=" CA ALA B 89 " pdb=" C ALA B 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA E 89 " pdb=" CA ALA E 89 " pdb=" C ALA E 89 " ideal model delta sigma weight residual 112.72 107.03 5.69 1.14e+00 7.69e-01 2.49e+01 angle pdb=" N ALA G 89 " pdb=" CA ALA G 89 " pdb=" C ALA G 89 " ideal model delta sigma weight residual 112.72 107.04 5.68 1.14e+00 7.69e-01 2.49e+01 ... (remaining 23760 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 7805 17.06 - 34.12: 532 34.12 - 51.18: 140 51.18 - 68.24: 70 68.24 - 85.30: 70 Dihedral angle restraints: 8617 sinusoidal: 3472 harmonic: 5145 Sorted by residual: dihedral pdb=" CA PRO E 29 " pdb=" C PRO E 29 " pdb=" N PRO E 30 " pdb=" CA PRO E 30 " ideal model delta harmonic sigma weight residual 180.00 149.12 30.88 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO D 29 " pdb=" C PRO D 29 " pdb=" N PRO D 30 " pdb=" CA PRO D 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 dihedral pdb=" CA PRO F 29 " pdb=" C PRO F 29 " pdb=" N PRO F 30 " pdb=" CA PRO F 30 " ideal model delta harmonic sigma weight residual 180.00 149.14 30.86 0 5.00e+00 4.00e-02 3.81e+01 ... (remaining 8614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1529 0.053 - 0.106: 504 0.106 - 0.159: 83 0.159 - 0.211: 5 0.211 - 0.264: 7 Chirality restraints: 2128 Sorted by residual: chirality pdb=" CA LEU F 88 " pdb=" N LEU F 88 " pdb=" C LEU F 88 " pdb=" CB LEU F 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA LEU E 88 " pdb=" N LEU E 88 " pdb=" C LEU E 88 " pdb=" CB LEU E 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA LEU A 88 " pdb=" N LEU A 88 " pdb=" C LEU A 88 " pdb=" CB LEU A 88 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 2125 not shown) Planarity restraints: 2912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR C 87 " -0.026 2.00e-02 2.50e+03 5.46e-02 2.98e+01 pdb=" C THR C 87 " 0.094 2.00e-02 2.50e+03 pdb=" O THR C 87 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU C 88 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR D 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR D 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 88 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 87 " 0.026 2.00e-02 2.50e+03 5.45e-02 2.97e+01 pdb=" C THR F 87 " -0.094 2.00e-02 2.50e+03 pdb=" O THR F 87 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU F 88 " 0.031 2.00e-02 2.50e+03 ... (remaining 2909 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 119 2.33 - 2.97: 8192 2.97 - 3.61: 25248 3.61 - 4.26: 36880 4.26 - 4.90: 57180 Nonbonded interactions: 127619 Sorted by model distance: nonbonded pdb=" CE1 HIS F 207 " pdb="FE HEC F 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS G 207 " pdb="FE HEC G 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS B 207 " pdb="FE HEC B 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS A 207 " pdb="FE HEC A 606 " model vdw 1.684 3.220 nonbonded pdb=" CE1 HIS E 207 " pdb="FE HEC E 606 " model vdw 1.684 3.220 ... (remaining 127614 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 12.300 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 43.840 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.007 0.098 16772 Z= 0.440 Angle : 1.023 8.233 23765 Z= 0.459 Chirality : 0.051 0.264 2128 Planarity : 0.008 0.116 2912 Dihedral : 16.461 85.304 5299 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 31.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.19 % Favored : 82.81 % Rotamer: Outliers : 0.45 % Allowed : 0.45 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -2.61 (0.19), residues: 1792 helix: -1.74 (0.25), residues: 294 sheet: -1.24 (0.28), residues: 154 loop : -1.93 (0.18), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G 270 HIS 0.015 0.002 HIS D 135 PHE 0.021 0.003 PHE G 42 TYR 0.012 0.003 TYR E 147 ARG 0.002 0.000 ARG C 227 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 408 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 VAL cc_start: 0.9141 (m) cc_final: 0.8908 (p) REVERT: B 79 ASN cc_start: 0.7926 (t0) cc_final: 0.7480 (t0) REVERT: B 95 MET cc_start: 0.8635 (mmm) cc_final: 0.8231 (mmm) REVERT: B 129 LYS cc_start: 0.9358 (ptpp) cc_final: 0.8984 (mttp) REVERT: B 176 GLN cc_start: 0.7279 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 203 GLN cc_start: 0.8910 (tp40) cc_final: 0.8348 (tp40) REVERT: B 204 ASP cc_start: 0.8815 (m-30) cc_final: 0.8484 (m-30) REVERT: B 269 ASN cc_start: 0.8206 (m-40) cc_final: 0.7723 (t0) REVERT: B 277 TRP cc_start: 0.8261 (t-100) cc_final: 0.7740 (t-100) REVERT: C 51 LEU cc_start: 0.7716 (mt) cc_final: 0.7515 (mt) REVERT: C 79 ASN cc_start: 0.7750 (t0) cc_final: 0.7429 (t0) REVERT: C 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8129 (mmp) REVERT: C 116 THR cc_start: 0.8837 (m) cc_final: 0.8339 (t) REVERT: C 148 ILE cc_start: 0.9148 (mm) cc_final: 0.8879 (mm) REVERT: C 179 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7394 (mt-10) REVERT: C 203 GLN cc_start: 0.8920 (tp40) cc_final: 0.8226 (tp40) REVERT: C 216 LEU cc_start: 0.8639 (tp) cc_final: 0.8395 (mp) REVERT: C 269 ASN cc_start: 0.8340 (m-40) cc_final: 0.7806 (m-40) REVERT: D 51 LEU cc_start: 0.7633 (mt) cc_final: 0.7420 (mt) REVERT: D 79 ASN cc_start: 0.7874 (t0) cc_final: 0.7501 (t0) REVERT: D 108 PHE cc_start: 0.8734 (p90) cc_final: 0.8469 (p90) REVERT: D 133 TYR cc_start: 0.8739 (t80) cc_final: 0.8533 (t80) REVERT: D 179 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7591 (mt-10) REVERT: D 203 GLN cc_start: 0.8905 (tp40) cc_final: 0.8300 (tp40) REVERT: D 216 LEU cc_start: 0.8666 (tp) cc_final: 0.8459 (mp) REVERT: D 269 ASN cc_start: 0.8414 (m-40) cc_final: 0.7938 (m-40) REVERT: A 37 ILE cc_start: 0.8675 (pt) cc_final: 0.8428 (pt) REVERT: A 61 VAL cc_start: 0.9208 (m) cc_final: 0.9005 (p) REVERT: A 176 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 203 GLN cc_start: 0.9054 (tp40) cc_final: 0.8529 (tp40) REVERT: A 226 ILE cc_start: 0.8978 (tp) cc_final: 0.8730 (tp) REVERT: A 227 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8411 (mmt180) REVERT: A 230 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.7703 (m-40) REVERT: E 61 VAL cc_start: 0.9144 (m) cc_final: 0.8926 (p) REVERT: E 79 ASN cc_start: 0.7914 (t0) cc_final: 0.7386 (t0) REVERT: E 95 MET cc_start: 0.8653 (mmm) cc_final: 0.8449 (mmm) REVERT: E 148 ILE cc_start: 0.9194 (mm) cc_final: 0.8987 (mm) REVERT: E 179 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7364 (mt-10) REVERT: E 203 GLN cc_start: 0.8933 (tp40) cc_final: 0.8544 (tp40) REVERT: E 204 ASP cc_start: 0.8724 (m-30) cc_final: 0.8522 (m-30) REVERT: E 269 ASN cc_start: 0.8388 (m-40) cc_final: 0.7526 (t0) REVERT: E 273 GLN cc_start: 0.8770 (mt0) cc_final: 0.8496 (mt0) REVERT: F 79 ASN cc_start: 0.7905 (t0) cc_final: 0.7596 (t0) REVERT: F 95 MET cc_start: 0.8712 (mmm) cc_final: 0.8372 (mmm) REVERT: F 108 PHE cc_start: 0.8878 (p90) cc_final: 0.8554 (p90) REVERT: F 176 GLN cc_start: 0.7762 (tm-30) cc_final: 0.7377 (tm-30) REVERT: F 204 ASP cc_start: 0.8773 (m-30) cc_final: 0.8570 (m-30) REVERT: F 269 ASN cc_start: 0.8581 (m-40) cc_final: 0.8046 (m-40) REVERT: G 37 ILE cc_start: 0.8742 (pt) cc_final: 0.8505 (pt) REVERT: G 79 ASN cc_start: 0.7957 (t0) cc_final: 0.7669 (t0) REVERT: G 107 ASP cc_start: 0.8263 (t70) cc_final: 0.8020 (t0) REVERT: G 141 ASN cc_start: 0.8852 (t0) cc_final: 0.8601 (t0) REVERT: G 203 GLN cc_start: 0.9043 (tp40) cc_final: 0.8394 (tp40) REVERT: G 204 ASP cc_start: 0.8831 (m-30) cc_final: 0.8593 (m-30) REVERT: G 216 LEU cc_start: 0.8629 (tp) cc_final: 0.8381 (mt) REVERT: G 269 ASN cc_start: 0.8420 (m-40) cc_final: 0.7827 (m-40) outliers start: 7 outliers final: 7 residues processed: 415 average time/residue: 0.3056 time to fit residues: 179.6678 Evaluate side-chains 361 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 354 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 142 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.1980 chunk 165 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 63 GLN D 146 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 146 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.1688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 16772 Z= 0.320 Angle : 0.925 14.816 23765 Z= 0.332 Chirality : 0.046 0.141 2128 Planarity : 0.005 0.067 2912 Dihedral : 17.976 89.964 2303 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.56 % Favored : 86.44 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.08 % 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: -2.39 (0.19), residues: 1792 helix: -1.24 (0.28), residues: 287 sheet: -1.44 (0.29), residues: 154 loop : -1.82 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 279 HIS 0.007 0.001 HIS B 64 PHE 0.015 0.002 PHE C 105 TYR 0.014 0.002 TYR E 133 ARG 0.002 0.000 ARG E 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 440 time to evaluate : 1.614 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 PHE cc_start: 0.8110 (t80) cc_final: 0.7514 (t80) REVERT: B 61 VAL cc_start: 0.9198 (m) cc_final: 0.8974 (p) REVERT: B 63 GLN cc_start: 0.8540 (mt0) cc_final: 0.8263 (mt0) REVERT: B 79 ASN cc_start: 0.7968 (t0) cc_final: 0.7523 (t0) REVERT: B 95 MET cc_start: 0.8503 (mmm) cc_final: 0.8200 (mmm) REVERT: B 129 LYS cc_start: 0.9355 (ptpp) cc_final: 0.9029 (mttp) REVERT: B 203 GLN cc_start: 0.8960 (tp40) cc_final: 0.8360 (tp40) REVERT: B 204 ASP cc_start: 0.8973 (m-30) cc_final: 0.8579 (m-30) REVERT: B 228 GLN cc_start: 0.8568 (tt0) cc_final: 0.8245 (tt0) REVERT: B 230 GLU cc_start: 0.8255 (mt-10) cc_final: 0.8015 (mt-10) REVERT: B 238 LEU cc_start: 0.9081 (mp) cc_final: 0.8873 (mp) REVERT: B 243 LYS cc_start: 0.8809 (tmtt) cc_final: 0.8598 (tptp) REVERT: B 263 TRP cc_start: 0.8252 (m100) cc_final: 0.7627 (m100) REVERT: B 269 ASN cc_start: 0.8070 (m-40) cc_final: 0.7433 (t0) REVERT: C 51 LEU cc_start: 0.7530 (mt) cc_final: 0.7322 (mt) REVERT: C 79 ASN cc_start: 0.7829 (t0) cc_final: 0.7305 (t0) REVERT: C 95 MET cc_start: 0.8633 (mmm) cc_final: 0.8195 (mmm) REVERT: C 108 PHE cc_start: 0.8815 (p90) cc_final: 0.8384 (p90) REVERT: C 116 THR cc_start: 0.8861 (m) cc_final: 0.8330 (t) REVERT: C 117 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8065 (mm-40) REVERT: C 179 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7495 (mt-10) REVERT: C 203 GLN cc_start: 0.8953 (tp40) cc_final: 0.8345 (tp40) REVERT: C 228 GLN cc_start: 0.8766 (tt0) cc_final: 0.8124 (tm-30) REVERT: C 263 TRP cc_start: 0.8337 (m100) cc_final: 0.7442 (m100) REVERT: C 269 ASN cc_start: 0.7652 (m-40) cc_final: 0.7017 (t0) REVERT: C 279 TRP cc_start: 0.7655 (t-100) cc_final: 0.7276 (t-100) REVERT: D 79 ASN cc_start: 0.7911 (t0) cc_final: 0.7520 (t0) REVERT: D 108 PHE cc_start: 0.8786 (p90) cc_final: 0.8524 (p90) REVERT: D 179 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7603 (mt-10) REVERT: D 182 HIS cc_start: 0.8259 (m-70) cc_final: 0.7464 (m170) REVERT: D 203 GLN cc_start: 0.9040 (tp40) cc_final: 0.8496 (tp40) REVERT: D 204 ASP cc_start: 0.8859 (m-30) cc_final: 0.8582 (m-30) REVERT: D 226 ILE cc_start: 0.9015 (tp) cc_final: 0.8785 (tp) REVERT: D 227 ARG cc_start: 0.8803 (mmt180) cc_final: 0.8584 (mtt180) REVERT: D 230 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7746 (mt-10) REVERT: D 242 GLN cc_start: 0.8156 (tp40) cc_final: 0.7899 (tp-100) REVERT: D 269 ASN cc_start: 0.7829 (m-40) cc_final: 0.7188 (t0) REVERT: D 273 GLN cc_start: 0.8487 (mt0) cc_final: 0.8163 (mt0) REVERT: A 34 PHE cc_start: 0.8619 (p90) cc_final: 0.8398 (p90) REVERT: A 37 ILE cc_start: 0.8620 (pt) cc_final: 0.8276 (pt) REVERT: A 61 VAL cc_start: 0.9252 (m) cc_final: 0.9034 (p) REVERT: A 197 ARG cc_start: 0.6657 (ttp-170) cc_final: 0.6436 (ttt-90) REVERT: A 203 GLN cc_start: 0.8967 (tp40) cc_final: 0.8649 (tp40) REVERT: A 226 ILE cc_start: 0.8995 (tp) cc_final: 0.8594 (tp) REVERT: A 227 ARG cc_start: 0.8963 (mtt180) cc_final: 0.8511 (mtt180) REVERT: A 230 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7412 (mt-10) REVERT: A 269 ASN cc_start: 0.7695 (m-40) cc_final: 0.7357 (t0) REVERT: E 37 ILE cc_start: 0.8397 (pt) cc_final: 0.8130 (pt) REVERT: E 61 VAL cc_start: 0.9166 (m) cc_final: 0.8965 (p) REVERT: E 79 ASN cc_start: 0.8037 (t0) cc_final: 0.7485 (t0) REVERT: E 129 LYS cc_start: 0.9187 (ptpp) cc_final: 0.8925 (mttp) REVERT: E 133 TYR cc_start: 0.8708 (t80) cc_final: 0.8490 (t80) REVERT: E 203 GLN cc_start: 0.8880 (tp40) cc_final: 0.8572 (tp40) REVERT: E 273 GLN cc_start: 0.8639 (mt0) cc_final: 0.8377 (mt0) REVERT: F 79 ASN cc_start: 0.7939 (t0) cc_final: 0.7590 (t0) REVERT: F 95 MET cc_start: 0.8617 (mmm) cc_final: 0.8270 (mmm) REVERT: F 108 PHE cc_start: 0.8899 (p90) cc_final: 0.8617 (p90) REVERT: F 176 GLN cc_start: 0.7700 (tm-30) cc_final: 0.7393 (tm-30) REVERT: F 203 GLN cc_start: 0.8928 (tp40) cc_final: 0.8655 (tp40) REVERT: F 204 ASP cc_start: 0.8898 (m-30) cc_final: 0.8584 (m-30) REVERT: F 226 ILE cc_start: 0.9001 (tp) cc_final: 0.8641 (tp) REVERT: F 227 ARG cc_start: 0.8802 (mmt180) cc_final: 0.8483 (mtt180) REVERT: F 228 GLN cc_start: 0.8686 (tt0) cc_final: 0.8143 (tm-30) REVERT: F 230 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7522 (mt-10) REVERT: F 269 ASN cc_start: 0.7823 (m-40) cc_final: 0.7583 (t0) REVERT: G 37 ILE cc_start: 0.8521 (pt) cc_final: 0.8194 (pt) REVERT: G 42 PHE cc_start: 0.8009 (t80) cc_final: 0.7775 (t80) REVERT: G 79 ASN cc_start: 0.7971 (t0) cc_final: 0.7598 (t0) REVERT: G 141 ASN cc_start: 0.8834 (t0) cc_final: 0.8469 (t0) REVERT: G 179 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7493 (mt-10) REVERT: G 182 HIS cc_start: 0.8236 (m-70) cc_final: 0.7578 (m170) REVERT: G 183 GLN cc_start: 0.5068 (pm20) cc_final: 0.4831 (pm20) REVERT: G 190 ASP cc_start: 0.9143 (t0) cc_final: 0.8875 (t0) REVERT: G 203 GLN cc_start: 0.9117 (tp40) cc_final: 0.8408 (tp40) REVERT: G 204 ASP cc_start: 0.8942 (m-30) cc_final: 0.8630 (m-30) REVERT: G 226 ILE cc_start: 0.8960 (tp) cc_final: 0.8654 (tp) REVERT: G 227 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8399 (mmt180) REVERT: G 228 GLN cc_start: 0.8631 (tt0) cc_final: 0.8127 (tm-30) REVERT: G 230 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7779 (mt-10) REVERT: G 238 LEU cc_start: 0.8904 (mt) cc_final: 0.8700 (mp) REVERT: G 241 ILE cc_start: 0.9031 (pt) cc_final: 0.8786 (pt) REVERT: G 242 GLN cc_start: 0.8131 (tp40) cc_final: 0.7743 (tp-100) REVERT: G 269 ASN cc_start: 0.7656 (m-40) cc_final: 0.7076 (t0) REVERT: G 279 TRP cc_start: 0.7643 (t-100) cc_final: 0.7368 (t-100) outliers start: 0 outliers final: 0 residues processed: 440 average time/residue: 0.3014 time to fit residues: 188.2200 Evaluate side-chains 405 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 0.2980 chunk 51 optimal weight: 0.4980 chunk 137 optimal weight: 0.6980 chunk 112 optimal weight: 0.0040 chunk 45 optimal weight: 0.5980 chunk 165 optimal weight: 0.8980 chunk 178 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 164 optimal weight: 0.0470 chunk 56 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.2890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 135 HIS B 273 GLN C 63 GLN D 63 GLN D 228 GLN D 273 GLN A 64 HIS A 117 GLN A 146 HIS A 228 GLN ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN F 135 HIS ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN G 135 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16772 Z= 0.246 Angle : 0.827 9.032 23765 Z= 0.313 Chirality : 0.046 0.158 2128 Planarity : 0.005 0.055 2912 Dihedral : 17.779 89.756 2303 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 0.06 % Allowed : 1.80 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -2.09 (0.19), residues: 1792 helix: -1.18 (0.28), residues: 294 sheet: -1.88 (0.42), residues: 84 loop : -1.51 (0.17), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 279 HIS 0.005 0.001 HIS A 64 PHE 0.014 0.001 PHE G 108 TYR 0.016 0.002 TYR A 133 ARG 0.003 0.001 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 422 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 61 VAL cc_start: 0.9173 (m) cc_final: 0.8917 (p) REVERT: B 63 GLN cc_start: 0.8508 (mt0) cc_final: 0.8172 (mt0) REVERT: B 79 ASN cc_start: 0.7882 (t0) cc_final: 0.7396 (t0) REVERT: B 95 MET cc_start: 0.8494 (mmm) cc_final: 0.8249 (mmm) REVERT: B 112 PHE cc_start: 0.7282 (m-80) cc_final: 0.7044 (m-80) REVERT: B 129 LYS cc_start: 0.9289 (ptpp) cc_final: 0.8989 (mttp) REVERT: B 135 HIS cc_start: 0.7234 (p90) cc_final: 0.6710 (p90) REVERT: B 203 GLN cc_start: 0.8966 (tp40) cc_final: 0.8710 (tp40) REVERT: B 204 ASP cc_start: 0.8858 (m-30) cc_final: 0.8567 (m-30) REVERT: B 243 LYS cc_start: 0.8774 (tmtt) cc_final: 0.8403 (tptp) REVERT: B 263 TRP cc_start: 0.8259 (m100) cc_final: 0.7873 (m100) REVERT: C 62 GLN cc_start: 0.8387 (mm110) cc_final: 0.8112 (mm110) REVERT: C 79 ASN cc_start: 0.7733 (t0) cc_final: 0.7393 (t0) REVERT: C 108 PHE cc_start: 0.8797 (p90) cc_final: 0.8528 (p90) REVERT: C 116 THR cc_start: 0.8803 (m) cc_final: 0.8327 (t) REVERT: C 117 GLN cc_start: 0.8299 (mm-40) cc_final: 0.8021 (mm-40) REVERT: C 179 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7283 (mt-10) REVERT: C 183 GLN cc_start: 0.6534 (pm20) cc_final: 0.6016 (pm20) REVERT: C 203 GLN cc_start: 0.8800 (tp40) cc_final: 0.8219 (tp40) REVERT: C 263 TRP cc_start: 0.8288 (m100) cc_final: 0.7516 (m100) REVERT: C 269 ASN cc_start: 0.7481 (m-40) cc_final: 0.6929 (m-40) REVERT: C 279 TRP cc_start: 0.7645 (t-100) cc_final: 0.7292 (t-100) REVERT: D 79 ASN cc_start: 0.7845 (t0) cc_final: 0.7371 (t0) REVERT: D 108 PHE cc_start: 0.8778 (p90) cc_final: 0.8481 (p90) REVERT: D 179 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7413 (mt-10) REVERT: D 182 HIS cc_start: 0.8076 (m-70) cc_final: 0.7310 (m170) REVERT: D 183 GLN cc_start: 0.6912 (pm20) cc_final: 0.6259 (pm20) REVERT: D 203 GLN cc_start: 0.9010 (tp40) cc_final: 0.8494 (tp40) REVERT: D 204 ASP cc_start: 0.8746 (m-30) cc_final: 0.8505 (m-30) REVERT: D 226 ILE cc_start: 0.9053 (tp) cc_final: 0.8757 (tp) REVERT: D 230 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7545 (mt-10) REVERT: D 242 GLN cc_start: 0.8222 (tp40) cc_final: 0.7960 (tp-100) REVERT: D 269 ASN cc_start: 0.7750 (m-40) cc_final: 0.7212 (m-40) REVERT: A 37 ILE cc_start: 0.8458 (pt) cc_final: 0.8105 (pt) REVERT: A 42 PHE cc_start: 0.7734 (t80) cc_final: 0.7221 (t80) REVERT: A 129 LYS cc_start: 0.9320 (ptpp) cc_final: 0.8917 (mttm) REVERT: A 135 HIS cc_start: 0.7316 (p-80) cc_final: 0.6968 (p-80) REVERT: A 176 GLN cc_start: 0.7495 (tm-30) cc_final: 0.7110 (tm-30) REVERT: A 203 GLN cc_start: 0.8866 (tp40) cc_final: 0.8622 (tp40) REVERT: A 226 ILE cc_start: 0.8993 (tp) cc_final: 0.8695 (tp) REVERT: A 227 ARG cc_start: 0.8840 (mtt180) cc_final: 0.8424 (mtt180) REVERT: A 230 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7330 (mt-10) REVERT: A 269 ASN cc_start: 0.7539 (m-40) cc_final: 0.7001 (m-40) REVERT: E 61 VAL cc_start: 0.9217 (m) cc_final: 0.8961 (p) REVERT: E 63 GLN cc_start: 0.8529 (mt0) cc_final: 0.8279 (mt0) REVERT: E 79 ASN cc_start: 0.7897 (t0) cc_final: 0.7358 (t0) REVERT: E 133 TYR cc_start: 0.8669 (t80) cc_final: 0.8364 (t80) REVERT: E 135 HIS cc_start: 0.7042 (p90) cc_final: 0.6665 (p-80) REVERT: E 203 GLN cc_start: 0.8770 (tp40) cc_final: 0.8529 (tp40) REVERT: E 204 ASP cc_start: 0.8531 (m-30) cc_final: 0.8293 (m-30) REVERT: E 269 ASN cc_start: 0.7663 (m-40) cc_final: 0.6645 (m-40) REVERT: E 273 GLN cc_start: 0.8583 (mt0) cc_final: 0.8230 (mt0) REVERT: F 79 ASN cc_start: 0.7761 (t0) cc_final: 0.7332 (t0) REVERT: F 95 MET cc_start: 0.8667 (mmm) cc_final: 0.8342 (mmm) REVERT: F 108 PHE cc_start: 0.8801 (p90) cc_final: 0.8131 (p90) REVERT: F 135 HIS cc_start: 0.7069 (p90) cc_final: 0.6635 (p90) REVERT: F 203 GLN cc_start: 0.8906 (tp40) cc_final: 0.8645 (tp40) REVERT: F 204 ASP cc_start: 0.8849 (m-30) cc_final: 0.8457 (m-30) REVERT: F 226 ILE cc_start: 0.9001 (tp) cc_final: 0.8648 (tp) REVERT: F 228 GLN cc_start: 0.8799 (tt0) cc_final: 0.8250 (tm-30) REVERT: F 230 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7532 (mt-10) REVERT: F 269 ASN cc_start: 0.7570 (m-40) cc_final: 0.7053 (m-40) REVERT: G 79 ASN cc_start: 0.7933 (t0) cc_final: 0.7613 (t0) REVERT: G 108 PHE cc_start: 0.9020 (p90) cc_final: 0.8803 (p90) REVERT: G 116 THR cc_start: 0.8764 (t) cc_final: 0.8460 (t) REVERT: G 179 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7417 (mt-10) REVERT: G 182 HIS cc_start: 0.8186 (m-70) cc_final: 0.7434 (m-70) REVERT: G 190 ASP cc_start: 0.9102 (t0) cc_final: 0.8823 (t0) REVERT: G 203 GLN cc_start: 0.9059 (tp40) cc_final: 0.8774 (tp40) REVERT: G 204 ASP cc_start: 0.8846 (m-30) cc_final: 0.8554 (m-30) REVERT: G 228 GLN cc_start: 0.8807 (tt0) cc_final: 0.8557 (tt0) REVERT: G 231 VAL cc_start: 0.8637 (t) cc_final: 0.8416 (p) REVERT: G 238 LEU cc_start: 0.8944 (mt) cc_final: 0.8714 (mt) REVERT: G 241 ILE cc_start: 0.9018 (pt) cc_final: 0.8788 (pt) REVERT: G 242 GLN cc_start: 0.8245 (tp40) cc_final: 0.8002 (tp40) REVERT: G 263 TRP cc_start: 0.8219 (m100) cc_final: 0.7940 (m100) REVERT: G 269 ASN cc_start: 0.7544 (m-40) cc_final: 0.6949 (m-40) REVERT: G 279 TRP cc_start: 0.7559 (t-100) cc_final: 0.7158 (t-100) outliers start: 1 outliers final: 0 residues processed: 422 average time/residue: 0.3273 time to fit residues: 197.8443 Evaluate side-chains 379 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 1.9990 chunk 124 optimal weight: 0.7980 chunk 85 optimal weight: 0.0050 chunk 18 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.3980 chunk 86 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.4512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 GLN B 228 GLN B 273 GLN C 228 GLN D 117 GLN D 146 HIS ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 64 HIS A 146 HIS A 228 GLN A 273 GLN E 64 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN F 273 GLN ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16772 Z= 0.281 Angle : 0.826 10.933 23765 Z= 0.312 Chirality : 0.046 0.135 2128 Planarity : 0.005 0.048 2912 Dihedral : 17.768 89.847 2303 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.78 % Favored : 86.22 % Rotamer: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.20), residues: 1792 helix: -1.25 (0.27), residues: 301 sheet: -1.61 (0.34), residues: 154 loop : -1.62 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 279 HIS 0.008 0.001 HIS G 276 PHE 0.013 0.001 PHE F 103 TYR 0.017 0.002 TYR D 133 ARG 0.003 0.001 ARG D 197 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 426 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLN cc_start: 0.8508 (mt0) cc_final: 0.8159 (mt0) REVERT: B 79 ASN cc_start: 0.7842 (t0) cc_final: 0.7362 (t0) REVERT: B 112 PHE cc_start: 0.7284 (m-80) cc_final: 0.7046 (m-80) REVERT: B 129 LYS cc_start: 0.9284 (ptpp) cc_final: 0.8968 (mttp) REVERT: B 135 HIS cc_start: 0.7083 (p90) cc_final: 0.6702 (p-80) REVERT: B 203 GLN cc_start: 0.8902 (tp40) cc_final: 0.8683 (tp40) REVERT: B 204 ASP cc_start: 0.8850 (m-30) cc_final: 0.8548 (m-30) REVERT: B 230 GLU cc_start: 0.8412 (tt0) cc_final: 0.8180 (tt0) REVERT: B 243 LYS cc_start: 0.8750 (tmtt) cc_final: 0.8390 (tptp) REVERT: B 263 TRP cc_start: 0.8264 (m100) cc_final: 0.7932 (m100) REVERT: C 62 GLN cc_start: 0.8420 (mm110) cc_final: 0.8160 (mm110) REVERT: C 79 ASN cc_start: 0.7759 (t0) cc_final: 0.7162 (t0) REVERT: C 108 PHE cc_start: 0.8803 (p90) cc_final: 0.8480 (p90) REVERT: C 116 THR cc_start: 0.8798 (m) cc_final: 0.8297 (t) REVERT: C 117 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7919 (mm110) REVERT: C 135 HIS cc_start: 0.7256 (p90) cc_final: 0.6976 (p90) REVERT: C 179 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7311 (mt-10) REVERT: C 182 HIS cc_start: 0.8096 (m-70) cc_final: 0.7545 (m170) REVERT: C 203 GLN cc_start: 0.8799 (tp40) cc_final: 0.8160 (tp40) REVERT: C 204 ASP cc_start: 0.8655 (m-30) cc_final: 0.8453 (m-30) REVERT: C 263 TRP cc_start: 0.8301 (m100) cc_final: 0.7589 (m100) REVERT: C 269 ASN cc_start: 0.7498 (m-40) cc_final: 0.6943 (m-40) REVERT: C 279 TRP cc_start: 0.7655 (t-100) cc_final: 0.7322 (t-100) REVERT: D 51 LEU cc_start: 0.7244 (mt) cc_final: 0.7036 (mt) REVERT: D 79 ASN cc_start: 0.7916 (t0) cc_final: 0.7499 (t0) REVERT: D 108 PHE cc_start: 0.8783 (p90) cc_final: 0.8522 (p90) REVERT: D 130 ASP cc_start: 0.7996 (t0) cc_final: 0.7588 (t0) REVERT: D 179 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7362 (mt-10) REVERT: D 182 HIS cc_start: 0.8112 (m-70) cc_final: 0.7364 (m170) REVERT: D 183 GLN cc_start: 0.6166 (pm20) cc_final: 0.5720 (pm20) REVERT: D 203 GLN cc_start: 0.9009 (tp40) cc_final: 0.8508 (tp40) REVERT: D 204 ASP cc_start: 0.8747 (m-30) cc_final: 0.8492 (m-30) REVERT: D 226 ILE cc_start: 0.8997 (tp) cc_final: 0.8697 (mp) REVERT: D 230 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7587 (mt-10) REVERT: D 242 GLN cc_start: 0.8203 (tp40) cc_final: 0.7890 (tp-100) REVERT: A 37 ILE cc_start: 0.8423 (pt) cc_final: 0.8104 (pt) REVERT: A 62 GLN cc_start: 0.8533 (mm110) cc_final: 0.8077 (mm110) REVERT: A 129 LYS cc_start: 0.9255 (ptpp) cc_final: 0.8870 (mttm) REVERT: A 133 TYR cc_start: 0.8582 (t80) cc_final: 0.8291 (t80) REVERT: A 135 HIS cc_start: 0.7497 (p-80) cc_final: 0.6953 (p-80) REVERT: A 203 GLN cc_start: 0.8850 (tp40) cc_final: 0.8629 (tp40) REVERT: A 226 ILE cc_start: 0.8994 (tp) cc_final: 0.8647 (tp) REVERT: A 230 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7291 (mt-10) REVERT: A 269 ASN cc_start: 0.7586 (m-40) cc_final: 0.7054 (m-40) REVERT: E 61 VAL cc_start: 0.9233 (m) cc_final: 0.9029 (p) REVERT: E 63 GLN cc_start: 0.8503 (mt0) cc_final: 0.8254 (mt0) REVERT: E 79 ASN cc_start: 0.7961 (t0) cc_final: 0.7414 (t0) REVERT: E 133 TYR cc_start: 0.8692 (t80) cc_final: 0.8397 (t80) REVERT: E 146 HIS cc_start: 0.8316 (p90) cc_final: 0.8060 (p-80) REVERT: E 179 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7397 (mt-10) REVERT: E 203 GLN cc_start: 0.8776 (tp40) cc_final: 0.8479 (tp40) REVERT: E 204 ASP cc_start: 0.8542 (m-30) cc_final: 0.8289 (m-30) REVERT: E 216 LEU cc_start: 0.8999 (tt) cc_final: 0.8743 (tt) REVERT: E 255 LYS cc_start: 0.8896 (pttm) cc_final: 0.8691 (ptpp) REVERT: E 260 ASP cc_start: 0.7971 (t0) cc_final: 0.7769 (t0) REVERT: E 261 LEU cc_start: 0.8167 (pt) cc_final: 0.7916 (pt) REVERT: E 269 ASN cc_start: 0.7676 (m-40) cc_final: 0.6820 (m-40) REVERT: F 79 ASN cc_start: 0.7808 (t0) cc_final: 0.7426 (t0) REVERT: F 95 MET cc_start: 0.8543 (mmm) cc_final: 0.8127 (mmp) REVERT: F 105 PHE cc_start: 0.8561 (m-80) cc_final: 0.8293 (m-80) REVERT: F 108 PHE cc_start: 0.8804 (p90) cc_final: 0.8398 (p90) REVERT: F 109 ARG cc_start: 0.8821 (mmt180) cc_final: 0.8497 (mmt180) REVERT: F 129 LYS cc_start: 0.9259 (mttp) cc_final: 0.8979 (tppt) REVERT: F 135 HIS cc_start: 0.7022 (p90) cc_final: 0.6796 (p90) REVERT: F 203 GLN cc_start: 0.8886 (tp40) cc_final: 0.8634 (tp40) REVERT: F 204 ASP cc_start: 0.8902 (m-30) cc_final: 0.8493 (m-30) REVERT: F 226 ILE cc_start: 0.8989 (tp) cc_final: 0.8686 (tp) REVERT: F 227 ARG cc_start: 0.8826 (mmt180) cc_final: 0.8221 (mmm160) REVERT: F 230 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7609 (mt-10) REVERT: F 242 GLN cc_start: 0.8196 (tp40) cc_final: 0.7900 (tp-100) REVERT: F 269 ASN cc_start: 0.7624 (m-40) cc_final: 0.6958 (m-40) REVERT: G 46 THR cc_start: 0.7919 (t) cc_final: 0.7464 (p) REVERT: G 79 ASN cc_start: 0.8035 (t0) cc_final: 0.7643 (t0) REVERT: G 116 THR cc_start: 0.8751 (t) cc_final: 0.8310 (t) REVERT: G 129 LYS cc_start: 0.9271 (mttp) cc_final: 0.9052 (mttp) REVERT: G 176 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6966 (tm-30) REVERT: G 190 ASP cc_start: 0.9085 (t0) cc_final: 0.8766 (t0) REVERT: G 203 GLN cc_start: 0.9054 (tp40) cc_final: 0.8759 (tp40) REVERT: G 204 ASP cc_start: 0.8821 (m-30) cc_final: 0.8557 (m-30) REVERT: G 213 ASP cc_start: 0.8691 (t0) cc_final: 0.8475 (t0) REVERT: G 226 ILE cc_start: 0.8886 (mt) cc_final: 0.8462 (mt) REVERT: G 230 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 241 ILE cc_start: 0.9012 (pt) cc_final: 0.8756 (pt) REVERT: G 242 GLN cc_start: 0.8210 (tp40) cc_final: 0.7764 (tp-100) REVERT: G 263 TRP cc_start: 0.8244 (m100) cc_final: 0.7899 (m100) REVERT: G 269 ASN cc_start: 0.7502 (m-40) cc_final: 0.6932 (m-40) outliers start: 0 outliers final: 0 residues processed: 426 average time/residue: 0.3000 time to fit residues: 181.9348 Evaluate side-chains 384 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 157 optimal weight: 0.4980 chunk 44 optimal weight: 0.0770 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 228 GLN B 273 GLN ** C 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN D 228 GLN D 273 GLN ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN A 273 GLN ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 GLN F 63 GLN ** F 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 228 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.139 16772 Z= 0.606 Angle : 1.121 17.828 23765 Z= 0.415 Chirality : 0.052 0.151 2128 Planarity : 0.005 0.049 2912 Dihedral : 18.488 89.695 2303 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 24.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.85 % Favored : 83.15 % Rotamer: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % 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: -2.64 (0.19), residues: 1792 helix: -1.59 (0.27), residues: 294 sheet: -2.53 (0.32), residues: 140 loop : -1.83 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP F 279 HIS 0.015 0.002 HIS G 276 PHE 0.028 0.003 PHE E 34 TYR 0.025 0.002 TYR B 151 ARG 0.008 0.001 ARG E 197 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 51 LEU cc_start: 0.8038 (mt) cc_final: 0.7821 (mt) REVERT: B 63 GLN cc_start: 0.8688 (mt0) cc_final: 0.8267 (mp10) REVERT: B 95 MET cc_start: 0.8639 (mmp) cc_final: 0.8313 (mmm) REVERT: B 129 LYS cc_start: 0.9271 (ptpp) cc_final: 0.9008 (mttp) REVERT: B 151 TYR cc_start: 0.8743 (p90) cc_final: 0.8475 (p90) REVERT: B 203 GLN cc_start: 0.8980 (tp40) cc_final: 0.8544 (tp40) REVERT: B 204 ASP cc_start: 0.9078 (m-30) cc_final: 0.8690 (m-30) REVERT: B 238 LEU cc_start: 0.8983 (mp) cc_final: 0.8749 (mp) REVERT: C 62 GLN cc_start: 0.8583 (mm110) cc_final: 0.8367 (mm110) REVERT: C 79 ASN cc_start: 0.8114 (t0) cc_final: 0.7844 (t0) REVERT: C 108 PHE cc_start: 0.8860 (p90) cc_final: 0.8544 (p90) REVERT: C 116 THR cc_start: 0.8804 (m) cc_final: 0.8418 (t) REVERT: C 117 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7974 (mm-40) REVERT: C 149 PRO cc_start: 0.9018 (Cg_exo) cc_final: 0.8503 (Cg_endo) REVERT: C 179 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 182 HIS cc_start: 0.8185 (m-70) cc_final: 0.7707 (m-70) REVERT: C 203 GLN cc_start: 0.8972 (tp40) cc_final: 0.7892 (tp40) REVERT: C 204 ASP cc_start: 0.9011 (m-30) cc_final: 0.8720 (m-30) REVERT: C 230 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7895 (mt-10) REVERT: C 238 LEU cc_start: 0.8865 (mt) cc_final: 0.8616 (mt) REVERT: C 269 ASN cc_start: 0.7806 (m-40) cc_final: 0.7326 (m-40) REVERT: D 46 THR cc_start: 0.8688 (t) cc_final: 0.8346 (t) REVERT: D 51 LEU cc_start: 0.7924 (mt) cc_final: 0.7714 (mt) REVERT: D 135 HIS cc_start: 0.7300 (p90) cc_final: 0.6613 (p90) REVERT: D 203 GLN cc_start: 0.9038 (tp40) cc_final: 0.8490 (tp40) REVERT: D 204 ASP cc_start: 0.9019 (m-30) cc_final: 0.8759 (m-30) REVERT: D 226 ILE cc_start: 0.9178 (tp) cc_final: 0.8975 (tp) REVERT: D 228 GLN cc_start: 0.8242 (tt0) cc_final: 0.7942 (tm-30) REVERT: D 230 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7773 (mt-10) REVERT: D 269 ASN cc_start: 0.8164 (m-40) cc_final: 0.7568 (m-40) REVERT: A 51 LEU cc_start: 0.8033 (mt) cc_final: 0.7815 (mt) REVERT: A 95 MET cc_start: 0.8592 (mmm) cc_final: 0.8309 (mmp) REVERT: A 108 PHE cc_start: 0.8891 (p90) cc_final: 0.8683 (p90) REVERT: A 129 LYS cc_start: 0.9304 (ptpp) cc_final: 0.8909 (mttm) REVERT: A 133 TYR cc_start: 0.8792 (t80) cc_final: 0.8468 (t80) REVERT: A 135 HIS cc_start: 0.7830 (p-80) cc_final: 0.7368 (p-80) REVERT: A 176 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7153 (tm-30) REVERT: A 197 ARG cc_start: 0.6663 (ttt180) cc_final: 0.6341 (ttt180) REVERT: A 203 GLN cc_start: 0.8933 (tp40) cc_final: 0.8584 (tp40) REVERT: A 227 ARG cc_start: 0.8902 (mtt180) cc_final: 0.8506 (mtt180) REVERT: A 230 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7509 (mt-10) REVERT: A 269 ASN cc_start: 0.7993 (m-40) cc_final: 0.7598 (m-40) REVERT: E 46 THR cc_start: 0.8542 (t) cc_final: 0.7992 (p) REVERT: E 51 LEU cc_start: 0.7813 (mt) cc_final: 0.7577 (mt) REVERT: E 63 GLN cc_start: 0.8593 (mt0) cc_final: 0.8224 (mt0) REVERT: E 133 TYR cc_start: 0.8803 (t80) cc_final: 0.8514 (t80) REVERT: E 146 HIS cc_start: 0.8217 (p90) cc_final: 0.7938 (p-80) REVERT: E 176 GLN cc_start: 0.7547 (tm-30) cc_final: 0.6998 (tm-30) REVERT: E 200 PHE cc_start: 0.8267 (m-80) cc_final: 0.7374 (m-10) REVERT: E 203 GLN cc_start: 0.8925 (tp40) cc_final: 0.8464 (tp40) REVERT: E 204 ASP cc_start: 0.8846 (m-30) cc_final: 0.7981 (t0) REVERT: E 269 ASN cc_start: 0.8039 (m-40) cc_final: 0.7686 (m-40) REVERT: F 51 LEU cc_start: 0.7850 (mt) cc_final: 0.7615 (mt) REVERT: F 60 LEU cc_start: 0.9228 (mm) cc_final: 0.9000 (mm) REVERT: F 62 GLN cc_start: 0.8654 (mm110) cc_final: 0.8390 (mm110) REVERT: F 79 ASN cc_start: 0.8055 (t0) cc_final: 0.7737 (t0) REVERT: F 95 MET cc_start: 0.8159 (mmm) cc_final: 0.7710 (mmm) REVERT: F 176 GLN cc_start: 0.7381 (tm-30) cc_final: 0.7109 (tm-30) REVERT: F 200 PHE cc_start: 0.8330 (m-80) cc_final: 0.7962 (m-10) REVERT: F 203 GLN cc_start: 0.8931 (tp40) cc_final: 0.8015 (tp40) REVERT: F 204 ASP cc_start: 0.9070 (m-30) cc_final: 0.8128 (t0) REVERT: F 226 ILE cc_start: 0.9076 (tp) cc_final: 0.8741 (tp) REVERT: F 227 ARG cc_start: 0.8521 (mmt90) cc_final: 0.7921 (mmt90) REVERT: F 230 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7583 (mt-10) REVERT: F 263 TRP cc_start: 0.8611 (m100) cc_final: 0.8211 (m100) REVERT: F 269 ASN cc_start: 0.8402 (m-40) cc_final: 0.7623 (m-40) REVERT: G 37 ILE cc_start: 0.8326 (pt) cc_final: 0.7735 (mt) REVERT: G 51 LEU cc_start: 0.7883 (mt) cc_final: 0.7658 (mt) REVERT: G 79 ASN cc_start: 0.8251 (t0) cc_final: 0.8043 (t0) REVERT: G 117 GLN cc_start: 0.8340 (mm110) cc_final: 0.8041 (mm110) REVERT: G 135 HIS cc_start: 0.7229 (p-80) cc_final: 0.6974 (p90) REVERT: G 141 ASN cc_start: 0.8940 (t0) cc_final: 0.8475 (t0) REVERT: G 146 HIS cc_start: 0.8216 (p90) cc_final: 0.7969 (p90) REVERT: G 190 ASP cc_start: 0.8995 (t0) cc_final: 0.8674 (t0) REVERT: G 204 ASP cc_start: 0.9087 (m-30) cc_final: 0.8747 (m-30) REVERT: G 213 ASP cc_start: 0.8861 (t0) cc_final: 0.8513 (t0) REVERT: G 216 LEU cc_start: 0.9090 (tt) cc_final: 0.8848 (tt) REVERT: G 226 ILE cc_start: 0.9090 (mt) cc_final: 0.8676 (mt) REVERT: G 230 GLU cc_start: 0.8420 (mt-10) cc_final: 0.8022 (mt-10) REVERT: G 241 ILE cc_start: 0.9092 (pt) cc_final: 0.8553 (pt) REVERT: G 242 GLN cc_start: 0.8012 (tp40) cc_final: 0.7475 (tp-100) REVERT: G 269 ASN cc_start: 0.7855 (m-40) cc_final: 0.7399 (m-40) outliers start: 0 outliers final: 0 residues processed: 441 average time/residue: 0.3203 time to fit residues: 201.4812 Evaluate side-chains 400 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 43 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN ** C 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS E 228 GLN F 63 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 273 GLN ** G 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 16772 Z= 0.375 Angle : 0.925 14.070 23765 Z= 0.354 Chirality : 0.049 0.140 2128 Planarity : 0.004 0.044 2912 Dihedral : 18.439 89.481 2303 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.79 % Favored : 85.21 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 4.76 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.71 (0.19), residues: 1792 helix: -1.74 (0.25), residues: 294 sheet: -2.50 (0.34), residues: 140 loop : -1.87 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 279 HIS 0.009 0.001 HIS B 64 PHE 0.018 0.002 PHE G 42 TYR 0.014 0.002 TYR B 151 ARG 0.004 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8464 (t) cc_final: 0.8048 (p) REVERT: B 51 LEU cc_start: 0.7811 (mt) cc_final: 0.7603 (mt) REVERT: B 57 ASP cc_start: 0.7612 (t0) cc_final: 0.7309 (t70) REVERT: B 63 GLN cc_start: 0.8559 (mt0) cc_final: 0.8122 (mp10) REVERT: B 95 MET cc_start: 0.8663 (mmp) cc_final: 0.8393 (mmp) REVERT: B 108 PHE cc_start: 0.8867 (p90) cc_final: 0.8514 (p90) REVERT: B 129 LYS cc_start: 0.9225 (ptpp) cc_final: 0.9015 (mttp) REVERT: B 151 TYR cc_start: 0.8850 (p90) cc_final: 0.8614 (p90) REVERT: B 200 PHE cc_start: 0.8274 (m-80) cc_final: 0.7405 (m-10) REVERT: B 203 GLN cc_start: 0.8980 (tp40) cc_final: 0.8570 (tp40) REVERT: B 204 ASP cc_start: 0.9019 (m-30) cc_final: 0.8056 (t0) REVERT: B 228 GLN cc_start: 0.8395 (tt0) cc_final: 0.8009 (tm-30) REVERT: C 46 THR cc_start: 0.8481 (t) cc_final: 0.8192 (t) REVERT: C 51 LEU cc_start: 0.7575 (mt) cc_final: 0.7291 (mt) REVERT: C 79 ASN cc_start: 0.8003 (t0) cc_final: 0.7718 (t0) REVERT: C 108 PHE cc_start: 0.8889 (p90) cc_final: 0.8320 (p90) REVERT: C 117 GLN cc_start: 0.8261 (mm-40) cc_final: 0.8028 (mm-40) REVERT: C 135 HIS cc_start: 0.7402 (p90) cc_final: 0.7056 (p90) REVERT: C 179 GLU cc_start: 0.7697 (mt-10) cc_final: 0.7479 (mt-10) REVERT: C 182 HIS cc_start: 0.7931 (m-70) cc_final: 0.7326 (m170) REVERT: C 203 GLN cc_start: 0.8938 (tp40) cc_final: 0.8032 (tp40) REVERT: C 227 ARG cc_start: 0.8769 (mtt180) cc_final: 0.8216 (mmt90) REVERT: C 230 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7731 (mt-10) REVERT: C 238 LEU cc_start: 0.8922 (mt) cc_final: 0.8680 (mt) REVERT: C 269 ASN cc_start: 0.7744 (m-40) cc_final: 0.7239 (m-40) REVERT: D 62 GLN cc_start: 0.8573 (mm110) cc_final: 0.8276 (mm110) REVERT: D 179 GLU cc_start: 0.7668 (mt-10) cc_final: 0.7274 (mt-10) REVERT: D 182 HIS cc_start: 0.7975 (m-70) cc_final: 0.7276 (m170) REVERT: D 203 GLN cc_start: 0.9065 (tp40) cc_final: 0.8526 (tp40) REVERT: D 204 ASP cc_start: 0.8993 (m-30) cc_final: 0.8705 (m-30) REVERT: D 226 ILE cc_start: 0.9077 (tp) cc_final: 0.8815 (tp) REVERT: D 230 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 238 LEU cc_start: 0.8968 (mt) cc_final: 0.8756 (mt) REVERT: D 269 ASN cc_start: 0.8014 (m-40) cc_final: 0.7799 (m-40) REVERT: A 46 THR cc_start: 0.8609 (t) cc_final: 0.8326 (t) REVERT: A 51 LEU cc_start: 0.7797 (mt) cc_final: 0.7573 (mt) REVERT: A 108 PHE cc_start: 0.8866 (p90) cc_final: 0.8621 (p90) REVERT: A 129 LYS cc_start: 0.9242 (ptpp) cc_final: 0.9005 (mttm) REVERT: A 133 TYR cc_start: 0.8698 (t80) cc_final: 0.8351 (t80) REVERT: A 135 HIS cc_start: 0.7668 (p-80) cc_final: 0.7211 (p-80) REVERT: A 176 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7369 (tm-30) REVERT: A 203 GLN cc_start: 0.8892 (tp40) cc_final: 0.8598 (tp40) REVERT: A 226 ILE cc_start: 0.9027 (tp) cc_final: 0.8720 (tp) REVERT: A 227 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8168 (mtt180) REVERT: A 230 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7385 (mt-10) REVERT: A 269 ASN cc_start: 0.7992 (m-40) cc_final: 0.7454 (m-40) REVERT: E 46 THR cc_start: 0.8445 (t) cc_final: 0.7719 (p) REVERT: E 51 LEU cc_start: 0.7842 (mt) cc_final: 0.7633 (mt) REVERT: E 63 GLN cc_start: 0.8593 (mt0) cc_final: 0.8245 (mt0) REVERT: E 129 LYS cc_start: 0.9034 (ptpp) cc_final: 0.8826 (mttp) REVERT: E 133 TYR cc_start: 0.8740 (t80) cc_final: 0.8444 (t80) REVERT: E 176 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7156 (tm-30) REVERT: E 203 GLN cc_start: 0.8872 (tp40) cc_final: 0.8508 (tp40) REVERT: E 228 GLN cc_start: 0.8342 (tt0) cc_final: 0.7586 (tm-30) REVERT: F 46 THR cc_start: 0.8377 (t) cc_final: 0.7867 (p) REVERT: F 51 LEU cc_start: 0.7671 (mt) cc_final: 0.7438 (mt) REVERT: F 60 LEU cc_start: 0.9070 (mm) cc_final: 0.8737 (mt) REVERT: F 79 ASN cc_start: 0.8049 (t0) cc_final: 0.7716 (t0) REVERT: F 95 MET cc_start: 0.8636 (mmm) cc_final: 0.8366 (mmm) REVERT: F 108 PHE cc_start: 0.8902 (p90) cc_final: 0.8605 (p90) REVERT: F 129 LYS cc_start: 0.9181 (mmtp) cc_final: 0.8950 (tppt) REVERT: F 130 ASP cc_start: 0.8032 (t0) cc_final: 0.7625 (t0) REVERT: F 203 GLN cc_start: 0.8898 (tp40) cc_final: 0.8512 (tp40) REVERT: F 204 ASP cc_start: 0.9063 (m-30) cc_final: 0.8711 (m-30) REVERT: F 226 ILE cc_start: 0.8986 (tp) cc_final: 0.8550 (tp) REVERT: F 227 ARG cc_start: 0.8362 (mmt90) cc_final: 0.8095 (mmt90) REVERT: F 228 GLN cc_start: 0.8592 (tt0) cc_final: 0.8228 (tm-30) REVERT: F 230 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7550 (mt-10) REVERT: F 238 LEU cc_start: 0.8914 (mt) cc_final: 0.8704 (mt) REVERT: F 243 LYS cc_start: 0.8755 (tmtt) cc_final: 0.8554 (tptp) REVERT: F 263 TRP cc_start: 0.8502 (m100) cc_final: 0.8271 (m100) REVERT: F 269 ASN cc_start: 0.7861 (m-40) cc_final: 0.7244 (m-40) REVERT: G 37 ILE cc_start: 0.8291 (pt) cc_final: 0.7782 (mt) REVERT: G 62 GLN cc_start: 0.8670 (mm110) cc_final: 0.8189 (mm110) REVERT: G 79 ASN cc_start: 0.8396 (t0) cc_final: 0.8023 (t0) REVERT: G 107 ASP cc_start: 0.8398 (t0) cc_final: 0.8008 (t0) REVERT: G 117 GLN cc_start: 0.8263 (mm110) cc_final: 0.8035 (mm110) REVERT: G 129 LYS cc_start: 0.9272 (mttp) cc_final: 0.9005 (mttp) REVERT: G 141 ASN cc_start: 0.8902 (t0) cc_final: 0.8459 (t0) REVERT: G 149 PRO cc_start: 0.9051 (Cg_exo) cc_final: 0.8675 (Cg_endo) REVERT: G 190 ASP cc_start: 0.9070 (t0) cc_final: 0.8738 (t0) REVERT: G 204 ASP cc_start: 0.9037 (m-30) cc_final: 0.8772 (m-30) REVERT: G 213 ASP cc_start: 0.8769 (t0) cc_final: 0.8381 (t0) REVERT: G 226 ILE cc_start: 0.8918 (mt) cc_final: 0.8411 (mt) REVERT: G 228 GLN cc_start: 0.8757 (tt0) cc_final: 0.8469 (tt0) REVERT: G 230 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7942 (mt-10) REVERT: G 241 ILE cc_start: 0.9027 (pt) cc_final: 0.8513 (pt) REVERT: G 242 GLN cc_start: 0.8094 (tp40) cc_final: 0.7429 (tp-100) REVERT: G 266 ILE cc_start: 0.8681 (mp) cc_final: 0.8421 (mp) REVERT: G 269 ASN cc_start: 0.7781 (m-40) cc_final: 0.7283 (m-40) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.3049 time to fit residues: 187.6709 Evaluate side-chains 395 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 0.0870 chunk 19 optimal weight: 0.8980 chunk 100 optimal weight: 0.0270 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 148 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 175 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 228 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS E 146 HIS E 228 GLN F 63 GLN F 117 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 16772 Z= 0.311 Angle : 0.880 11.096 23765 Z= 0.339 Chirality : 0.047 0.140 2128 Planarity : 0.004 0.043 2912 Dihedral : 18.299 89.876 2303 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.51 % Favored : 85.49 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 3.40 % 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: -2.64 (0.19), residues: 1792 helix: -1.85 (0.24), residues: 294 sheet: -2.47 (0.36), residues: 140 loop : -1.77 (0.18), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP F 279 HIS 0.008 0.001 HIS G 276 PHE 0.019 0.002 PHE G 108 TYR 0.018 0.002 TYR G 133 ARG 0.004 0.001 ARG G 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8648 (t) cc_final: 0.8201 (p) REVERT: B 47 LYS cc_start: 0.8827 (tttp) cc_final: 0.8472 (tttp) REVERT: B 57 ASP cc_start: 0.7611 (t0) cc_final: 0.7305 (t70) REVERT: B 63 GLN cc_start: 0.8513 (mt0) cc_final: 0.8145 (mp10) REVERT: B 95 MET cc_start: 0.8685 (mmp) cc_final: 0.8402 (mmp) REVERT: B 108 PHE cc_start: 0.8877 (p90) cc_final: 0.8382 (p90) REVERT: B 151 TYR cc_start: 0.8854 (p90) cc_final: 0.8650 (p90) REVERT: B 200 PHE cc_start: 0.8234 (m-80) cc_final: 0.7513 (m-10) REVERT: B 203 GLN cc_start: 0.8984 (tp40) cc_final: 0.8585 (tp40) REVERT: B 204 ASP cc_start: 0.9006 (m-30) cc_final: 0.8029 (t0) REVERT: C 51 LEU cc_start: 0.7281 (mt) cc_final: 0.7049 (mt) REVERT: C 79 ASN cc_start: 0.7971 (t0) cc_final: 0.7666 (t0) REVERT: C 108 PHE cc_start: 0.8885 (p90) cc_final: 0.8040 (p90) REVERT: C 109 ARG cc_start: 0.9071 (mmt180) cc_final: 0.8624 (mmt180) REVERT: C 135 HIS cc_start: 0.7379 (p90) cc_final: 0.6975 (p90) REVERT: C 182 HIS cc_start: 0.7929 (m-70) cc_final: 0.7379 (m170) REVERT: C 203 GLN cc_start: 0.8903 (tp40) cc_final: 0.8005 (tp40) REVERT: C 204 ASP cc_start: 0.8883 (m-30) cc_final: 0.8660 (m-30) REVERT: C 227 ARG cc_start: 0.8664 (mtt180) cc_final: 0.8141 (mmt90) REVERT: C 230 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7565 (mt-10) REVERT: C 238 LEU cc_start: 0.8932 (mt) cc_final: 0.8697 (mt) REVERT: C 269 ASN cc_start: 0.7706 (m-40) cc_final: 0.7175 (m-40) REVERT: D 46 THR cc_start: 0.8158 (t) cc_final: 0.7872 (t) REVERT: D 62 GLN cc_start: 0.8462 (mm110) cc_final: 0.8125 (mm-40) REVERT: D 79 ASN cc_start: 0.7941 (t0) cc_final: 0.7608 (t0) REVERT: D 129 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8843 (tppt) REVERT: D 135 HIS cc_start: 0.7383 (p-80) cc_final: 0.6930 (p-80) REVERT: D 149 PRO cc_start: 0.9069 (Cg_exo) cc_final: 0.8711 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 182 HIS cc_start: 0.7819 (m-70) cc_final: 0.7190 (m170) REVERT: D 203 GLN cc_start: 0.9037 (tp40) cc_final: 0.8463 (tp40) REVERT: D 204 ASP cc_start: 0.8945 (m-30) cc_final: 0.8344 (t0) REVERT: D 226 ILE cc_start: 0.9062 (tp) cc_final: 0.8796 (tp) REVERT: D 227 ARG cc_start: 0.8788 (mtt180) cc_final: 0.8512 (mtt180) REVERT: D 228 GLN cc_start: 0.8167 (tt0) cc_final: 0.7943 (tm-30) REVERT: D 230 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7569 (mt-10) REVERT: D 238 LEU cc_start: 0.8957 (mt) cc_final: 0.8740 (mt) REVERT: A 108 PHE cc_start: 0.8848 (p90) cc_final: 0.8620 (p90) REVERT: A 109 ARG cc_start: 0.8802 (mmt90) cc_final: 0.8323 (tpp80) REVERT: A 129 LYS cc_start: 0.9228 (ptpp) cc_final: 0.9009 (mttm) REVERT: A 133 TYR cc_start: 0.8658 (t80) cc_final: 0.8326 (t80) REVERT: A 135 HIS cc_start: 0.7779 (p-80) cc_final: 0.7246 (p-80) REVERT: A 176 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7393 (tm-30) REVERT: A 203 GLN cc_start: 0.8853 (tp40) cc_final: 0.8601 (tp40) REVERT: A 226 ILE cc_start: 0.9059 (tp) cc_final: 0.8735 (tp) REVERT: A 227 ARG cc_start: 0.8683 (mtt180) cc_final: 0.8245 (mtt180) REVERT: A 230 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7315 (mt-10) REVERT: A 269 ASN cc_start: 0.7953 (m-40) cc_final: 0.7364 (m-40) REVERT: E 63 GLN cc_start: 0.8420 (mt0) cc_final: 0.8134 (mt0) REVERT: E 79 ASN cc_start: 0.7923 (t0) cc_final: 0.7650 (t0) REVERT: E 108 PHE cc_start: 0.8966 (p90) cc_final: 0.8631 (p90) REVERT: E 133 TYR cc_start: 0.8702 (t80) cc_final: 0.8396 (t80) REVERT: E 203 GLN cc_start: 0.8847 (tp40) cc_final: 0.8519 (tp40) REVERT: E 204 ASP cc_start: 0.8750 (m-30) cc_final: 0.8515 (m-30) REVERT: E 261 LEU cc_start: 0.8075 (pt) cc_final: 0.7859 (pt) REVERT: E 269 ASN cc_start: 0.7814 (m-40) cc_final: 0.7225 (m-40) REVERT: E 270 TRP cc_start: 0.8181 (t-100) cc_final: 0.7945 (t-100) REVERT: F 46 THR cc_start: 0.8424 (t) cc_final: 0.7900 (p) REVERT: F 79 ASN cc_start: 0.7960 (t0) cc_final: 0.7609 (t0) REVERT: F 95 MET cc_start: 0.8505 (mmm) cc_final: 0.8120 (mmm) REVERT: F 108 PHE cc_start: 0.8912 (p90) cc_final: 0.8612 (p90) REVERT: F 129 LYS cc_start: 0.9170 (mmtp) cc_final: 0.8962 (tppt) REVERT: F 176 GLN cc_start: 0.7328 (tm-30) cc_final: 0.6982 (tm-30) REVERT: F 203 GLN cc_start: 0.8883 (tp40) cc_final: 0.8516 (tp40) REVERT: F 204 ASP cc_start: 0.9024 (m-30) cc_final: 0.8673 (m-30) REVERT: F 228 GLN cc_start: 0.8570 (tt0) cc_final: 0.8167 (tm-30) REVERT: F 269 ASN cc_start: 0.8313 (m-40) cc_final: 0.7241 (m-40) REVERT: F 273 GLN cc_start: 0.8844 (mt0) cc_final: 0.8545 (mt0) REVERT: G 37 ILE cc_start: 0.8157 (pt) cc_final: 0.7600 (mt) REVERT: G 79 ASN cc_start: 0.8317 (t0) cc_final: 0.7963 (t0) REVERT: G 107 ASP cc_start: 0.8332 (t0) cc_final: 0.7867 (t0) REVERT: G 116 THR cc_start: 0.8802 (t) cc_final: 0.8368 (t) REVERT: G 117 GLN cc_start: 0.8362 (mm110) cc_final: 0.8138 (mm110) REVERT: G 129 LYS cc_start: 0.9279 (mttp) cc_final: 0.9070 (mttp) REVERT: G 135 HIS cc_start: 0.7110 (p90) cc_final: 0.6902 (p90) REVERT: G 141 ASN cc_start: 0.8859 (t0) cc_final: 0.8470 (t0) REVERT: G 149 PRO cc_start: 0.9046 (Cg_exo) cc_final: 0.8677 (Cg_endo) REVERT: G 190 ASP cc_start: 0.9061 (t0) cc_final: 0.8766 (t0) REVERT: G 204 ASP cc_start: 0.8992 (m-30) cc_final: 0.8732 (m-30) REVERT: G 213 ASP cc_start: 0.8764 (t0) cc_final: 0.8381 (t0) REVERT: G 226 ILE cc_start: 0.8887 (mt) cc_final: 0.8472 (mt) REVERT: G 228 GLN cc_start: 0.8797 (tt0) cc_final: 0.8523 (tt0) REVERT: G 230 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7832 (mt-10) REVERT: G 241 ILE cc_start: 0.9038 (pt) cc_final: 0.8590 (pt) REVERT: G 242 GLN cc_start: 0.8184 (tp40) cc_final: 0.7573 (tp-100) REVERT: G 266 ILE cc_start: 0.8668 (mp) cc_final: 0.8388 (mp) outliers start: 0 outliers final: 0 residues processed: 431 average time/residue: 0.2985 time to fit residues: 183.0444 Evaluate side-chains 399 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 399 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 0.0870 chunk 33 optimal weight: 0.7980 chunk 111 optimal weight: 0.0970 chunk 119 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS E 146 HIS ** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 63 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS G 146 HIS ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16772 Z= 0.289 Angle : 0.866 12.305 23765 Z= 0.333 Chirality : 0.047 0.138 2128 Planarity : 0.004 0.042 2912 Dihedral : 18.221 89.589 2303 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.57 (0.19), residues: 1792 helix: -1.93 (0.23), residues: 301 sheet: -3.34 (0.39), residues: 70 loop : -1.71 (0.17), residues: 1421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 279 HIS 0.008 0.001 HIS G 64 PHE 0.012 0.001 PHE B 103 TYR 0.011 0.001 TYR B 151 ARG 0.003 0.001 ARG D 109 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8673 (t) cc_final: 0.8099 (p) REVERT: B 47 LYS cc_start: 0.8795 (tttp) cc_final: 0.8415 (tttp) REVERT: B 57 ASP cc_start: 0.7624 (t0) cc_final: 0.7374 (t70) REVERT: B 63 GLN cc_start: 0.8495 (mt0) cc_final: 0.8140 (mp10) REVERT: B 95 MET cc_start: 0.8714 (mmp) cc_final: 0.8400 (mmp) REVERT: B 108 PHE cc_start: 0.8887 (p90) cc_final: 0.8180 (p90) REVERT: B 146 HIS cc_start: 0.8227 (p-80) cc_final: 0.7872 (p90) REVERT: B 151 TYR cc_start: 0.8838 (p90) cc_final: 0.8631 (p90) REVERT: B 156 VAL cc_start: 0.8704 (t) cc_final: 0.8391 (p) REVERT: B 200 PHE cc_start: 0.8218 (m-80) cc_final: 0.7490 (m-10) REVERT: B 203 GLN cc_start: 0.8963 (tp40) cc_final: 0.8553 (tp40) REVERT: B 204 ASP cc_start: 0.9008 (m-30) cc_final: 0.8002 (t0) REVERT: C 51 LEU cc_start: 0.7268 (mt) cc_final: 0.7048 (mt) REVERT: C 79 ASN cc_start: 0.7939 (t0) cc_final: 0.7629 (t0) REVERT: C 108 PHE cc_start: 0.8958 (p90) cc_final: 0.7931 (p90) REVERT: C 109 ARG cc_start: 0.9051 (mmt180) cc_final: 0.8506 (mmt180) REVERT: C 135 HIS cc_start: 0.7378 (p90) cc_final: 0.7113 (p90) REVERT: C 139 ILE cc_start: 0.8918 (tp) cc_final: 0.8712 (tp) REVERT: C 203 GLN cc_start: 0.8882 (tp40) cc_final: 0.8527 (tp40) REVERT: C 230 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7552 (mt-10) REVERT: C 238 LEU cc_start: 0.8944 (mt) cc_final: 0.8702 (mt) REVERT: C 269 ASN cc_start: 0.7721 (m-40) cc_final: 0.7184 (m-40) REVERT: D 46 THR cc_start: 0.8288 (t) cc_final: 0.8020 (t) REVERT: D 62 GLN cc_start: 0.8405 (mm110) cc_final: 0.8073 (mm-40) REVERT: D 79 ASN cc_start: 0.7920 (t0) cc_final: 0.7550 (t0) REVERT: D 117 GLN cc_start: 0.8621 (tp40) cc_final: 0.8362 (tp-100) REVERT: D 129 LYS cc_start: 0.9167 (mmtm) cc_final: 0.8905 (tppt) REVERT: D 135 HIS cc_start: 0.7323 (p-80) cc_final: 0.6876 (p-80) REVERT: D 149 PRO cc_start: 0.9125 (Cg_exo) cc_final: 0.8762 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7588 (mt-10) cc_final: 0.7170 (mt-10) REVERT: D 182 HIS cc_start: 0.7644 (m-70) cc_final: 0.7029 (m170) REVERT: D 183 GLN cc_start: 0.7042 (pm20) cc_final: 0.6534 (pm20) REVERT: D 200 PHE cc_start: 0.8142 (m-10) cc_final: 0.7657 (m-10) REVERT: D 203 GLN cc_start: 0.9013 (tp40) cc_final: 0.8436 (tp40) REVERT: D 204 ASP cc_start: 0.8928 (m-30) cc_final: 0.8150 (t0) REVERT: D 230 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 238 LEU cc_start: 0.8963 (mt) cc_final: 0.8757 (mt) REVERT: D 269 ASN cc_start: 0.7971 (m-40) cc_final: 0.7615 (m-40) REVERT: A 133 TYR cc_start: 0.8633 (t80) cc_final: 0.8335 (t80) REVERT: A 135 HIS cc_start: 0.7647 (p-80) cc_final: 0.7250 (p90) REVERT: A 146 HIS cc_start: 0.7943 (p90) cc_final: 0.7539 (p90) REVERT: A 176 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7262 (tm-30) REVERT: A 204 ASP cc_start: 0.8797 (m-30) cc_final: 0.8580 (m-30) REVERT: A 226 ILE cc_start: 0.9004 (tp) cc_final: 0.8642 (tp) REVERT: A 227 ARG cc_start: 0.8632 (mtt180) cc_final: 0.8220 (mtt180) REVERT: A 230 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7252 (mt-10) REVERT: A 269 ASN cc_start: 0.7649 (m-40) cc_final: 0.7015 (m-40) REVERT: E 46 THR cc_start: 0.8177 (t) cc_final: 0.7554 (p) REVERT: E 63 GLN cc_start: 0.8379 (mt0) cc_final: 0.8060 (mt0) REVERT: E 79 ASN cc_start: 0.7857 (t0) cc_final: 0.7495 (t0) REVERT: E 129 LYS cc_start: 0.9123 (mttp) cc_final: 0.8918 (mmtp) REVERT: E 133 TYR cc_start: 0.8672 (t80) cc_final: 0.8358 (t80) REVERT: E 135 HIS cc_start: 0.7523 (p90) cc_final: 0.7027 (p-80) REVERT: E 176 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7095 (tm-30) REVERT: E 203 GLN cc_start: 0.8849 (tp40) cc_final: 0.8499 (tp40) REVERT: E 204 ASP cc_start: 0.8720 (m-30) cc_final: 0.8494 (m-30) REVERT: E 228 GLN cc_start: 0.8277 (tt0) cc_final: 0.7957 (tm-30) REVERT: E 269 ASN cc_start: 0.7823 (m-40) cc_final: 0.7150 (m-40) REVERT: E 270 TRP cc_start: 0.8188 (t-100) cc_final: 0.7547 (t-100) REVERT: F 46 THR cc_start: 0.8423 (t) cc_final: 0.7731 (p) REVERT: F 60 LEU cc_start: 0.9022 (mm) cc_final: 0.8746 (mt) REVERT: F 79 ASN cc_start: 0.7917 (t0) cc_final: 0.7586 (t0) REVERT: F 108 PHE cc_start: 0.8894 (p90) cc_final: 0.8599 (p90) REVERT: F 176 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7213 (tm-30) REVERT: F 183 GLN cc_start: 0.7158 (pm20) cc_final: 0.6902 (pm20) REVERT: F 203 GLN cc_start: 0.8896 (tp40) cc_final: 0.8535 (tp40) REVERT: F 204 ASP cc_start: 0.8997 (m-30) cc_final: 0.8646 (m-30) REVERT: F 226 ILE cc_start: 0.9046 (tp) cc_final: 0.8839 (tp) REVERT: F 228 GLN cc_start: 0.8500 (tt0) cc_final: 0.8140 (tm-30) REVERT: F 230 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7556 (mt-10) REVERT: F 243 LYS cc_start: 0.8746 (tmtt) cc_final: 0.8460 (tptp) REVERT: F 269 ASN cc_start: 0.8294 (m-40) cc_final: 0.7070 (m-40) REVERT: F 273 GLN cc_start: 0.8852 (mt0) cc_final: 0.8530 (mt0) REVERT: G 37 ILE cc_start: 0.8265 (pt) cc_final: 0.7755 (mt) REVERT: G 46 THR cc_start: 0.8328 (t) cc_final: 0.7982 (t) REVERT: G 79 ASN cc_start: 0.8332 (t0) cc_final: 0.7963 (t0) REVERT: G 107 ASP cc_start: 0.8385 (t0) cc_final: 0.7914 (t0) REVERT: G 116 THR cc_start: 0.8792 (t) cc_final: 0.8396 (t) REVERT: G 117 GLN cc_start: 0.8348 (mm110) cc_final: 0.8123 (mm110) REVERT: G 129 LYS cc_start: 0.9267 (mttp) cc_final: 0.9032 (mttp) REVERT: G 141 ASN cc_start: 0.8775 (t0) cc_final: 0.8496 (t0) REVERT: G 149 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8539 (Cg_endo) REVERT: G 190 ASP cc_start: 0.9054 (t0) cc_final: 0.8743 (t0) REVERT: G 204 ASP cc_start: 0.8983 (m-30) cc_final: 0.8703 (m-30) REVERT: G 213 ASP cc_start: 0.8736 (t0) cc_final: 0.8347 (t0) REVERT: G 226 ILE cc_start: 0.8955 (mt) cc_final: 0.8511 (mt) REVERT: G 228 GLN cc_start: 0.8807 (tt0) cc_final: 0.8524 (tt0) REVERT: G 230 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7770 (mt-10) REVERT: G 241 ILE cc_start: 0.9027 (pt) cc_final: 0.8720 (pt) REVERT: G 242 GLN cc_start: 0.8160 (tp40) cc_final: 0.7515 (tp-100) REVERT: G 266 ILE cc_start: 0.8734 (mp) cc_final: 0.8480 (mp) outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.2980 time to fit residues: 184.7659 Evaluate side-chains 405 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.5980 chunk 168 optimal weight: 0.0980 chunk 153 optimal weight: 0.9980 chunk 163 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 147 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 162 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 64 HIS ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS D 228 GLN D 273 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 228 GLN F 33 GLN F 63 GLN ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 16772 Z= 0.346 Angle : 0.898 12.845 23765 Z= 0.342 Chirality : 0.048 0.152 2128 Planarity : 0.004 0.041 2912 Dihedral : 18.189 89.690 2303 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.84 % Favored : 85.16 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.72 % 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: -2.75 (0.19), residues: 1792 helix: -1.92 (0.24), residues: 301 sheet: -2.62 (0.36), residues: 140 loop : -1.84 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 279 HIS 0.008 0.001 HIS E 276 PHE 0.016 0.002 PHE F 103 TYR 0.017 0.002 TYR G 133 ARG 0.005 0.001 ARG E 109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 423 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8600 (t) cc_final: 0.7896 (p) REVERT: B 57 ASP cc_start: 0.7797 (t0) cc_final: 0.7535 (t70) REVERT: B 63 GLN cc_start: 0.8579 (mt0) cc_final: 0.8174 (mp10) REVERT: B 79 ASN cc_start: 0.8056 (t0) cc_final: 0.7785 (t0) REVERT: B 95 MET cc_start: 0.8718 (mmp) cc_final: 0.8356 (mmp) REVERT: B 108 PHE cc_start: 0.8940 (p90) cc_final: 0.8442 (p90) REVERT: B 117 GLN cc_start: 0.8843 (tp40) cc_final: 0.8547 (tp-100) REVERT: B 146 HIS cc_start: 0.8228 (p-80) cc_final: 0.7996 (p-80) REVERT: B 156 VAL cc_start: 0.8772 (t) cc_final: 0.8464 (p) REVERT: B 176 GLN cc_start: 0.7295 (tm-30) cc_final: 0.7095 (tm-30) REVERT: B 203 GLN cc_start: 0.8973 (tp40) cc_final: 0.8536 (tp40) REVERT: B 204 ASP cc_start: 0.9025 (m-30) cc_final: 0.8254 (t0) REVERT: B 228 GLN cc_start: 0.8369 (tt0) cc_final: 0.8049 (tm-30) REVERT: C 79 ASN cc_start: 0.7982 (t0) cc_final: 0.7666 (t0) REVERT: C 108 PHE cc_start: 0.9019 (p90) cc_final: 0.7713 (p90) REVERT: C 109 ARG cc_start: 0.9029 (mmt180) cc_final: 0.8329 (mmt180) REVERT: C 135 HIS cc_start: 0.7357 (p90) cc_final: 0.6959 (p90) REVERT: C 149 PRO cc_start: 0.8864 (Cg_exo) cc_final: 0.8408 (Cg_endo) REVERT: C 203 GLN cc_start: 0.8893 (tp40) cc_final: 0.8483 (tp40) REVERT: C 238 LEU cc_start: 0.8933 (mt) cc_final: 0.8468 (mp) REVERT: C 269 ASN cc_start: 0.7759 (m-40) cc_final: 0.7298 (m-40) REVERT: D 62 GLN cc_start: 0.8390 (mm110) cc_final: 0.8072 (mm-40) REVERT: D 108 PHE cc_start: 0.8833 (p90) cc_final: 0.7867 (p90) REVERT: D 109 ARG cc_start: 0.9082 (mmt180) cc_final: 0.8663 (mmt180) REVERT: D 117 GLN cc_start: 0.8642 (tp40) cc_final: 0.8382 (tp-100) REVERT: D 129 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8938 (tppt) REVERT: D 135 HIS cc_start: 0.7515 (p90) cc_final: 0.7040 (p-80) REVERT: D 149 PRO cc_start: 0.9023 (Cg_exo) cc_final: 0.8628 (Cg_endo) REVERT: D 179 GLU cc_start: 0.7630 (mt-10) cc_final: 0.7265 (mt-10) REVERT: D 182 HIS cc_start: 0.7725 (m-70) cc_final: 0.7095 (m170) REVERT: D 183 GLN cc_start: 0.6947 (pm20) cc_final: 0.6420 (pm20) REVERT: D 203 GLN cc_start: 0.9010 (tp40) cc_final: 0.8432 (tp40) REVERT: D 204 ASP cc_start: 0.8949 (m-30) cc_final: 0.8241 (t0) REVERT: D 226 ILE cc_start: 0.9143 (tp) cc_final: 0.8899 (tp) REVERT: D 227 ARG cc_start: 0.8703 (mtt180) cc_final: 0.8244 (mtt180) REVERT: D 230 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7610 (mt-10) REVERT: D 238 LEU cc_start: 0.8941 (mt) cc_final: 0.8690 (mt) REVERT: A 46 THR cc_start: 0.8462 (t) cc_final: 0.8196 (t) REVERT: A 108 PHE cc_start: 0.8862 (p90) cc_final: 0.8636 (p90) REVERT: A 109 ARG cc_start: 0.8727 (mmt90) cc_final: 0.8339 (tpp80) REVERT: A 133 TYR cc_start: 0.8647 (t80) cc_final: 0.8317 (t80) REVERT: A 135 HIS cc_start: 0.7739 (p-80) cc_final: 0.7223 (p-80) REVERT: A 176 GLN cc_start: 0.7661 (tm-30) cc_final: 0.7268 (tm-30) REVERT: A 226 ILE cc_start: 0.9017 (tp) cc_final: 0.8638 (tp) REVERT: A 227 ARG cc_start: 0.8655 (mtt180) cc_final: 0.8227 (mtt180) REVERT: A 230 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7247 (mt-10) REVERT: A 269 ASN cc_start: 0.8256 (m-40) cc_final: 0.7427 (m-40) REVERT: E 46 THR cc_start: 0.8383 (t) cc_final: 0.7621 (p) REVERT: E 60 LEU cc_start: 0.8957 (mm) cc_final: 0.8713 (mt) REVERT: E 63 GLN cc_start: 0.8427 (mt0) cc_final: 0.8090 (mt0) REVERT: E 79 ASN cc_start: 0.7966 (t0) cc_final: 0.7650 (t0) REVERT: E 109 ARG cc_start: 0.9011 (mmt90) cc_final: 0.8785 (mmm-85) REVERT: E 129 LYS cc_start: 0.9076 (mttp) cc_final: 0.8833 (mmtm) REVERT: E 133 TYR cc_start: 0.8691 (t80) cc_final: 0.8384 (t80) REVERT: E 200 PHE cc_start: 0.8149 (m-80) cc_final: 0.7929 (m-10) REVERT: E 203 GLN cc_start: 0.8848 (tp40) cc_final: 0.8410 (tp40) REVERT: E 204 ASP cc_start: 0.8796 (m-30) cc_final: 0.8109 (t0) REVERT: E 228 GLN cc_start: 0.8277 (tt0) cc_final: 0.8045 (tm-30) REVERT: E 230 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7549 (mt-10) REVERT: E 269 ASN cc_start: 0.8011 (m-40) cc_final: 0.7354 (m-40) REVERT: E 270 TRP cc_start: 0.8218 (t-100) cc_final: 0.7634 (t-100) REVERT: F 79 ASN cc_start: 0.7912 (t0) cc_final: 0.7576 (t0) REVERT: F 108 PHE cc_start: 0.8930 (p90) cc_final: 0.8606 (p90) REVERT: F 176 GLN cc_start: 0.7657 (tm-30) cc_final: 0.7168 (tm-30) REVERT: F 183 GLN cc_start: 0.7180 (pm20) cc_final: 0.6939 (pm20) REVERT: F 197 ARG cc_start: 0.7208 (ttt180) cc_final: 0.6880 (ttt180) REVERT: F 204 ASP cc_start: 0.9010 (m-30) cc_final: 0.8644 (m-30) REVERT: F 227 ARG cc_start: 0.8671 (mmt180) cc_final: 0.8448 (mtt180) REVERT: F 228 GLN cc_start: 0.8501 (tt0) cc_final: 0.8116 (tm-30) REVERT: F 230 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7649 (mt-10) REVERT: F 243 LYS cc_start: 0.8776 (tmtt) cc_final: 0.8365 (tptp) REVERT: F 269 ASN cc_start: 0.8240 (m-40) cc_final: 0.7081 (m-40) REVERT: F 273 GLN cc_start: 0.8910 (mt0) cc_final: 0.8573 (mt0) REVERT: G 37 ILE cc_start: 0.8318 (pt) cc_final: 0.7820 (mt) REVERT: G 79 ASN cc_start: 0.8397 (t0) cc_final: 0.8078 (t0) REVERT: G 107 ASP cc_start: 0.8425 (t0) cc_final: 0.7936 (t0) REVERT: G 116 THR cc_start: 0.8795 (t) cc_final: 0.8381 (t) REVERT: G 117 GLN cc_start: 0.8355 (mm110) cc_final: 0.8138 (mm110) REVERT: G 129 LYS cc_start: 0.9269 (mttp) cc_final: 0.9053 (mttp) REVERT: G 149 PRO cc_start: 0.9023 (Cg_exo) cc_final: 0.8655 (Cg_endo) REVERT: G 179 GLU cc_start: 0.7266 (tm-30) cc_final: 0.7043 (tm-30) REVERT: G 190 ASP cc_start: 0.8982 (t0) cc_final: 0.8691 (t0) REVERT: G 204 ASP cc_start: 0.9004 (m-30) cc_final: 0.8668 (m-30) REVERT: G 213 ASP cc_start: 0.8745 (t0) cc_final: 0.8365 (t0) REVERT: G 226 ILE cc_start: 0.8964 (mt) cc_final: 0.8248 (mt) REVERT: G 228 GLN cc_start: 0.8842 (tt0) cc_final: 0.8630 (tt0) REVERT: G 230 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7762 (mt-10) REVERT: G 238 LEU cc_start: 0.8788 (mt) cc_final: 0.8473 (mp) REVERT: G 241 ILE cc_start: 0.9051 (pt) cc_final: 0.8589 (pt) REVERT: G 242 GLN cc_start: 0.8140 (tp40) cc_final: 0.7527 (tp-100) REVERT: G 266 ILE cc_start: 0.8650 (mp) cc_final: 0.8370 (mp) REVERT: G 269 ASN cc_start: 0.7809 (m-40) cc_final: 0.7273 (m-40) outliers start: 1 outliers final: 0 residues processed: 424 average time/residue: 0.3011 time to fit residues: 182.0976 Evaluate side-chains 398 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.9990 chunk 172 optimal weight: 7.9990 chunk 105 optimal weight: 0.4980 chunk 82 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 0.5980 chunk 166 optimal weight: 3.9990 chunk 144 optimal weight: 0.0050 chunk 14 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 GLN C 62 GLN ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 GLN E 228 GLN F 63 GLN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 16772 Z= 0.302 Angle : 0.872 12.845 23765 Z= 0.337 Chirality : 0.047 0.140 2128 Planarity : 0.004 0.042 2912 Dihedral : 18.176 89.995 2303 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.34 % Favored : 86.66 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.19), residues: 1792 helix: -2.00 (0.23), residues: 301 sheet: -2.63 (0.36), residues: 140 loop : -1.86 (0.18), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 279 HIS 0.007 0.001 HIS C 146 PHE 0.014 0.002 PHE F 103 TYR 0.012 0.002 TYR B 151 ARG 0.004 0.001 ARG E 109 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 46 THR cc_start: 0.8605 (t) cc_final: 0.8078 (p) REVERT: B 57 ASP cc_start: 0.7801 (t0) cc_final: 0.7528 (t70) REVERT: B 63 GLN cc_start: 0.8481 (mt0) cc_final: 0.8034 (mp10) REVERT: B 79 ASN cc_start: 0.8054 (t0) cc_final: 0.7771 (t0) REVERT: B 95 MET cc_start: 0.8704 (mmp) cc_final: 0.8189 (mmm) REVERT: B 108 PHE cc_start: 0.8950 (p90) cc_final: 0.8661 (p90) REVERT: B 117 GLN cc_start: 0.8861 (tp40) cc_final: 0.8532 (tp-100) REVERT: B 146 HIS cc_start: 0.8225 (p-80) cc_final: 0.7893 (p90) REVERT: B 151 TYR cc_start: 0.8926 (p90) cc_final: 0.8678 (p90) REVERT: B 156 VAL cc_start: 0.8778 (t) cc_final: 0.8475 (p) REVERT: B 176 GLN cc_start: 0.7272 (tm-30) cc_final: 0.7054 (tm-30) REVERT: B 203 GLN cc_start: 0.8962 (tp40) cc_final: 0.8545 (tp40) REVERT: B 204 ASP cc_start: 0.9009 (m-30) cc_final: 0.8006 (t0) REVERT: B 227 ARG cc_start: 0.9036 (mmt180) cc_final: 0.8679 (mmt180) REVERT: B 228 GLN cc_start: 0.8340 (tt0) cc_final: 0.7972 (tm-30) REVERT: C 62 GLN cc_start: 0.8419 (mm110) cc_final: 0.8132 (mm-40) REVERT: C 79 ASN cc_start: 0.7973 (t0) cc_final: 0.7644 (t0) REVERT: C 108 PHE cc_start: 0.9005 (p90) cc_final: 0.7800 (p90) REVERT: C 109 ARG cc_start: 0.8951 (mmt180) cc_final: 0.8431 (mmt180) REVERT: C 135 HIS cc_start: 0.7347 (p90) cc_final: 0.6927 (p90) REVERT: C 149 PRO cc_start: 0.8888 (Cg_exo) cc_final: 0.8389 (Cg_endo) REVERT: C 203 GLN cc_start: 0.8834 (tp40) cc_final: 0.8453 (tp40) REVERT: C 230 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7779 (mt-10) REVERT: C 238 LEU cc_start: 0.8905 (mt) cc_final: 0.8484 (mp) REVERT: D 46 THR cc_start: 0.8425 (t) cc_final: 0.8033 (t) REVERT: D 62 GLN cc_start: 0.8324 (mm110) cc_final: 0.7977 (mm-40) REVERT: D 108 PHE cc_start: 0.8868 (p90) cc_final: 0.7927 (p90) REVERT: D 109 ARG cc_start: 0.9124 (mmt180) cc_final: 0.8626 (mmt180) REVERT: D 117 GLN cc_start: 0.8685 (tp40) cc_final: 0.8419 (tp-100) REVERT: D 129 LYS cc_start: 0.9200 (mmtm) cc_final: 0.8926 (tppt) REVERT: D 179 GLU cc_start: 0.7564 (mt-10) cc_final: 0.7171 (mt-10) REVERT: D 182 HIS cc_start: 0.7692 (m-70) cc_final: 0.7076 (m170) REVERT: D 183 GLN cc_start: 0.6872 (pm20) cc_final: 0.6349 (pm20) REVERT: D 203 GLN cc_start: 0.8986 (tp40) cc_final: 0.8392 (tp40) REVERT: D 204 ASP cc_start: 0.8888 (m-30) cc_final: 0.8054 (t0) REVERT: D 226 ILE cc_start: 0.9126 (tp) cc_final: 0.8919 (tp) REVERT: D 227 ARG cc_start: 0.8684 (mtt180) cc_final: 0.8319 (mtt180) REVERT: D 230 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7553 (mt-10) REVERT: D 238 LEU cc_start: 0.8965 (mt) cc_final: 0.8719 (mt) REVERT: A 108 PHE cc_start: 0.8857 (p90) cc_final: 0.8608 (p90) REVERT: A 109 ARG cc_start: 0.8727 (mmt90) cc_final: 0.8373 (tpp80) REVERT: A 129 LYS cc_start: 0.9343 (mttp) cc_final: 0.9120 (mmtm) REVERT: A 133 TYR cc_start: 0.8636 (t80) cc_final: 0.8336 (t80) REVERT: A 135 HIS cc_start: 0.7725 (p-80) cc_final: 0.7280 (p90) REVERT: A 179 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7280 (mt-10) REVERT: A 204 ASP cc_start: 0.8809 (m-30) cc_final: 0.8598 (m-30) REVERT: A 226 ILE cc_start: 0.8981 (tp) cc_final: 0.8589 (tp) REVERT: A 227 ARG cc_start: 0.8561 (mtt180) cc_final: 0.8160 (mtt180) REVERT: A 230 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7116 (mt-10) REVERT: A 269 ASN cc_start: 0.7782 (m-40) cc_final: 0.7082 (m-40) REVERT: E 46 THR cc_start: 0.8317 (t) cc_final: 0.7544 (p) REVERT: E 60 LEU cc_start: 0.8976 (mm) cc_final: 0.8703 (mt) REVERT: E 63 GLN cc_start: 0.8423 (mt0) cc_final: 0.8055 (mt0) REVERT: E 108 PHE cc_start: 0.8975 (p90) cc_final: 0.8509 (p90) REVERT: E 129 LYS cc_start: 0.9103 (mttp) cc_final: 0.8875 (mmtm) REVERT: E 133 TYR cc_start: 0.8635 (t80) cc_final: 0.8326 (t80) REVERT: E 182 HIS cc_start: 0.7810 (m170) cc_final: 0.7448 (m170) REVERT: E 203 GLN cc_start: 0.8844 (tp40) cc_final: 0.8397 (tp40) REVERT: E 204 ASP cc_start: 0.8799 (m-30) cc_final: 0.8098 (t0) REVERT: E 269 ASN cc_start: 0.7950 (m-40) cc_final: 0.7283 (m-40) REVERT: E 270 TRP cc_start: 0.8162 (t-100) cc_final: 0.7628 (t-100) REVERT: F 46 THR cc_start: 0.8248 (t) cc_final: 0.8036 (t) REVERT: F 79 ASN cc_start: 0.7836 (t0) cc_final: 0.7458 (t0) REVERT: F 108 PHE cc_start: 0.8930 (p90) cc_final: 0.8645 (p90) REVERT: F 176 GLN cc_start: 0.7617 (tm-30) cc_final: 0.7214 (tm-30) REVERT: F 183 GLN cc_start: 0.6957 (pm20) cc_final: 0.6734 (pm20) REVERT: F 204 ASP cc_start: 0.8996 (m-30) cc_final: 0.8613 (m-30) REVERT: F 226 ILE cc_start: 0.9057 (tp) cc_final: 0.8842 (tp) REVERT: F 228 GLN cc_start: 0.8548 (tt0) cc_final: 0.8140 (tm-30) REVERT: F 230 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7657 (mt-10) REVERT: F 243 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8372 (tptp) REVERT: F 269 ASN cc_start: 0.8214 (m-40) cc_final: 0.6982 (m-40) REVERT: F 273 GLN cc_start: 0.8856 (mt0) cc_final: 0.8535 (mt0) REVERT: G 79 ASN cc_start: 0.8404 (t0) cc_final: 0.8070 (t0) REVERT: G 107 ASP cc_start: 0.8481 (t0) cc_final: 0.7990 (t0) REVERT: G 116 THR cc_start: 0.8788 (t) cc_final: 0.8372 (t) REVERT: G 117 GLN cc_start: 0.8339 (mm110) cc_final: 0.8112 (mm110) REVERT: G 141 ASN cc_start: 0.8868 (t0) cc_final: 0.8513 (t0) REVERT: G 149 PRO cc_start: 0.9031 (Cg_exo) cc_final: 0.8639 (Cg_endo) REVERT: G 190 ASP cc_start: 0.8996 (t0) cc_final: 0.8701 (t0) REVERT: G 204 ASP cc_start: 0.8961 (m-30) cc_final: 0.8647 (m-30) REVERT: G 213 ASP cc_start: 0.8721 (t0) cc_final: 0.8382 (t0) REVERT: G 226 ILE cc_start: 0.8988 (mt) cc_final: 0.8490 (mt) REVERT: G 227 ARG cc_start: 0.9053 (mtt180) cc_final: 0.8764 (mtt180) REVERT: G 228 GLN cc_start: 0.8815 (tt0) cc_final: 0.8557 (tt0) REVERT: G 230 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7804 (mt-10) REVERT: G 238 LEU cc_start: 0.8815 (mt) cc_final: 0.8510 (mp) REVERT: G 241 ILE cc_start: 0.9055 (pt) cc_final: 0.8570 (pt) REVERT: G 242 GLN cc_start: 0.8159 (tp40) cc_final: 0.7465 (tp-100) REVERT: G 260 ASP cc_start: 0.7908 (t0) cc_final: 0.6608 (p0) REVERT: G 261 LEU cc_start: 0.7815 (pt) cc_final: 0.7535 (pt) REVERT: G 263 TRP cc_start: 0.8264 (m100) cc_final: 0.7866 (m100) REVERT: G 266 ILE cc_start: 0.8648 (mp) cc_final: 0.8423 (mp) REVERT: G 269 ASN cc_start: 0.7763 (m-40) cc_final: 0.7216 (m-40) outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.2970 time to fit residues: 182.4111 Evaluate side-chains 409 residues out of total 1554 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 409 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 144 optimal weight: 0.0270 chunk 60 optimal weight: 1.9990 chunk 148 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN B 228 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 HIS ** D 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 117 GLN ** A 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.084141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.069406 restraints weight = 46448.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072367 restraints weight = 26571.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074424 restraints weight = 17524.274| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 16772 Z= 0.336 Angle : 0.890 12.921 23765 Z= 0.341 Chirality : 0.048 0.146 2128 Planarity : 0.004 0.042 2912 Dihedral : 18.188 89.981 2303 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 19.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.68 % Favored : 85.32 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.04 % 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: -2.92 (0.19), residues: 1792 helix: -2.12 (0.23), residues: 301 sheet: -2.35 (0.38), residues: 154 loop : -1.98 (0.18), residues: 1337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP F 279 HIS 0.007 0.001 HIS E 276 PHE 0.015 0.002 PHE E 108 TYR 0.013 0.002 TYR B 151 ARG 0.007 0.001 ARG F 197 =============================================================================== Job complete usr+sys time: 3924.54 seconds wall clock time: 70 minutes 54.79 seconds (4254.79 seconds total)