Starting phenix.real_space_refine on Wed Sep 25 23:37:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/09_2024/6pwe_20506.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 14 5.16 5 C 6576 2.51 5 N 2231 2.21 5 O 2808 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 11923 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 626 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 789 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 743 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Restraints were copied for chains: E, F, G, H Time building chain proxies: 7.54, per 1000 atoms: 0.63 Number of scatterers: 11923 At special positions: 0 Unit cell: (108.36, 113.4, 120.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 294 15.00 O 2808 8.00 N 2231 7.00 C 6576 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 879.1 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1392 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 59.4% alpha, 1.6% beta 95 base pairs and 208 stacking pairs defined. Time for finding SS restraints: 5.54 Creating SS restraints... Processing helix chain 'A' and resid 46 through 50 Processing helix chain 'A' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 105 removed outlier: 3.841A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN A 93 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.602A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 128 removed outlier: 3.589A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 39 removed outlier: 3.533A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N PHE B 61 " --> pdb=" O VAL B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.853A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.699A pdb=" N ALA C 20 " --> pdb=" O ARG C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU C 32 " --> pdb=" O ARG C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 72 removed outlier: 3.700A pdb=" N ALA C 51 " --> pdb=" O PRO C 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 63 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 66 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 68 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU C 82 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 83 " --> pdb=" O PRO C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS C 94 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.690A pdb=" N ILE D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 43 " --> pdb=" O TYR D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN D 60 " --> pdb=" O MET D 56 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR D 80 " --> pdb=" O ARG D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS D 113 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 50 Processing helix chain 'E' and resid 64 through 75 removed outlier: 4.620A pdb=" N LEU E 70 " --> pdb=" O PRO E 66 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 73 " --> pdb=" O ARG E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 105 removed outlier: 3.842A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU E 94 " --> pdb=" O MET E 90 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU E 97 " --> pdb=" O GLN E 93 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.601A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 128 removed outlier: 3.590A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN E 125 " --> pdb=" O PRO E 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.516A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 39 removed outlier: 3.534A pdb=" N LEU F 37 " --> pdb=" O ALA F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 63 removed outlier: 4.463A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL F 60 " --> pdb=" O GLY F 56 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE F 61 " --> pdb=" O VAL F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.921A pdb=" N THR F 71 " --> pdb=" O ARG F 67 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TYR F 72 " --> pdb=" O ASP F 68 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR F 73 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.854A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.698A pdb=" N ALA G 20 " --> pdb=" O ARG G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 33 removed outlier: 3.888A pdb=" N LEU G 32 " --> pdb=" O ARG G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 72 removed outlier: 3.701A pdb=" N ALA G 51 " --> pdb=" O PRO G 47 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL G 53 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU G 63 " --> pdb=" O ALA G 59 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 88 removed outlier: 3.955A pdb=" N LEU G 82 " --> pdb=" O ILE G 78 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN G 83 " --> pdb=" O PRO G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 94 removed outlier: 3.970A pdb=" N LYS G 94 " --> pdb=" O GLU G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 43 removed outlier: 3.689A pdb=" N ILE H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 54 through 80 removed outlier: 3.535A pdb=" N ASN H 60 " --> pdb=" O MET H 56 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA H 72 " --> pdb=" O GLU H 68 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR H 80 " --> pdb=" O ARG H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 94 removed outlier: 3.699A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.602A pdb=" N VAL H 108 " --> pdb=" O ALA H 104 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.787A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42 removed outlier: 7.109A pdb=" N ARG C 41 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.536A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42 removed outlier: 7.395A pdb=" N ARG G 41 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77 206 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 225 hydrogen bonds 438 hydrogen bond angles 0 basepair planarities 95 basepair parallelities 208 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.32: 1843 1.32 - 1.44: 4466 1.44 - 1.56: 5815 1.56 - 1.68: 586 1.68 - 1.80: 26 Bond restraints: 12736 Sorted by residual: bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.98e+00 bond pdb=" CB PRO A 66 " pdb=" CG PRO A 66 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.09e+00 bond pdb=" CB PRO E 66 " pdb=" CG PRO E 66 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.06e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.472 -0.050 3.00e-02 1.11e+03 2.82e+00 bond pdb=" C3' DG I 38 " pdb=" O3' DG I 38 " ideal model delta sigma weight residual 1.422 1.373 0.049 3.00e-02 1.11e+03 2.68e+00 ... (remaining 12731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 17147 1.74 - 3.49: 1166 3.49 - 5.23: 120 5.23 - 6.97: 16 6.97 - 8.71: 12 Bond angle restraints: 18461 Sorted by residual: angle pdb=" C ARG H 30 " pdb=" N LYS H 31 " pdb=" CA LYS H 31 " ideal model delta sigma weight residual 121.54 130.25 -8.71 1.91e+00 2.74e-01 2.08e+01 angle pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta sigma weight residual 121.54 130.24 -8.70 1.91e+00 2.74e-01 2.07e+01 angle pdb=" N LYS D 31 " pdb=" CA LYS D 31 " pdb=" CB LYS D 31 " ideal model delta sigma weight residual 110.49 117.07 -6.58 1.69e+00 3.50e-01 1.52e+01 angle pdb=" N LYS H 31 " pdb=" CA LYS H 31 " pdb=" CB LYS H 31 " ideal model delta sigma weight residual 110.49 117.03 -6.54 1.69e+00 3.50e-01 1.50e+01 angle pdb=" C ALA C 102 " pdb=" N GLN C 103 " pdb=" CA GLN C 103 " ideal model delta sigma weight residual 122.46 127.42 -4.96 1.41e+00 5.03e-01 1.24e+01 ... (remaining 18456 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.76: 5440 31.76 - 63.52: 1415 63.52 - 95.29: 44 95.29 - 127.05: 0 127.05 - 158.81: 3 Dihedral angle restraints: 6902 sinusoidal: 4744 harmonic: 2158 Sorted by residual: dihedral pdb=" CA LYS D 29 " pdb=" C LYS D 29 " pdb=" N ARG D 30 " pdb=" CA ARG D 30 " ideal model delta harmonic sigma weight residual -180.00 -127.05 -52.95 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA LYS H 29 " pdb=" C LYS H 29 " pdb=" N ARG H 30 " pdb=" CA ARG H 30 " ideal model delta harmonic sigma weight residual -180.00 -127.10 -52.90 0 5.00e+00 4.00e-02 1.12e+02 dihedral pdb=" CA ARG D 30 " pdb=" C ARG D 30 " pdb=" N LYS D 31 " pdb=" CA LYS D 31 " ideal model delta harmonic sigma weight residual 180.00 140.19 39.81 0 5.00e+00 4.00e-02 6.34e+01 ... (remaining 6899 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1265 0.044 - 0.088: 667 0.088 - 0.133: 129 0.133 - 0.177: 27 0.177 - 0.221: 10 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CB VAL G 106 " pdb=" CA VAL G 106 " pdb=" CG1 VAL G 106 " pdb=" CG2 VAL G 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CB VAL C 106 " pdb=" CA VAL C 106 " pdb=" CG1 VAL C 106 " pdb=" CG2 VAL C 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB VAL C 99 " pdb=" CA VAL C 99 " pdb=" CG1 VAL C 99 " pdb=" CG2 VAL C 99 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 2095 not shown) Planarity restraints: 1318 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 65 " -0.046 5.00e-02 4.00e+02 6.89e-02 7.60e+00 pdb=" N PRO A 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 66 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " 0.046 5.00e-02 4.00e+02 6.88e-02 7.58e+00 pdb=" N PRO E 66 " -0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 101 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.15e+00 pdb=" C GLY H 101 " -0.043 2.00e-02 2.50e+03 pdb=" O GLY H 101 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU H 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 1315 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2734 2.79 - 3.32: 10074 3.32 - 3.85: 22518 3.85 - 4.37: 26262 4.37 - 4.90: 37230 Nonbonded interactions: 98818 Sorted by model distance: nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 48 " model vdw 2.264 3.040 nonbonded pdb=" OH TYR H 37 " pdb=" OP1 DG I 48 " model vdw 2.281 3.040 nonbonded pdb=" O TYR F 51 " pdb=" NH1 ARG F 55 " model vdw 2.317 3.120 nonbonded pdb=" O TYR B 51 " pdb=" NH1 ARG B 55 " model vdw 2.318 3.120 nonbonded pdb=" N2 DG I 21 " pdb=" O2 DC J -21 " model vdw 2.330 2.496 ... (remaining 98813 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.860 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 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 : 0.010 0.088 12736 Z= 0.556 Angle : 0.929 8.715 18461 Z= 0.526 Chirality : 0.053 0.221 2098 Planarity : 0.007 0.069 1318 Dihedral : 27.121 158.809 5510 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.42 % Favored : 92.31 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -6.65 (0.18), residues: 728 helix: -4.66 (0.11), residues: 440 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS H 106 PHE 0.019 0.003 PHE A 104 TYR 0.018 0.004 TYR F 51 ARG 0.008 0.001 ARG H 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7194 (tt0) cc_final: 0.6709 (tp30) REVERT: B 31 LYS cc_start: 0.8599 (tttt) cc_final: 0.8096 (mptt) REVERT: B 51 TYR cc_start: 0.8455 (m-80) cc_final: 0.7977 (m-80) REVERT: B 79 LYS cc_start: 0.7955 (mttp) cc_final: 0.7747 (mtpt) REVERT: C 109 ASN cc_start: 0.7057 (t0) cc_final: 0.6806 (m-40) REVERT: D 48 ASP cc_start: 0.8152 (p0) cc_final: 0.7794 (p0) REVERT: D 106 HIS cc_start: 0.7772 (m90) cc_final: 0.7565 (m-70) REVERT: E 41 TYR cc_start: 0.8455 (m-80) cc_final: 0.8156 (m-80) REVERT: E 49 ARG cc_start: 0.7485 (mtm180) cc_final: 0.7270 (tpp-160) REVERT: E 118 THR cc_start: 0.9373 (m) cc_final: 0.9075 (p) REVERT: F 80 THR cc_start: 0.8638 (m) cc_final: 0.8278 (p) REVERT: F 84 MET cc_start: 0.6704 (mmm) cc_final: 0.6013 (mmm) REVERT: F 88 TYR cc_start: 0.8433 (m-10) cc_final: 0.7793 (m-80) REVERT: F 98 TYR cc_start: 0.8948 (m-10) cc_final: 0.8633 (m-10) REVERT: H 40 LYS cc_start: 0.9155 (mttt) cc_final: 0.8815 (mtpt) REVERT: H 80 TYR cc_start: 0.7785 (m-10) cc_final: 0.7496 (m-10) REVERT: H 97 LEU cc_start: 0.8873 (mt) cc_final: 0.8648 (mp) outliers start: 0 outliers final: 0 residues processed: 260 average time/residue: 0.3779 time to fit residues: 123.4018 Evaluate side-chains 171 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 57 optimal weight: 0.0000 chunk 88 optimal weight: 5.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 23 GLN D 60 ASN D 64 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 23 GLN G 88 ASN H 60 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12736 Z= 0.198 Angle : 0.626 5.640 18461 Z= 0.375 Chirality : 0.037 0.181 2098 Planarity : 0.005 0.046 1318 Dihedral : 30.744 158.655 4040 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.53 % Favored : 95.33 % Rotamer: Outliers : 1.94 % Allowed : 13.75 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.96 (0.23), residues: 728 helix: -3.11 (0.18), residues: 468 sheet: None (None), residues: 0 loop : -3.34 (0.29), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.010 0.001 PHE E 104 TYR 0.015 0.001 TYR C 56 ARG 0.009 0.001 ARG A 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 212 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.9074 (m-80) cc_final: 0.8822 (m-80) REVERT: A 73 GLU cc_start: 0.7228 (tt0) cc_final: 0.6923 (tp30) REVERT: B 31 LYS cc_start: 0.8851 (tttt) cc_final: 0.8286 (mptt) REVERT: B 35 ARG cc_start: 0.8161 (tpp80) cc_final: 0.7745 (tpp80) REVERT: B 59 LYS cc_start: 0.8273 (tttt) cc_final: 0.7980 (tttt) REVERT: B 82 THR cc_start: 0.8552 (t) cc_final: 0.8078 (m) REVERT: B 88 TYR cc_start: 0.8281 (m-80) cc_final: 0.7562 (m-10) REVERT: C 109 ASN cc_start: 0.7150 (t0) cc_final: 0.6788 (m-40) REVERT: D 48 ASP cc_start: 0.7996 (p0) cc_final: 0.7596 (p0) REVERT: F 84 MET cc_start: 0.6392 (mmm) cc_final: 0.4709 (tpp) REVERT: F 88 TYR cc_start: 0.8306 (m-10) cc_final: 0.7651 (m-80) REVERT: H 39 TYR cc_start: 0.7827 (t80) cc_final: 0.7539 (t80) REVERT: H 40 LYS cc_start: 0.9133 (mttt) cc_final: 0.8414 (mtpt) REVERT: H 65 ASP cc_start: 0.8588 (t70) cc_final: 0.8256 (t0) REVERT: H 80 TYR cc_start: 0.8040 (m-10) cc_final: 0.7557 (m-10) outliers start: 12 outliers final: 4 residues processed: 217 average time/residue: 0.2981 time to fit residues: 85.4853 Evaluate side-chains 164 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 160 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain E residue 96 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 30 optimal weight: 0.7980 chunk 71 optimal weight: 10.0000 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 HIS C 93 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 ASN ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 12736 Z= 0.364 Angle : 0.696 8.073 18461 Z= 0.401 Chirality : 0.040 0.176 2098 Planarity : 0.005 0.041 1318 Dihedral : 30.895 161.728 4040 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.73 % Favored : 93.13 % Rotamer: Outliers : 4.85 % Allowed : 17.80 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.18 (0.26), residues: 728 helix: -2.49 (0.21), residues: 458 sheet: None (None), residues: 0 loop : -3.06 (0.31), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 106 PHE 0.012 0.002 PHE E 104 TYR 0.018 0.003 TYR D 37 ARG 0.006 0.001 ARG E 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 174 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7425 (tt0) cc_final: 0.6993 (tp30) REVERT: B 31 LYS cc_start: 0.8814 (tttt) cc_final: 0.8269 (mptt) REVERT: B 82 THR cc_start: 0.8627 (t) cc_final: 0.8265 (m) REVERT: B 84 MET cc_start: 0.8613 (tpp) cc_final: 0.8331 (tpp) REVERT: B 88 TYR cc_start: 0.8176 (m-80) cc_final: 0.7454 (m-10) REVERT: D 48 ASP cc_start: 0.8229 (p0) cc_final: 0.7934 (p0) REVERT: E 49 ARG cc_start: 0.7521 (ttm-80) cc_final: 0.6571 (tpm170) REVERT: E 59 GLU cc_start: 0.8224 (pm20) cc_final: 0.8004 (mt-10) REVERT: F 84 MET cc_start: 0.6579 (mmm) cc_final: 0.5327 (tpp) REVERT: F 88 TYR cc_start: 0.8430 (m-10) cc_final: 0.7769 (m-80) REVERT: G 34 ARG cc_start: 0.8494 (ttm170) cc_final: 0.8080 (mtm-85) REVERT: H 31 LYS cc_start: 0.7448 (mtpp) cc_final: 0.7216 (mtpp) REVERT: H 37 TYR cc_start: 0.8706 (m-80) cc_final: 0.8291 (m-80) REVERT: H 54 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8534 (tptm) REVERT: H 80 TYR cc_start: 0.8094 (m-10) cc_final: 0.7771 (m-10) REVERT: H 98 LEU cc_start: 0.8591 (mp) cc_final: 0.8223 (mp) outliers start: 30 outliers final: 19 residues processed: 194 average time/residue: 0.2732 time to fit residues: 71.5815 Evaluate side-chains 186 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 167 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 62 ILE Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 57 VAL Chi-restraints excluded: chain H residue 49 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 94 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 93 ASN E 93 GLN G 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12736 Z= 0.258 Angle : 0.607 6.530 18461 Z= 0.357 Chirality : 0.036 0.137 2098 Planarity : 0.004 0.039 1318 Dihedral : 30.556 162.318 4040 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.05 % Allowed : 20.71 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.28), residues: 728 helix: -2.04 (0.22), residues: 466 sheet: None (None), residues: 0 loop : -2.80 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 106 PHE 0.007 0.001 PHE H 62 TYR 0.020 0.002 TYR H 118 ARG 0.006 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8548 (mtp-110) cc_final: 0.7924 (mtp85) REVERT: A 73 GLU cc_start: 0.7482 (tt0) cc_final: 0.6848 (tp30) REVERT: B 31 LYS cc_start: 0.8609 (tttt) cc_final: 0.8218 (mptt) REVERT: B 82 THR cc_start: 0.8511 (t) cc_final: 0.8232 (m) REVERT: B 88 TYR cc_start: 0.8158 (m-10) cc_final: 0.7579 (m-10) REVERT: C 101 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8724 (mp) REVERT: D 48 ASP cc_start: 0.8178 (p0) cc_final: 0.7891 (p0) REVERT: E 49 ARG cc_start: 0.7525 (ttm-80) cc_final: 0.6123 (tpm170) REVERT: F 84 MET cc_start: 0.6542 (mmm) cc_final: 0.5309 (tpp) REVERT: F 88 TYR cc_start: 0.8417 (m-10) cc_final: 0.7402 (m-80) REVERT: G 22 LEU cc_start: 0.7624 (mp) cc_final: 0.7418 (mt) REVERT: H 39 TYR cc_start: 0.7883 (t80) cc_final: 0.7432 (t80) REVERT: H 54 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8481 (tptm) REVERT: H 80 TYR cc_start: 0.8116 (m-10) cc_final: 0.7588 (m-10) outliers start: 25 outliers final: 18 residues processed: 183 average time/residue: 0.2884 time to fit residues: 70.4395 Evaluate side-chains 169 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 150 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.3980 chunk 1 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.4980 chunk 85 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.0000 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS C 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12736 Z= 0.187 Angle : 0.552 6.174 18461 Z= 0.327 Chirality : 0.033 0.131 2098 Planarity : 0.004 0.037 1318 Dihedral : 30.159 159.694 4040 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.56 % Allowed : 21.68 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.80 (0.29), residues: 728 helix: -1.51 (0.23), residues: 470 sheet: None (None), residues: 0 loop : -2.28 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 46 PHE 0.005 0.001 PHE H 67 TYR 0.023 0.001 TYR H 118 ARG 0.007 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7361 (tt0) cc_final: 0.6631 (tp30) REVERT: B 72 TYR cc_start: 0.8778 (m-80) cc_final: 0.8449 (m-80) REVERT: B 82 THR cc_start: 0.8488 (t) cc_final: 0.8134 (m) REVERT: B 88 TYR cc_start: 0.7933 (m-10) cc_final: 0.7520 (m-10) REVERT: C 49 TYR cc_start: 0.8488 (t80) cc_final: 0.8142 (t80) REVERT: C 109 ASN cc_start: 0.7447 (t0) cc_final: 0.7117 (m-40) REVERT: D 48 ASP cc_start: 0.8077 (p0) cc_final: 0.7787 (p0) REVERT: D 77 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8469 (tp) REVERT: E 49 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.5973 (tpm170) REVERT: E 57 SER cc_start: 0.8158 (OUTLIER) cc_final: 0.7949 (t) REVERT: F 25 ASN cc_start: 0.7660 (m-40) cc_final: 0.7426 (t0) REVERT: F 88 TYR cc_start: 0.8347 (m-10) cc_final: 0.7864 (m-80) REVERT: H 39 TYR cc_start: 0.7863 (t80) cc_final: 0.7403 (t80) REVERT: H 54 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8416 (tptp) REVERT: H 56 MET cc_start: 0.7813 (mmm) cc_final: 0.6884 (mtt) REVERT: H 80 TYR cc_start: 0.8083 (m-10) cc_final: 0.7649 (m-10) outliers start: 22 outliers final: 12 residues processed: 171 average time/residue: 0.2779 time to fit residues: 64.2049 Evaluate side-chains 155 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 10.0000 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 7 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN F 25 ASN G 23 GLN G 72 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12736 Z= 0.251 Angle : 0.585 7.317 18461 Z= 0.341 Chirality : 0.035 0.141 2098 Planarity : 0.004 0.036 1318 Dihedral : 30.332 160.934 4040 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.02 % Allowed : 21.20 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -2.56 (0.30), residues: 728 helix: -1.31 (0.23), residues: 472 sheet: None (None), residues: 0 loop : -2.24 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 106 PHE 0.008 0.001 PHE E 104 TYR 0.024 0.002 TYR H 118 ARG 0.006 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 154 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7330 (tt0) cc_final: 0.6579 (tp30) REVERT: B 82 THR cc_start: 0.8537 (t) cc_final: 0.8210 (m) REVERT: B 88 TYR cc_start: 0.7986 (m-10) cc_final: 0.7447 (m-10) REVERT: D 48 ASP cc_start: 0.8175 (p0) cc_final: 0.7909 (p0) REVERT: D 77 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8465 (tp) REVERT: E 49 ARG cc_start: 0.7483 (ttm-80) cc_final: 0.5993 (tpm170) REVERT: E 56 LYS cc_start: 0.8506 (mtpt) cc_final: 0.8280 (mtpt) REVERT: E 57 SER cc_start: 0.8237 (OUTLIER) cc_final: 0.7973 (t) REVERT: E 90 MET cc_start: 0.8286 (tpp) cc_final: 0.8002 (tpp) REVERT: F 25 ASN cc_start: 0.8068 (m-40) cc_final: 0.7428 (t0) REVERT: F 84 MET cc_start: 0.6648 (mmm) cc_final: 0.5921 (mmm) REVERT: F 88 TYR cc_start: 0.8386 (m-10) cc_final: 0.7577 (m-80) REVERT: H 39 TYR cc_start: 0.7968 (t80) cc_final: 0.7522 (t80) REVERT: H 56 MET cc_start: 0.7997 (mmm) cc_final: 0.7122 (mtt) REVERT: H 80 TYR cc_start: 0.8120 (m-10) cc_final: 0.7579 (m-10) outliers start: 31 outliers final: 20 residues processed: 171 average time/residue: 0.2797 time to fit residues: 64.3036 Evaluate side-chains 171 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 149 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 58 optimal weight: 2.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN G 23 GLN G 72 ASN G 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.179 Angle : 0.540 7.444 18461 Z= 0.319 Chirality : 0.033 0.148 2098 Planarity : 0.004 0.036 1318 Dihedral : 30.027 157.866 4040 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 4.85 % Allowed : 21.52 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.31), residues: 728 helix: -0.83 (0.24), residues: 468 sheet: None (None), residues: 0 loop : -1.91 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 79 PHE 0.004 0.001 PHE A 78 TYR 0.023 0.001 TYR H 118 ARG 0.005 0.000 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7179 (tt0) cc_final: 0.6552 (tp30) REVERT: B 82 THR cc_start: 0.8514 (t) cc_final: 0.8142 (m) REVERT: B 88 TYR cc_start: 0.7819 (m-10) cc_final: 0.7365 (m-10) REVERT: C 49 TYR cc_start: 0.8466 (t80) cc_final: 0.8122 (t80) REVERT: D 48 ASP cc_start: 0.8027 (p0) cc_final: 0.7735 (p0) REVERT: D 77 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8502 (tp) REVERT: E 42 ARG cc_start: 0.8243 (mtp180) cc_final: 0.7740 (mtp180) REVERT: E 49 ARG cc_start: 0.7459 (ttm-80) cc_final: 0.6044 (tpm170) REVERT: F 84 MET cc_start: 0.6490 (mmm) cc_final: 0.5721 (mmm) REVERT: F 88 TYR cc_start: 0.8316 (m-10) cc_final: 0.7732 (m-80) REVERT: H 39 TYR cc_start: 0.7864 (t80) cc_final: 0.7432 (t80) REVERT: H 56 MET cc_start: 0.7881 (mmm) cc_final: 0.7067 (mtt) REVERT: H 80 TYR cc_start: 0.8068 (m-10) cc_final: 0.7578 (m-10) outliers start: 30 outliers final: 20 residues processed: 169 average time/residue: 0.2579 time to fit residues: 60.0544 Evaluate side-chains 164 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12736 Z= 0.218 Angle : 0.568 8.102 18461 Z= 0.330 Chirality : 0.034 0.147 2098 Planarity : 0.004 0.035 1318 Dihedral : 30.113 158.141 4040 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.72 % Allowed : 22.33 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.31), residues: 728 helix: -0.72 (0.24), residues: 472 sheet: None (None), residues: 0 loop : -1.92 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.006 0.001 PHE E 104 TYR 0.023 0.002 TYR H 118 ARG 0.005 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 145 time to evaluate : 0.973 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7161 (tt0) cc_final: 0.6425 (tp30) REVERT: B 82 THR cc_start: 0.8564 (t) cc_final: 0.8189 (m) REVERT: B 88 TYR cc_start: 0.7848 (m-10) cc_final: 0.7420 (m-10) REVERT: D 48 ASP cc_start: 0.8091 (p0) cc_final: 0.7816 (p0) REVERT: D 77 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8477 (tp) REVERT: E 49 ARG cc_start: 0.7461 (ttm-80) cc_final: 0.5967 (tpm170) REVERT: F 84 MET cc_start: 0.6598 (mmm) cc_final: 0.5870 (mmm) REVERT: F 88 TYR cc_start: 0.8353 (m-10) cc_final: 0.7648 (m-80) REVERT: H 39 TYR cc_start: 0.7881 (t80) cc_final: 0.7454 (t80) REVERT: H 56 MET cc_start: 0.7907 (mmm) cc_final: 0.7120 (mtt) REVERT: H 80 TYR cc_start: 0.8018 (m-10) cc_final: 0.7538 (m-10) outliers start: 23 outliers final: 19 residues processed: 158 average time/residue: 0.2712 time to fit residues: 58.9671 Evaluate side-chains 163 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 90 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 103 GLN G 72 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.182 Angle : 0.544 8.114 18461 Z= 0.319 Chirality : 0.033 0.148 2098 Planarity : 0.003 0.036 1318 Dihedral : 29.976 156.221 4040 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.88 % Allowed : 22.82 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.32), residues: 728 helix: -0.31 (0.25), residues: 468 sheet: None (None), residues: 0 loop : -1.68 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 106 PHE 0.005 0.001 PHE E 104 TYR 0.023 0.001 TYR H 118 ARG 0.003 0.000 ARG B 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8963 (pt) cc_final: 0.8667 (mt) REVERT: A 73 GLU cc_start: 0.6911 (tt0) cc_final: 0.6169 (tp30) REVERT: B 82 THR cc_start: 0.8538 (t) cc_final: 0.8142 (m) REVERT: B 88 TYR cc_start: 0.7787 (m-10) cc_final: 0.7346 (m-10) REVERT: D 48 ASP cc_start: 0.8058 (p0) cc_final: 0.7772 (p0) REVERT: F 84 MET cc_start: 0.6513 (mmm) cc_final: 0.5641 (mmm) REVERT: F 88 TYR cc_start: 0.8258 (m-10) cc_final: 0.7689 (m-80) REVERT: G 103 GLN cc_start: 0.8457 (pt0) cc_final: 0.8199 (pt0) REVERT: H 31 LYS cc_start: 0.7601 (mmmt) cc_final: 0.6934 (mmmt) REVERT: H 39 TYR cc_start: 0.7869 (t80) cc_final: 0.7455 (t80) REVERT: H 56 MET cc_start: 0.7891 (mmm) cc_final: 0.7118 (mtt) REVERT: H 80 TYR cc_start: 0.7989 (m-10) cc_final: 0.7522 (m-10) outliers start: 24 outliers final: 21 residues processed: 163 average time/residue: 0.2743 time to fit residues: 61.9142 Evaluate side-chains 161 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 140 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 8.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 60 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 93 ASN C 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12736 Z= 0.211 Angle : 0.567 7.684 18461 Z= 0.329 Chirality : 0.034 0.150 2098 Planarity : 0.003 0.035 1318 Dihedral : 30.019 156.657 4040 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.72 % Allowed : 23.30 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.32), residues: 728 helix: -0.24 (0.25), residues: 470 sheet: None (None), residues: 0 loop : -1.72 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 106 PHE 0.006 0.001 PHE E 104 TYR 0.033 0.002 TYR F 51 ARG 0.004 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8986 (pt) cc_final: 0.8685 (mt) REVERT: A 73 GLU cc_start: 0.7016 (tt0) cc_final: 0.6304 (tp30) REVERT: B 82 THR cc_start: 0.8559 (t) cc_final: 0.8166 (m) REVERT: B 88 TYR cc_start: 0.7807 (m-10) cc_final: 0.7366 (m-10) REVERT: D 48 ASP cc_start: 0.8098 (p0) cc_final: 0.7818 (p0) REVERT: E 49 ARG cc_start: 0.7436 (ttm-80) cc_final: 0.5995 (tpm170) REVERT: F 84 MET cc_start: 0.6565 (mmm) cc_final: 0.5653 (mmm) REVERT: F 88 TYR cc_start: 0.8289 (m-10) cc_final: 0.7690 (m-80) REVERT: G 103 GLN cc_start: 0.8491 (pt0) cc_final: 0.8243 (pt0) REVERT: H 39 TYR cc_start: 0.7912 (t80) cc_final: 0.7478 (t80) REVERT: H 56 MET cc_start: 0.7924 (mmm) cc_final: 0.7119 (mtt) REVERT: H 80 TYR cc_start: 0.8003 (m-10) cc_final: 0.7519 (m-10) outliers start: 23 outliers final: 21 residues processed: 156 average time/residue: 0.2709 time to fit residues: 58.8111 Evaluate side-chains 160 residues out of total 618 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain C residue 30 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 82 LEU Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 99 VAL Chi-restraints excluded: chain G residue 106 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 32 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.0980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.133579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110341 restraints weight = 24951.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112117 restraints weight = 15180.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113286 restraints weight = 11073.126| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.5261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12736 Z= 0.221 Angle : 0.570 7.351 18461 Z= 0.330 Chirality : 0.034 0.153 2098 Planarity : 0.004 0.035 1318 Dihedral : 30.073 156.960 4040 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.05 % Allowed : 22.82 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.32), residues: 728 helix: -0.21 (0.25), residues: 472 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 106 PHE 0.006 0.001 PHE E 104 TYR 0.032 0.002 TYR F 51 ARG 0.004 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2146.68 seconds wall clock time: 39 minutes 10.92 seconds (2350.92 seconds total)