Starting phenix.real_space_refine on Thu Jul 31 05:17:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.map" model { file = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t9h_41111/07_2025/8t9h_41111.cif" } resolution = 3.37 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= -0.001 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1622 atoms to isotropic. 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 201 5.49 5 S 29 5.16 5 C 6930 2.51 5 N 2237 2.21 5 O 2642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 750 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "H" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 709 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2012 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "J" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 2110 Classifications: {'DNA': 102} Link IDs: {'rna3p': 101} Chain: "K" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1969 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 7.16, per 1000 atoms: 0.59 Number of scatterers: 12039 At special positions: 0 Unit cell: (92.064, 118.368, 127.136, 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 29 16.00 P 201 15.00 O 2642 8.00 N 2237 7.00 C 6930 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: 2.76 Conformation dependent library (CDL) restraints added in 1.1 seconds 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 65.9% alpha, 5.5% beta 96 base pairs and 141 stacking pairs defined. Time for finding SS restraints: 4.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.990A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.523A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.569A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.530A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.511A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.505A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.173A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.669A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.492A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 39 through 50 removed outlier: 3.524A pdb=" N TYR H 43 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.609A pdb=" N ALA H 108 " --> pdb=" O PRO H 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 134 through 148 removed outlier: 3.697A pdb=" N LYS K 138 " --> pdb=" O GLN K 134 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU K 142 " --> pdb=" O LYS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 158 Processing helix chain 'K' and resid 160 through 169 removed outlier: 3.652A pdb=" N LEU K 168 " --> pdb=" O ARG K 164 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN K 169 " --> pdb=" O HIS K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 188 removed outlier: 3.509A pdb=" N ILE K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 243 removed outlier: 3.709A pdb=" N ASN K 240 " --> pdb=" O GLU K 236 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET K 241 " --> pdb=" O ILE K 237 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.683A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 328 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 354 through 361 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.154A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 22 removed outlier: 3.570A pdb=" N CYS K 260 " --> pdb=" O SER K 255 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA K 232 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU K 265 " --> pdb=" O CYS K 230 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.652A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA6, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.453A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.049A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AB1, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.287A pdb=" N ARG G 42 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB3, first strand: chain 'K' and resid 195 through 199 removed outlier: 3.697A pdb=" N GLU K 301 " --> pdb=" O ALA K 214 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 279 through 283 483 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 247 hydrogen bonds 486 hydrogen bond angles 0 basepair planarities 96 basepair parallelities 141 stacking parallelities Total time for adding SS restraints: 4.36 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2831 1.33 - 1.45: 3313 1.45 - 1.57: 6062 1.57 - 1.69: 400 1.69 - 1.81: 44 Bond restraints: 12650 Sorted by residual: bond pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " ideal model delta sigma weight residual 1.422 1.460 -0.038 3.00e-02 1.11e+03 1.64e+00 bond pdb=" C3' DA J 44 " pdb=" O3' DA J 44 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" CA ILE C 79 " pdb=" CB ILE C 79 " ideal model delta sigma weight residual 1.546 1.536 0.010 8.80e-03 1.29e+04 1.23e+00 bond pdb=" O5' DA I 49 " pdb=" C5' DA I 49 " ideal model delta sigma weight residual 1.423 1.455 -0.032 3.00e-02 1.11e+03 1.15e+00 bond pdb=" C3' DT I 48 " pdb=" O3' DT I 48 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.75e-01 ... (remaining 12645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.11: 17096 1.11 - 2.23: 695 2.23 - 3.34: 119 3.34 - 4.46: 10 4.46 - 5.57: 8 Bond angle restraints: 17928 Sorted by residual: angle pdb=" N GLY D 104 " pdb=" CA GLY D 104 " pdb=" C GLY D 104 " ideal model delta sigma weight residual 111.02 116.36 -5.34 1.86e+00 2.89e-01 8.23e+00 angle pdb=" C3' DT I 48 " pdb=" C2' DT I 48 " pdb=" C1' DT I 48 " ideal model delta sigma weight residual 101.60 97.33 4.27 1.50e+00 4.44e-01 8.12e+00 angle pdb=" C ASN G 73 " pdb=" N LYS G 74 " pdb=" CA LYS G 74 " ideal model delta sigma weight residual 121.54 126.03 -4.49 1.91e+00 2.74e-01 5.52e+00 angle pdb=" C4' DA I 49 " pdb=" C3' DA I 49 " pdb=" C2' DA I 49 " ideal model delta sigma weight residual 102.40 98.93 3.47 1.50e+00 4.44e-01 5.36e+00 angle pdb=" N PRO D 103 " pdb=" CA PRO D 103 " pdb=" C PRO D 103 " ideal model delta sigma weight residual 110.21 113.95 -3.74 1.64e+00 3.72e-01 5.21e+00 ... (remaining 17923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.17: 6152 35.17 - 70.34: 927 70.34 - 105.50: 42 105.50 - 140.67: 0 140.67 - 175.84: 3 Dihedral angle restraints: 7124 sinusoidal: 4214 harmonic: 2910 Sorted by residual: dihedral pdb=" C4' DA J 44 " pdb=" C3' DA J 44 " pdb=" O3' DA J 44 " pdb=" P DT J 45 " ideal model delta sinusoidal sigma weight residual 220.00 44.16 175.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 94 " pdb=" C3' DG I 94 " pdb=" O3' DG I 94 " pdb=" P DC I 95 " ideal model delta sinusoidal sigma weight residual 220.00 51.01 168.99 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DG I 85 " pdb=" C3' DG I 85 " pdb=" O3' DG I 85 " pdb=" P DT I 86 " ideal model delta sinusoidal sigma weight residual 220.00 55.01 164.99 1 3.50e+01 8.16e-04 1.54e+01 ... (remaining 7121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1456 0.031 - 0.063: 428 0.063 - 0.094: 89 0.094 - 0.125: 53 0.125 - 0.156: 5 Chirality restraints: 2031 Sorted by residual: chirality pdb=" C3' DT I 48 " pdb=" C4' DT I 48 " pdb=" O3' DT I 48 " pdb=" C2' DT I 48 " both_signs ideal model delta sigma weight residual False -2.66 -2.82 0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" P DT I 86 " pdb=" OP1 DT I 86 " pdb=" OP2 DT I 86 " pdb=" O5' DT I 86 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2028 not shown) Planarity restraints: 1592 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 49 " 0.031 2.00e-02 2.50e+03 1.38e-02 5.22e+00 pdb=" N9 DA I 49 " -0.029 2.00e-02 2.50e+03 pdb=" C8 DA I 49 " 0.000 2.00e-02 2.50e+03 pdb=" N7 DA I 49 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DA I 49 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 49 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 49 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I 49 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 49 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 49 " -0.008 2.00e-02 2.50e+03 pdb=" C4 DA I 49 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 98 " 0.001 2.00e-02 2.50e+03 1.40e-02 4.44e+00 pdb=" N1 DC J 98 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DC J 98 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 98 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 98 " -0.013 2.00e-02 2.50e+03 pdb=" N4 DC J 98 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC J 98 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DC J 98 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " -0.024 2.00e-02 2.50e+03 1.15e-02 3.31e+00 pdb=" N1 DT I 88 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " 0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.004 2.00e-02 2.50e+03 ... (remaining 1589 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.78: 2498 2.78 - 3.31: 11748 3.31 - 3.84: 23449 3.84 - 4.37: 25860 4.37 - 4.90: 39469 Nonbonded interactions: 103024 Sorted by model distance: nonbonded pdb=" OD1 ASP B 85 " pdb=" OH TYR D 83 " model vdw 2.255 3.040 nonbonded pdb=" NE2 GLN K 262 " pdb=" O LEU K 263 " model vdw 2.256 3.120 nonbonded pdb=" OG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 2.256 3.040 nonbonded pdb=" O GLU K 236 " pdb=" ND2 ASN K 240 " model vdw 2.264 3.120 nonbonded pdb=" O ILE K 271 " pdb=" OH TYR K 307 " model vdw 2.264 3.040 ... (remaining 103019 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' and resid 44 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 125) 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.920 Find NCS groups from input model: 0.300 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12650 Z= 0.149 Angle : 0.519 5.574 17928 Z= 0.317 Chirality : 0.035 0.156 2031 Planarity : 0.004 0.034 1592 Dihedral : 24.898 175.838 5244 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 6.18 % Favored : 92.85 % 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: 1.98 (0.27), residues: 981 helix: 2.29 (0.21), residues: 624 sheet: -0.80 (0.82), residues: 44 loop : -0.37 (0.33), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE E 78 TYR 0.008 0.001 TYR G 57 ARG 0.002 0.000 ARG H 100 Details of bonding type rmsd hydrogen bonds : bond 0.11301 ( 730) hydrogen bonds : angle 4.85681 ( 1905) covalent geometry : bond 0.00314 (12650) covalent geometry : angle 0.51903 (17928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 196 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8935 (tp-100) cc_final: 0.8624 (tp-100) REVERT: C 90 ASP cc_start: 0.8267 (t70) cc_final: 0.7652 (t0) REVERT: C 92 GLU cc_start: 0.8607 (mp0) cc_final: 0.7966 (mp0) REVERT: C 104 GLN cc_start: 0.8060 (mp10) cc_final: 0.7564 (mp10) REVERT: D 51 ASP cc_start: 0.8292 (p0) cc_final: 0.7962 (p0) REVERT: D 68 ASP cc_start: 0.8875 (t70) cc_final: 0.8551 (t0) REVERT: D 93 GLU cc_start: 0.8430 (mp0) cc_final: 0.7859 (mp0) REVERT: D 123 SER cc_start: 0.7785 (m) cc_final: 0.7510 (p) REVERT: G 92 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8398 (mm-30) REVERT: K 185 TYR cc_start: 0.9105 (m-80) cc_final: 0.8396 (m-80) outliers start: 8 outliers final: 2 residues processed: 202 average time/residue: 0.2249 time to fit residues: 65.2520 Evaluate side-chains 173 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 171 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain G residue 27 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 40.0000 chunk 87 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 54 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN C 112 GLN G 112 GLN K 134 GLN K 174 GLN K 262 GLN K 346 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.068965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.045958 restraints weight = 56055.537| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.39 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12650 Z= 0.156 Angle : 0.548 5.984 17928 Z= 0.321 Chirality : 0.036 0.154 2031 Planarity : 0.004 0.034 1592 Dihedral : 29.619 176.299 3315 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.21 % Allowed : 11.39 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.27), residues: 981 helix: 2.45 (0.20), residues: 636 sheet: -0.87 (0.83), residues: 44 loop : -0.45 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE A 67 TYR 0.017 0.001 TYR H 84 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 730) hydrogen bonds : angle 3.60747 ( 1905) covalent geometry : bond 0.00341 (12650) covalent geometry : angle 0.54803 (17928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 190 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9313 (tt0) cc_final: 0.9097 (tt0) REVERT: A 76 GLN cc_start: 0.8972 (tp-100) cc_final: 0.8515 (tp-100) REVERT: B 84 MET cc_start: 0.8756 (mmm) cc_final: 0.8384 (mmm) REVERT: B 88 TYR cc_start: 0.8529 (m-80) cc_final: 0.8025 (m-80) REVERT: C 64 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7947 (tm-30) REVERT: C 90 ASP cc_start: 0.8203 (t70) cc_final: 0.7650 (t70) REVERT: C 92 GLU cc_start: 0.8834 (mp0) cc_final: 0.8357 (mp0) REVERT: C 104 GLN cc_start: 0.8141 (mp10) cc_final: 0.7561 (mp10) REVERT: D 37 TYR cc_start: 0.8942 (m-10) cc_final: 0.8728 (m-10) REVERT: D 51 ASP cc_start: 0.8981 (p0) cc_final: 0.8241 (p0) REVERT: D 68 ASP cc_start: 0.9186 (t70) cc_final: 0.8871 (t0) REVERT: D 93 GLU cc_start: 0.8901 (mp0) cc_final: 0.8061 (mp0) REVERT: D 123 SER cc_start: 0.8387 (m) cc_final: 0.7972 (p) REVERT: E 50 GLU cc_start: 0.9572 (tt0) cc_final: 0.8954 (tt0) REVERT: E 125 GLN cc_start: 0.9276 (pt0) cc_final: 0.8720 (pm20) REVERT: F 44 LYS cc_start: 0.9034 (mmtp) cc_final: 0.8603 (mmtp) REVERT: G 90 ASP cc_start: 0.8712 (t0) cc_final: 0.8296 (t0) REVERT: H 69 ASP cc_start: 0.9391 (t70) cc_final: 0.8997 (t0) REVERT: K 185 TYR cc_start: 0.9124 (m-80) cc_final: 0.8463 (m-80) outliers start: 10 outliers final: 6 residues processed: 191 average time/residue: 0.2375 time to fit residues: 64.6584 Evaluate side-chains 179 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 100 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 316 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.065800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.042412 restraints weight = 57815.682| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.40 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 12650 Z= 0.304 Angle : 0.626 5.828 17928 Z= 0.363 Chirality : 0.039 0.171 2031 Planarity : 0.004 0.037 1592 Dihedral : 30.041 179.067 3313 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.30 % Allowed : 11.39 % Favored : 86.30 % 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: 2.00 (0.27), residues: 981 helix: 2.34 (0.20), residues: 638 sheet: -1.09 (0.79), residues: 44 loop : -0.52 (0.33), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 264 HIS 0.005 0.001 HIS B 75 PHE 0.008 0.001 PHE A 78 TYR 0.016 0.002 TYR H 84 ARG 0.008 0.001 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.05219 ( 730) hydrogen bonds : angle 3.81033 ( 1905) covalent geometry : bond 0.00677 (12650) covalent geometry : angle 0.62599 (17928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9330 (tt0) cc_final: 0.9129 (tt0) REVERT: A 133 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8406 (mt-10) REVERT: B 88 TYR cc_start: 0.8856 (m-80) cc_final: 0.8596 (m-80) REVERT: C 64 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7950 (tm-30) REVERT: C 90 ASP cc_start: 0.8309 (t70) cc_final: 0.7542 (t0) REVERT: C 92 GLU cc_start: 0.8895 (mp0) cc_final: 0.8121 (mp0) REVERT: C 104 GLN cc_start: 0.8252 (mp10) cc_final: 0.7607 (mp10) REVERT: D 51 ASP cc_start: 0.9046 (p0) cc_final: 0.8335 (p0) REVERT: D 68 ASP cc_start: 0.9214 (t70) cc_final: 0.8860 (t0) REVERT: D 93 GLU cc_start: 0.8993 (mp0) cc_final: 0.8093 (mp0) REVERT: E 50 GLU cc_start: 0.9590 (tt0) cc_final: 0.9361 (tt0) REVERT: E 80 THR cc_start: 0.9545 (OUTLIER) cc_final: 0.9292 (m) REVERT: E 81 ASP cc_start: 0.9341 (p0) cc_final: 0.9053 (p0) REVERT: E 125 GLN cc_start: 0.9236 (pt0) cc_final: 0.8989 (pt0) REVERT: F 44 LYS cc_start: 0.9068 (mmtp) cc_final: 0.8634 (mmtp) REVERT: G 90 ASP cc_start: 0.8729 (t0) cc_final: 0.8350 (t0) REVERT: K 185 TYR cc_start: 0.8963 (m-80) cc_final: 0.8337 (m-80) REVERT: K 253 MET cc_start: 0.8568 (mpp) cc_final: 0.8128 (mpp) outliers start: 19 outliers final: 15 residues processed: 172 average time/residue: 0.2579 time to fit residues: 63.9653 Evaluate side-chains 174 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 92 optimal weight: 0.0980 chunk 91 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS E 125 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.068176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.045171 restraints weight = 55743.685| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 3.40 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.144 Angle : 0.545 7.032 17928 Z= 0.319 Chirality : 0.036 0.164 2031 Planarity : 0.003 0.034 1592 Dihedral : 29.765 178.335 3313 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.58 % Allowed : 13.58 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.27), residues: 981 helix: 2.45 (0.20), residues: 636 sheet: -0.97 (0.77), residues: 44 loop : -0.47 (0.34), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.008 0.001 PHE H 71 TYR 0.019 0.001 TYR H 41 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 730) hydrogen bonds : angle 3.35855 ( 1905) covalent geometry : bond 0.00315 (12650) covalent geometry : angle 0.54512 (17928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 178 time to evaluate : 1.422 Fit side-chains REVERT: A 50 GLU cc_start: 0.9330 (tt0) cc_final: 0.9091 (tt0) REVERT: A 76 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8436 (tp-100) REVERT: A 133 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8139 (mt-10) REVERT: B 84 MET cc_start: 0.8765 (mmm) cc_final: 0.8350 (mmm) REVERT: B 88 TYR cc_start: 0.8657 (m-80) cc_final: 0.8024 (m-80) REVERT: B 93 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8941 (mm-40) REVERT: C 64 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7991 (tm-30) REVERT: C 90 ASP cc_start: 0.8251 (t70) cc_final: 0.7444 (t0) REVERT: C 92 GLU cc_start: 0.8878 (mp0) cc_final: 0.7993 (mp0) REVERT: C 104 GLN cc_start: 0.8205 (mp10) cc_final: 0.7569 (mp10) REVERT: D 51 ASP cc_start: 0.9016 (p0) cc_final: 0.8326 (p0) REVERT: D 68 ASP cc_start: 0.9147 (t70) cc_final: 0.8853 (t0) REVERT: D 83 TYR cc_start: 0.8358 (t80) cc_final: 0.8041 (t80) REVERT: D 93 GLU cc_start: 0.8981 (mp0) cc_final: 0.8064 (mp0) REVERT: D 123 SER cc_start: 0.8423 (m) cc_final: 0.8046 (p) REVERT: E 50 GLU cc_start: 0.9595 (tt0) cc_final: 0.9329 (tt0) REVERT: E 125 GLN cc_start: 0.9257 (pt0) cc_final: 0.9048 (pt0) REVERT: F 44 LYS cc_start: 0.9022 (mmtp) cc_final: 0.8592 (mmtp) REVERT: G 90 ASP cc_start: 0.8718 (t0) cc_final: 0.8334 (t0) REVERT: H 69 ASP cc_start: 0.9409 (t70) cc_final: 0.9035 (t0) REVERT: K 185 TYR cc_start: 0.9042 (m-80) cc_final: 0.8462 (m-80) REVERT: K 188 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8922 (ppp) REVERT: K 253 MET cc_start: 0.8513 (mpp) cc_final: 0.8108 (mpp) outliers start: 13 outliers final: 7 residues processed: 183 average time/residue: 0.2617 time to fit residues: 69.0129 Evaluate side-chains 179 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 171 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 63 optimal weight: 0.0070 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.066235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.043162 restraints weight = 56777.186| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.37 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 12650 Z= 0.269 Angle : 0.600 6.782 17928 Z= 0.348 Chirality : 0.038 0.167 2031 Planarity : 0.004 0.037 1592 Dihedral : 29.969 179.750 3313 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.82 % Allowed : 14.30 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 981 helix: 2.40 (0.20), residues: 639 sheet: -1.05 (0.77), residues: 44 loop : -0.49 (0.33), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 218 HIS 0.005 0.001 HIS B 75 PHE 0.007 0.001 PHE E 78 TYR 0.024 0.002 TYR H 41 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04499 ( 730) hydrogen bonds : angle 3.57003 ( 1905) covalent geometry : bond 0.00600 (12650) covalent geometry : angle 0.59980 (17928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8516 (tp-100) REVERT: A 133 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8222 (mt-10) REVERT: B 23 ARG cc_start: 0.8006 (mmm-85) cc_final: 0.7736 (mmm-85) REVERT: B 44 LYS cc_start: 0.8724 (mtpt) cc_final: 0.8405 (mtpt) REVERT: B 84 MET cc_start: 0.8751 (mmm) cc_final: 0.8484 (mmm) REVERT: B 88 TYR cc_start: 0.8809 (m-80) cc_final: 0.8200 (m-80) REVERT: C 29 ARG cc_start: 0.8679 (ttm170) cc_final: 0.8285 (ttm170) REVERT: C 64 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7868 (tm-30) REVERT: C 90 ASP cc_start: 0.8302 (t70) cc_final: 0.7456 (t0) REVERT: C 92 GLU cc_start: 0.8901 (mp0) cc_final: 0.8090 (mp0) REVERT: C 104 GLN cc_start: 0.8303 (mp10) cc_final: 0.7686 (mp10) REVERT: D 51 ASP cc_start: 0.8987 (p0) cc_final: 0.8294 (p0) REVERT: D 68 ASP cc_start: 0.9242 (t70) cc_final: 0.8917 (t0) REVERT: D 83 TYR cc_start: 0.8371 (t80) cc_final: 0.8005 (t80) REVERT: E 50 GLU cc_start: 0.9580 (tt0) cc_final: 0.9346 (tt0) REVERT: E 125 GLN cc_start: 0.9181 (pt0) cc_final: 0.8936 (pt0) REVERT: F 44 LYS cc_start: 0.9030 (mmtp) cc_final: 0.8572 (mmtp) REVERT: G 90 ASP cc_start: 0.8765 (t0) cc_final: 0.8393 (t0) REVERT: K 188 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8828 (ppp) outliers start: 15 outliers final: 10 residues processed: 171 average time/residue: 0.2758 time to fit residues: 66.5949 Evaluate side-chains 171 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 160 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 291 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 43 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.066649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.043509 restraints weight = 57501.942| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 3.42 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12650 Z= 0.213 Angle : 0.575 7.438 17928 Z= 0.335 Chirality : 0.037 0.162 2031 Planarity : 0.004 0.034 1592 Dihedral : 29.993 179.868 3313 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.21 % Allowed : 16.12 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.27), residues: 981 helix: 2.44 (0.20), residues: 637 sheet: -0.99 (0.76), residues: 44 loop : -0.42 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.04135 ( 730) hydrogen bonds : angle 3.43360 ( 1905) covalent geometry : bond 0.00474 (12650) covalent geometry : angle 0.57518 (17928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 169 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9297 (tt0) cc_final: 0.8748 (tt0) REVERT: A 76 GLN cc_start: 0.8998 (tp-100) cc_final: 0.8469 (tp-100) REVERT: A 133 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 23 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7750 (mmm-85) REVERT: B 44 LYS cc_start: 0.8787 (mtpt) cc_final: 0.8423 (mtpt) REVERT: B 84 MET cc_start: 0.8799 (mmm) cc_final: 0.8500 (mmm) REVERT: B 88 TYR cc_start: 0.8775 (m-80) cc_final: 0.8232 (m-80) REVERT: B 93 GLN cc_start: 0.9084 (mm-40) cc_final: 0.8832 (mm-40) REVERT: C 64 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 90 ASP cc_start: 0.8304 (t70) cc_final: 0.7747 (t0) REVERT: C 92 GLU cc_start: 0.8887 (mp0) cc_final: 0.8301 (mp0) REVERT: C 104 GLN cc_start: 0.8289 (mp10) cc_final: 0.7666 (mp10) REVERT: D 51 ASP cc_start: 0.8946 (p0) cc_final: 0.8236 (p0) REVERT: D 68 ASP cc_start: 0.9214 (t70) cc_final: 0.8909 (t0) REVERT: D 71 GLU cc_start: 0.8865 (tp30) cc_final: 0.8571 (mm-30) REVERT: D 83 TYR cc_start: 0.8312 (t80) cc_final: 0.7909 (t80) REVERT: D 93 GLU cc_start: 0.8975 (mp0) cc_final: 0.8026 (mp0) REVERT: E 50 GLU cc_start: 0.9559 (tt0) cc_final: 0.9305 (tt0) REVERT: F 44 LYS cc_start: 0.9013 (mmtp) cc_final: 0.8562 (mmtp) REVERT: G 90 ASP cc_start: 0.8762 (t0) cc_final: 0.8356 (t0) REVERT: K 188 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8867 (ppp) REVERT: K 253 MET cc_start: 0.8209 (mpp) cc_final: 0.7868 (mpp) outliers start: 10 outliers final: 8 residues processed: 172 average time/residue: 0.3029 time to fit residues: 75.7318 Evaluate side-chains 178 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.066371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.043377 restraints weight = 56698.587| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 3.35 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12650 Z= 0.229 Angle : 0.590 8.776 17928 Z= 0.341 Chirality : 0.037 0.168 2031 Planarity : 0.004 0.033 1592 Dihedral : 30.033 179.555 3313 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.58 % Allowed : 16.24 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.27), residues: 981 helix: 2.43 (0.20), residues: 640 sheet: -0.97 (0.76), residues: 44 loop : -0.37 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE F 100 TYR 0.025 0.002 TYR H 41 ARG 0.007 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.04369 ( 730) hydrogen bonds : angle 3.46394 ( 1905) covalent geometry : bond 0.00511 (12650) covalent geometry : angle 0.59002 (17928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9291 (tt0) cc_final: 0.8720 (tt0) REVERT: A 76 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8463 (tp-100) REVERT: A 133 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8217 (mt-10) REVERT: B 20 MET cc_start: 0.8892 (mmm) cc_final: 0.8617 (mmm) REVERT: B 23 ARG cc_start: 0.7984 (mtm-85) cc_final: 0.7745 (mmm-85) REVERT: B 84 MET cc_start: 0.8812 (mmm) cc_final: 0.8506 (mmm) REVERT: B 88 TYR cc_start: 0.8808 (m-80) cc_final: 0.8292 (m-80) REVERT: C 29 ARG cc_start: 0.8756 (ttm170) cc_final: 0.8456 (ttm170) REVERT: C 64 GLU cc_start: 0.8246 (tm-30) cc_final: 0.7905 (tm-30) REVERT: C 72 ASP cc_start: 0.8859 (m-30) cc_final: 0.8560 (m-30) REVERT: C 90 ASP cc_start: 0.8288 (t70) cc_final: 0.7714 (t0) REVERT: C 92 GLU cc_start: 0.8902 (mp0) cc_final: 0.8338 (mp0) REVERT: C 104 GLN cc_start: 0.8279 (mp10) cc_final: 0.7625 (mp10) REVERT: D 51 ASP cc_start: 0.8968 (p0) cc_final: 0.8269 (p0) REVERT: D 68 ASP cc_start: 0.9202 (t70) cc_final: 0.8897 (t0) REVERT: D 83 TYR cc_start: 0.8331 (t80) cc_final: 0.7951 (t80) REVERT: D 93 GLU cc_start: 0.8970 (mp0) cc_final: 0.8007 (mp0) REVERT: E 50 GLU cc_start: 0.9552 (tt0) cc_final: 0.9284 (tt0) REVERT: F 44 LYS cc_start: 0.9023 (mmtp) cc_final: 0.8584 (mmtp) REVERT: G 90 ASP cc_start: 0.8723 (t0) cc_final: 0.8329 (t0) REVERT: H 84 TYR cc_start: 0.7855 (m-10) cc_final: 0.7349 (m-10) REVERT: K 188 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8837 (ppp) REVERT: K 253 MET cc_start: 0.8195 (mpp) cc_final: 0.7842 (mpp) outliers start: 13 outliers final: 11 residues processed: 177 average time/residue: 0.2558 time to fit residues: 63.9620 Evaluate side-chains 179 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 39 optimal weight: 0.8980 chunk 102 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.067945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.045062 restraints weight = 56512.879| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.40 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.152 Angle : 0.564 8.897 17928 Z= 0.323 Chirality : 0.036 0.165 2031 Planarity : 0.003 0.036 1592 Dihedral : 29.796 179.385 3313 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.21 % Allowed : 16.48 % Favored : 82.30 % 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: 2.29 (0.27), residues: 981 helix: 2.55 (0.20), residues: 636 sheet: -0.92 (0.75), residues: 44 loop : -0.39 (0.33), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE H 71 TYR 0.026 0.001 TYR H 41 ARG 0.004 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03650 ( 730) hydrogen bonds : angle 3.23210 ( 1905) covalent geometry : bond 0.00337 (12650) covalent geometry : angle 0.56388 (17928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8075 (mt-10) REVERT: B 20 MET cc_start: 0.8855 (mmm) cc_final: 0.8604 (mmm) REVERT: B 84 MET cc_start: 0.8829 (mmm) cc_final: 0.8605 (mmm) REVERT: B 88 TYR cc_start: 0.8736 (m-80) cc_final: 0.8318 (m-80) REVERT: B 93 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8826 (mm-40) REVERT: C 64 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7920 (tm-30) REVERT: C 90 ASP cc_start: 0.8278 (t70) cc_final: 0.7460 (t0) REVERT: C 92 GLU cc_start: 0.8882 (mp0) cc_final: 0.8015 (mp0) REVERT: D 51 ASP cc_start: 0.8924 (p0) cc_final: 0.8206 (p0) REVERT: D 68 ASP cc_start: 0.9159 (t70) cc_final: 0.8862 (t0) REVERT: D 83 TYR cc_start: 0.8275 (t80) cc_final: 0.7941 (t80) REVERT: D 93 GLU cc_start: 0.8931 (mp0) cc_final: 0.8054 (mp0) REVERT: D 123 SER cc_start: 0.8462 (m) cc_final: 0.8085 (p) REVERT: E 50 GLU cc_start: 0.9538 (tt0) cc_final: 0.9228 (tt0) REVERT: F 44 LYS cc_start: 0.9036 (mmtp) cc_final: 0.8585 (mmtp) REVERT: G 90 ASP cc_start: 0.8700 (t0) cc_final: 0.8262 (t0) REVERT: H 69 ASP cc_start: 0.9408 (t70) cc_final: 0.9052 (t0) REVERT: K 188 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8854 (ppp) REVERT: K 253 MET cc_start: 0.8226 (mpp) cc_final: 0.7940 (mpp) outliers start: 10 outliers final: 9 residues processed: 186 average time/residue: 0.2686 time to fit residues: 71.5714 Evaluate side-chains 183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 173 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 51 optimal weight: 0.0870 chunk 90 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.068119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.045309 restraints weight = 55968.924| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.37 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.152 Angle : 0.561 9.008 17928 Z= 0.321 Chirality : 0.036 0.173 2031 Planarity : 0.004 0.057 1592 Dihedral : 29.714 179.568 3313 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.45 % Allowed : 16.48 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 981 helix: 2.55 (0.20), residues: 639 sheet: -0.86 (0.75), residues: 44 loop : -0.33 (0.34), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE H 71 TYR 0.026 0.001 TYR H 41 ARG 0.014 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03627 ( 730) hydrogen bonds : angle 3.20844 ( 1905) covalent geometry : bond 0.00335 (12650) covalent geometry : angle 0.56072 (17928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9183 (tt0) cc_final: 0.8791 (tt0) REVERT: A 76 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8345 (tp-100) REVERT: A 133 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8058 (mt-10) REVERT: B 20 MET cc_start: 0.8916 (mmm) cc_final: 0.8638 (mmm) REVERT: B 84 MET cc_start: 0.8827 (mmm) cc_final: 0.8604 (mmm) REVERT: B 88 TYR cc_start: 0.8754 (m-80) cc_final: 0.8293 (m-80) REVERT: B 93 GLN cc_start: 0.9036 (mm-40) cc_final: 0.8827 (mm-40) REVERT: C 29 ARG cc_start: 0.8648 (ttm170) cc_final: 0.8282 (ttm170) REVERT: C 64 GLU cc_start: 0.8286 (tm-30) cc_final: 0.7977 (tm-30) REVERT: C 90 ASP cc_start: 0.8328 (t70) cc_final: 0.7741 (t0) REVERT: C 92 GLU cc_start: 0.8910 (mp0) cc_final: 0.8344 (mp0) REVERT: C 104 GLN cc_start: 0.8208 (mp10) cc_final: 0.7677 (mp10) REVERT: D 51 ASP cc_start: 0.8904 (p0) cc_final: 0.8169 (p0) REVERT: D 68 ASP cc_start: 0.9161 (t70) cc_final: 0.8868 (t0) REVERT: D 83 TYR cc_start: 0.8320 (t80) cc_final: 0.7985 (t80) REVERT: D 93 GLU cc_start: 0.8928 (mp0) cc_final: 0.8055 (mp0) REVERT: D 123 SER cc_start: 0.8328 (m) cc_final: 0.7978 (p) REVERT: E 50 GLU cc_start: 0.9538 (tt0) cc_final: 0.9245 (tt0) REVERT: F 44 LYS cc_start: 0.8989 (mmtp) cc_final: 0.8537 (mmtp) REVERT: G 90 ASP cc_start: 0.8721 (t0) cc_final: 0.8275 (t0) REVERT: K 188 MET cc_start: 0.9142 (OUTLIER) cc_final: 0.8846 (ppp) REVERT: K 253 MET cc_start: 0.8198 (mpp) cc_final: 0.7885 (mpp) outliers start: 12 outliers final: 11 residues processed: 182 average time/residue: 0.2495 time to fit residues: 63.7242 Evaluate side-chains 183 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Chi-restraints excluded: chain K residue 307 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 112 optimal weight: 10.0000 chunk 45 optimal weight: 0.9980 chunk 92 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 35 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.067881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.044851 restraints weight = 56422.100| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 3.39 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12650 Z= 0.169 Angle : 0.577 11.918 17928 Z= 0.327 Chirality : 0.036 0.163 2031 Planarity : 0.004 0.035 1592 Dihedral : 29.716 179.478 3313 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.82 % Allowed : 16.61 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.27), residues: 981 helix: 2.47 (0.20), residues: 643 sheet: -0.87 (0.74), residues: 44 loop : -0.34 (0.34), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.006 0.001 PHE H 71 TYR 0.027 0.001 TYR H 41 ARG 0.004 0.000 ARG D 33 Details of bonding type rmsd hydrogen bonds : bond 0.03727 ( 730) hydrogen bonds : angle 3.22609 ( 1905) covalent geometry : bond 0.00376 (12650) covalent geometry : angle 0.57652 (17928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1962 Ramachandran restraints generated. 981 Oldfield, 0 Emsley, 981 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.159 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9190 (tt0) cc_final: 0.8716 (tt0) REVERT: A 76 GLN cc_start: 0.8940 (tp-100) cc_final: 0.8373 (tp-100) REVERT: A 133 GLU cc_start: 0.8619 (mt-10) cc_final: 0.8092 (mt-10) REVERT: B 20 MET cc_start: 0.8950 (mmm) cc_final: 0.8679 (mmm) REVERT: B 23 ARG cc_start: 0.8018 (mmm-85) cc_final: 0.7717 (mmm-85) REVERT: B 84 MET cc_start: 0.8816 (mmm) cc_final: 0.8606 (mmm) REVERT: B 88 TYR cc_start: 0.8776 (m-80) cc_final: 0.8350 (m-80) REVERT: B 93 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8868 (mm-40) REVERT: C 64 GLU cc_start: 0.8252 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 90 ASP cc_start: 0.8346 (t70) cc_final: 0.7786 (t0) REVERT: C 92 GLU cc_start: 0.8940 (mp0) cc_final: 0.8383 (mp0) REVERT: C 104 GLN cc_start: 0.8227 (mp10) cc_final: 0.7693 (mp10) REVERT: D 51 ASP cc_start: 0.8939 (p0) cc_final: 0.8209 (p0) REVERT: D 68 ASP cc_start: 0.9161 (t70) cc_final: 0.8864 (t0) REVERT: D 83 TYR cc_start: 0.8291 (t80) cc_final: 0.7939 (t80) REVERT: D 93 GLU cc_start: 0.8933 (mp0) cc_final: 0.8053 (mp0) REVERT: D 123 SER cc_start: 0.8354 (m) cc_final: 0.8003 (p) REVERT: E 50 GLU cc_start: 0.9540 (tt0) cc_final: 0.9242 (tt0) REVERT: F 44 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8572 (mmtp) REVERT: H 84 TYR cc_start: 0.7851 (m-10) cc_final: 0.7361 (m-10) REVERT: K 188 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8824 (ppp) REVERT: K 253 MET cc_start: 0.8182 (mpp) cc_final: 0.7900 (mpp) outliers start: 15 outliers final: 11 residues processed: 176 average time/residue: 0.2448 time to fit residues: 61.9914 Evaluate side-chains 186 residues out of total 844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 173 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 77 GLU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 149 HIS Chi-restraints excluded: chain K residue 188 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 50 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.068302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.045575 restraints weight = 56272.735| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.37 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12650 Z= 0.154 Angle : 0.576 11.632 17928 Z= 0.325 Chirality : 0.036 0.160 2031 Planarity : 0.004 0.054 1592 Dihedral : 29.623 179.276 3313 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.58 % Allowed : 16.85 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.27), residues: 981 helix: 2.52 (0.20), residues: 644 sheet: -0.83 (0.75), residues: 44 loop : -0.29 (0.34), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 218 HIS 0.004 0.001 HIS B 75 PHE 0.007 0.001 PHE H 71 TYR 0.026 0.001 TYR H 41 ARG 0.012 0.000 ARG C 99 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 730) hydrogen bonds : angle 3.17518 ( 1905) covalent geometry : bond 0.00342 (12650) covalent geometry : angle 0.57612 (17928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5739.41 seconds wall clock time: 105 minutes 11.70 seconds (6311.70 seconds total)