Starting phenix.real_space_refine on Sun May 18 05:05:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.map" model { file = "/net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jhy_22340/05_2025/7jhy_22340.cif" } resolution = 3.9 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= 0.035 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 30 5.49 5 S 6 5.16 5 C 10361 2.51 5 N 3013 2.21 5 O 3187 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16597 Number of models: 1 Model: "" Number of chains: 3 Chain: "a" Number of atoms: 1725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1725 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "z" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 627 Classifications: {'RNA': 31} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 13, 'rna3p_pur': 1, 'rna3p_pyr': 13} Link IDs: {'rna2p': 16, 'rna3p': 14} Chain: "g" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1124 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PTRANS': 12, 'TRANS': 129} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: b, c, d, e, f, h, i, j, k Time building chain proxies: 6.34, per 1000 atoms: 0.38 Number of scatterers: 16597 At special positions: 0 Unit cell: (115.5, 108.9, 189.2, 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 6 16.00 P 30 15.00 O 3187 8.00 N 3013 7.00 C 10361 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: 4.38 Conformation dependent library (CDL) restraints added in 2.3 seconds 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3890 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 34.6% alpha, 9.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'e' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE e 70 " --> pdb=" O SER e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU e 125 " --> pdb=" O ASN e 121 " (cutoff:3.500A) Processing helix chain 'e' and resid 128 through 133 Processing helix chain 'e' and resid 232 through 248 Processing helix chain 'e' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY e 257 " --> pdb=" O SER e 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 254 through 257' Processing helix chain 'd' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE d 70 " --> pdb=" O SER d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU d 125 " --> pdb=" O ASN d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 133 Processing helix chain 'd' and resid 232 through 248 Processing helix chain 'd' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY d 257 " --> pdb=" O SER d 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 254 through 257' Processing helix chain 'c' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE c 70 " --> pdb=" O SER c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU c 125 " --> pdb=" O ASN c 121 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 133 Processing helix chain 'c' and resid 232 through 248 Processing helix chain 'c' and resid 254 through 257 removed outlier: 3.540A pdb=" N GLY c 257 " --> pdb=" O SER c 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 254 through 257' Processing helix chain 'f' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) Processing helix chain 'f' and resid 121 through 126 removed outlier: 3.624A pdb=" N LEU f 125 " --> pdb=" O ASN f 121 " (cutoff:3.500A) Processing helix chain 'f' and resid 128 through 133 Processing helix chain 'f' and resid 232 through 248 Processing helix chain 'f' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY f 257 " --> pdb=" O SER f 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 254 through 257' Processing helix chain 'b' and resid 66 through 83 removed outlier: 3.796A pdb=" N PHE b 70 " --> pdb=" O SER b 66 " (cutoff:3.500A) Processing helix chain 'b' and resid 121 through 126 removed outlier: 3.623A pdb=" N LEU b 125 " --> pdb=" O ASN b 121 " (cutoff:3.500A) Processing helix chain 'b' and resid 128 through 133 Processing helix chain 'b' and resid 232 through 248 Processing helix chain 'b' and resid 254 through 257 removed outlier: 3.538A pdb=" N GLY b 257 " --> pdb=" O SER b 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 257' Processing helix chain 'a' and resid 66 through 83 removed outlier: 3.795A pdb=" N PHE a 70 " --> pdb=" O SER a 66 " (cutoff:3.500A) Processing helix chain 'a' and resid 121 through 126 removed outlier: 3.625A pdb=" N LEU a 125 " --> pdb=" O ASN a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 133 Processing helix chain 'a' and resid 232 through 248 Processing helix chain 'a' and resid 254 through 257 removed outlier: 3.539A pdb=" N GLY a 257 " --> pdb=" O SER a 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 254 through 257' Processing helix chain 'h' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG h 11 " --> pdb=" O THR h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) Processing helix chain 'h' and resid 69 through 78 Processing helix chain 'h' and resid 83 through 94 Processing helix chain 'h' and resid 102 through 113 Processing helix chain 'h' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR h 122 " --> pdb=" O LEU h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 128 through 145 Processing helix chain 'g' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG g 11 " --> pdb=" O THR g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 30 through 44 removed outlier: 3.636A pdb=" N ALA g 34 " --> pdb=" O ALA g 30 " (cutoff:3.500A) Processing helix chain 'g' and resid 69 through 78 Processing helix chain 'g' and resid 83 through 94 Processing helix chain 'g' and resid 102 through 113 Processing helix chain 'g' and resid 118 through 127 removed outlier: 3.729A pdb=" N THR g 122 " --> pdb=" O LEU g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 128 through 145 Processing helix chain 'j' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG j 11 " --> pdb=" O THR j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA j 34 " --> pdb=" O ALA j 30 " (cutoff:3.500A) Processing helix chain 'j' and resid 69 through 78 Processing helix chain 'j' and resid 83 through 94 Processing helix chain 'j' and resid 102 through 113 Processing helix chain 'j' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR j 122 " --> pdb=" O LEU j 118 " (cutoff:3.500A) Processing helix chain 'j' and resid 128 through 145 Processing helix chain 'k' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG k 11 " --> pdb=" O THR k 7 " (cutoff:3.500A) Processing helix chain 'k' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA k 34 " --> pdb=" O ALA k 30 " (cutoff:3.500A) Processing helix chain 'k' and resid 69 through 78 Processing helix chain 'k' and resid 83 through 94 Processing helix chain 'k' and resid 102 through 113 Processing helix chain 'k' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR k 122 " --> pdb=" O LEU k 118 " (cutoff:3.500A) Processing helix chain 'k' and resid 128 through 145 Processing helix chain 'i' and resid 7 through 12 removed outlier: 3.833A pdb=" N ARG i 11 " --> pdb=" O THR i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 30 through 44 removed outlier: 3.635A pdb=" N ALA i 34 " --> pdb=" O ALA i 30 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 78 Processing helix chain 'i' and resid 83 through 94 Processing helix chain 'i' and resid 102 through 113 Processing helix chain 'i' and resid 118 through 127 removed outlier: 3.728A pdb=" N THR i 122 " --> pdb=" O LEU i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 128 through 145 Processing sheet with id=AA1, first strand: chain 'e' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG e 253 " --> pdb=" O HIS e 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN e 260 " --> pdb=" O GLY e 251 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N GLY e 251 " --> pdb=" O GLN e 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR e 262 " --> pdb=" O HIS e 249 " (cutoff:3.500A) removed outlier: 9.278A pdb=" N HIS e 249 " --> pdb=" O THR e 262 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'e' and resid 50 through 53 Processing sheet with id=AA3, first strand: chain 'd' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG d 253 " --> pdb=" O HIS d 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN d 260 " --> pdb=" O GLY d 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY d 251 " --> pdb=" O GLN d 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR d 262 " --> pdb=" O HIS d 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS d 249 " --> pdb=" O THR d 262 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'd' and resid 50 through 53 Processing sheet with id=AA5, first strand: chain 'c' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG c 253 " --> pdb=" O HIS c 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN c 260 " --> pdb=" O GLY c 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY c 251 " --> pdb=" O GLN c 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR c 262 " --> pdb=" O HIS c 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS c 249 " --> pdb=" O THR c 262 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 50 through 53 Processing sheet with id=AA7, first strand: chain 'f' and resid 145 through 147 removed outlier: 4.123A pdb=" N ARG f 253 " --> pdb=" O HIS f 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN f 260 " --> pdb=" O GLY f 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY f 251 " --> pdb=" O GLN f 260 " (cutoff:3.500A) removed outlier: 9.179A pdb=" N THR f 262 " --> pdb=" O HIS f 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS f 249 " --> pdb=" O THR f 262 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'f' and resid 50 through 53 Processing sheet with id=AA9, first strand: chain 'b' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG b 253 " --> pdb=" O HIS b 258 " (cutoff:3.500A) removed outlier: 8.902A pdb=" N GLN b 260 " --> pdb=" O GLY b 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY b 251 " --> pdb=" O GLN b 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR b 262 " --> pdb=" O HIS b 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS b 249 " --> pdb=" O THR b 262 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'b' and resid 50 through 53 Processing sheet with id=AB2, first strand: chain 'a' and resid 145 through 147 removed outlier: 4.122A pdb=" N ARG a 253 " --> pdb=" O HIS a 258 " (cutoff:3.500A) removed outlier: 8.901A pdb=" N GLN a 260 " --> pdb=" O GLY a 251 " (cutoff:3.500A) removed outlier: 8.934A pdb=" N GLY a 251 " --> pdb=" O GLN a 260 " (cutoff:3.500A) removed outlier: 9.180A pdb=" N THR a 262 " --> pdb=" O HIS a 249 " (cutoff:3.500A) removed outlier: 9.277A pdb=" N HIS a 249 " --> pdb=" O THR a 262 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 50 through 53 548 hydrogen bonds defined for protein. 1608 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4402 1.33 - 1.45: 2903 1.45 - 1.57: 9609 1.57 - 1.68: 60 1.68 - 1.80: 12 Bond restraints: 16986 Sorted by residual: bond pdb=" C ASP k 58 " pdb=" N PRO k 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.98e+00 bond pdb=" C ASP i 58 " pdb=" N PRO i 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.96e+00 bond pdb=" C ASP j 58 " pdb=" N PRO j 59 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.90e+00 bond pdb=" C THR d 168 " pdb=" N PRO d 169 " ideal model delta sigma weight residual 1.334 1.374 -0.040 2.34e-02 1.83e+03 2.89e+00 bond pdb=" C ASP h 58 " pdb=" N PRO h 59 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 ... (remaining 16981 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 22295 2.39 - 4.78: 747 4.78 - 7.17: 161 7.17 - 9.56: 58 9.56 - 11.95: 22 Bond angle restraints: 23283 Sorted by residual: angle pdb=" N PRO j 116 " pdb=" CA PRO j 116 " pdb=" CB PRO j 116 " ideal model delta sigma weight residual 103.26 109.92 -6.66 1.14e+00 7.69e-01 3.41e+01 angle pdb=" N PRO h 116 " pdb=" CA PRO h 116 " pdb=" CB PRO h 116 " ideal model delta sigma weight residual 103.26 109.90 -6.64 1.14e+00 7.69e-01 3.39e+01 angle pdb=" N PRO k 116 " pdb=" CA PRO k 116 " pdb=" CB PRO k 116 " ideal model delta sigma weight residual 103.26 109.88 -6.62 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO i 116 " pdb=" CA PRO i 116 " pdb=" CB PRO i 116 " ideal model delta sigma weight residual 103.26 109.87 -6.61 1.14e+00 7.69e-01 3.37e+01 angle pdb=" N PRO g 116 " pdb=" CA PRO g 116 " pdb=" CB PRO g 116 " ideal model delta sigma weight residual 103.26 109.85 -6.59 1.14e+00 7.69e-01 3.34e+01 ... (remaining 23278 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 9957 35.63 - 71.26: 276 71.26 - 106.89: 30 106.89 - 142.52: 3 142.52 - 178.15: 4 Dihedral angle restraints: 10270 sinusoidal: 4320 harmonic: 5950 Sorted by residual: dihedral pdb=" O4' U z 8 " pdb=" C1' U z 8 " pdb=" N1 U z 8 " pdb=" C2 U z 8 " ideal model delta sinusoidal sigma weight residual 232.00 53.85 178.15 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U z 3 " pdb=" C1' U z 3 " pdb=" N1 U z 3 " pdb=" C2 U z 3 " ideal model delta sinusoidal sigma weight residual 232.00 59.09 172.91 1 1.70e+01 3.46e-03 6.62e+01 dihedral pdb=" O4' U z 31 " pdb=" C1' U z 31 " pdb=" N1 U z 31 " pdb=" C2 U z 31 " ideal model delta sinusoidal sigma weight residual -128.00 35.51 -163.51 1 1.70e+01 3.46e-03 6.51e+01 ... (remaining 10267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2099 0.061 - 0.122: 568 0.122 - 0.183: 67 0.183 - 0.244: 31 0.244 - 0.305: 1 Chirality restraints: 2766 Sorted by residual: chirality pdb=" C3' A z 1 " pdb=" C4' A z 1 " pdb=" O3' A z 1 " pdb=" C2' A z 1 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA ARG b 276 " pdb=" N ARG b 276 " pdb=" C ARG b 276 " pdb=" CB ARG b 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ARG f 276 " pdb=" N ARG f 276 " pdb=" C ARG f 276 " pdb=" CB ARG f 276 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2763 not shown) Planarity restraints: 2903 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU b 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO b 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO b 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO b 162 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU f 161 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO f 162 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO f 162 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO f 162 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU a 161 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.01e+00 pdb=" N PRO a 162 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO a 162 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO a 162 " -0.041 5.00e-02 4.00e+02 ... (remaining 2900 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 913 2.73 - 3.27: 15867 3.27 - 3.81: 25430 3.81 - 4.36: 27686 4.36 - 4.90: 48153 Nonbonded interactions: 118049 Sorted by model distance: nonbonded pdb=" NH2 ARG h 114 " pdb=" O PRO g 18 " model vdw 2.185 3.120 nonbonded pdb=" NH2 ARG b 76 " pdb=" OP1 U z 31 " model vdw 2.295 3.120 nonbonded pdb=" NE ARG c 71 " pdb=" OP1 U z 19 " model vdw 2.320 3.120 nonbonded pdb=" NE ARG d 71 " pdb=" OP2 U z 13 " model vdw 2.357 3.120 nonbonded pdb=" O2' U z 10 " pdb=" O4' A z 11 " model vdw 2.373 3.040 ... (remaining 118044 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } 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: 1.240 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.620 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 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 : 0.005 0.061 16986 Z= 0.230 Angle : 1.144 11.948 23283 Z= 0.578 Chirality : 0.057 0.305 2766 Planarity : 0.007 0.075 2903 Dihedral : 17.137 178.149 6380 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.76 % Favored : 84.99 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.63 % 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: -2.88 (0.18), residues: 2005 helix: -0.18 (0.21), residues: 613 sheet: -1.50 (0.32), residues: 264 loop : -3.19 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP h 87 HIS 0.004 0.001 HIS f 249 PHE 0.007 0.001 PHE b 237 TYR 0.011 0.002 TYR g 47 ARG 0.020 0.001 ARG i 75 Details of bonding type rmsd hydrogen bonds : bond 0.13702 ( 548) hydrogen bonds : angle 6.84868 ( 1608) covalent geometry : bond 0.00485 (16986) covalent geometry : angle 1.14351 (23283) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 438 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 116 ASP cc_start: 0.6625 (m-30) cc_final: 0.6312 (m-30) REVERT: c 52 ILE cc_start: 0.8850 (pt) cc_final: 0.7990 (pt) REVERT: c 59 ILE cc_start: 0.8967 (mm) cc_final: 0.8747 (tt) REVERT: f 228 ASN cc_start: 0.8035 (m110) cc_final: 0.7720 (m110) REVERT: b 29 SER cc_start: 0.8255 (m) cc_final: 0.7814 (t) REVERT: b 118 GLU cc_start: 0.6012 (mm-30) cc_final: 0.5558 (mm-30) REVERT: b 276 ARG cc_start: 0.7554 (ptt90) cc_final: 0.7267 (ptt90) REVERT: a 19 ARG cc_start: 0.6931 (ptm-80) cc_final: 0.6226 (ptm-80) REVERT: a 223 TRP cc_start: 0.7773 (p-90) cc_final: 0.7523 (p-90) REVERT: h 8 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6455 (tp40) REVERT: h 136 ARG cc_start: 0.7476 (ttt-90) cc_final: 0.5898 (ttt-90) REVERT: g 104 ASP cc_start: 0.7238 (p0) cc_final: 0.6810 (p0) REVERT: g 106 ARG cc_start: 0.6864 (ttp-110) cc_final: 0.5791 (ttp80) REVERT: j 76 ARG cc_start: 0.8297 (tmm160) cc_final: 0.8091 (tpt170) REVERT: k 80 ARG cc_start: 0.7701 (mpt90) cc_final: 0.6685 (mpt-90) outliers start: 0 outliers final: 0 residues processed: 438 average time/residue: 0.3422 time to fit residues: 207.7125 Evaluate side-chains 356 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 173 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 159 HIS b 61 GLN b 159 HIS a 159 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 145 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.224356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.184053 restraints weight = 23065.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.187792 restraints weight = 14394.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.189952 restraints weight = 10538.004| |-----------------------------------------------------------------------------| r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16986 Z= 0.209 Angle : 0.853 12.032 23283 Z= 0.419 Chirality : 0.048 0.267 2766 Planarity : 0.007 0.095 2903 Dihedral : 15.857 176.017 2718 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 1.87 % Allowed : 15.16 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: -2.47 (0.19), residues: 2005 helix: 0.47 (0.22), residues: 619 sheet: -1.31 (0.33), residues: 264 loop : -3.14 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP c 281 HIS 0.007 0.001 HIS d 159 PHE 0.022 0.002 PHE d 70 TYR 0.016 0.002 TYR j 47 ARG 0.032 0.001 ARG h 103 Details of bonding type rmsd hydrogen bonds : bond 0.04493 ( 548) hydrogen bonds : angle 5.48293 ( 1608) covalent geometry : bond 0.00475 (16986) covalent geometry : angle 0.85257 (23283) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 384 time to evaluate : 1.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 141 MET cc_start: 0.7042 (mmp) cc_final: 0.6768 (mmp) REVERT: e 226 LEU cc_start: 0.8109 (mt) cc_final: 0.7884 (mt) REVERT: d 118 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: d 120 ARG cc_start: 0.5240 (mtm180) cc_final: 0.3833 (mtm180) REVERT: d 153 GLU cc_start: 0.6083 (tp30) cc_final: 0.5786 (tp30) REVERT: c 52 ILE cc_start: 0.8608 (pt) cc_final: 0.8329 (pt) REVERT: c 59 ILE cc_start: 0.9050 (mm) cc_final: 0.8784 (tt) REVERT: f 68 SER cc_start: 0.8224 (p) cc_final: 0.8023 (m) REVERT: b 29 SER cc_start: 0.8437 (m) cc_final: 0.7841 (t) REVERT: b 254 SER cc_start: 0.8841 (p) cc_final: 0.8124 (t) REVERT: a 19 ARG cc_start: 0.7083 (ptm-80) cc_final: 0.6270 (ptm-80) REVERT: a 223 TRP cc_start: 0.7826 (p-90) cc_final: 0.7522 (p-90) REVERT: h 8 GLN cc_start: 0.7284 (mm-40) cc_final: 0.6909 (tp40) REVERT: h 44 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7793 (tt) REVERT: h 107 LEU cc_start: 0.8907 (tp) cc_final: 0.8486 (mp) REVERT: h 122 THR cc_start: 0.7309 (p) cc_final: 0.7073 (t) REVERT: h 136 ARG cc_start: 0.7867 (ttt-90) cc_final: 0.6476 (ttt-90) REVERT: g 104 ASP cc_start: 0.7031 (p0) cc_final: 0.6686 (p0) REVERT: g 106 ARG cc_start: 0.6646 (ttp-110) cc_final: 0.5737 (ttp80) REVERT: j 47 TYR cc_start: 0.7071 (m-80) cc_final: 0.6725 (m-10) REVERT: j 76 ARG cc_start: 0.8280 (tmm160) cc_final: 0.7989 (tpt170) REVERT: j 109 LEU cc_start: 0.8780 (tp) cc_final: 0.8493 (tt) REVERT: k 47 TYR cc_start: 0.6466 (m-10) cc_final: 0.6022 (m-10) REVERT: k 103 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7320 (mtp180) outliers start: 31 outliers final: 23 residues processed: 393 average time/residue: 0.3257 time to fit residues: 181.2428 Evaluate side-chains 380 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 355 time to evaluate : 1.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 118 GLU Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 211 ILE Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 287 ASP Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 137 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 25 optimal weight: 0.7980 chunk 115 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 232 HIS f 159 HIS ** g 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.230783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.191170 restraints weight = 22867.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.194961 restraints weight = 14316.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.196688 restraints weight = 10692.231| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16986 Z= 0.166 Angle : 0.798 11.085 23283 Z= 0.388 Chirality : 0.046 0.267 2766 Planarity : 0.006 0.064 2903 Dihedral : 15.713 177.659 2718 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer: Outliers : 3.31 % Allowed : 19.13 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.31 (0.19), residues: 2005 helix: 0.76 (0.21), residues: 619 sheet: -1.25 (0.32), residues: 264 loop : -3.15 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 281 HIS 0.004 0.001 HIS d 159 PHE 0.017 0.001 PHE d 70 TYR 0.013 0.001 TYR j 47 ARG 0.008 0.001 ARG k 114 Details of bonding type rmsd hydrogen bonds : bond 0.04049 ( 548) hydrogen bonds : angle 5.19490 ( 1608) covalent geometry : bond 0.00370 (16986) covalent geometry : angle 0.79824 (23283) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 347 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 70 PHE cc_start: 0.9041 (t80) cc_final: 0.8823 (t80) REVERT: c 52 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8406 (pt) REVERT: c 59 ILE cc_start: 0.9083 (mm) cc_final: 0.8790 (tt) REVERT: f 236 PHE cc_start: 0.8460 (t80) cc_final: 0.8235 (t80) REVERT: b 29 SER cc_start: 0.8441 (m) cc_final: 0.7841 (t) REVERT: b 33 ARG cc_start: 0.7505 (tpp80) cc_final: 0.7224 (tpp80) REVERT: b 232 HIS cc_start: 0.7813 (m-70) cc_final: 0.6838 (m-70) REVERT: b 254 SER cc_start: 0.8857 (p) cc_final: 0.8210 (t) REVERT: a 141 MET cc_start: 0.7668 (mmm) cc_final: 0.7132 (mmm) REVERT: h 8 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6886 (tp40) REVERT: h 33 ARG cc_start: 0.7602 (mpt180) cc_final: 0.7294 (mpt180) REVERT: h 44 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7750 (tt) REVERT: h 107 LEU cc_start: 0.8742 (tp) cc_final: 0.8484 (mp) REVERT: h 113 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8057 (mt) REVERT: h 122 THR cc_start: 0.7532 (p) cc_final: 0.7246 (t) REVERT: h 136 ARG cc_start: 0.7854 (ttt-90) cc_final: 0.6082 (ttt-90) REVERT: g 104 ASP cc_start: 0.7076 (p0) cc_final: 0.6783 (p0) REVERT: g 106 ARG cc_start: 0.6642 (ttp-110) cc_final: 0.5708 (ttp80) REVERT: k 47 TYR cc_start: 0.6421 (m-10) cc_final: 0.5980 (m-10) outliers start: 55 outliers final: 38 residues processed: 369 average time/residue: 0.2984 time to fit residues: 159.1790 Evaluate side-chains 379 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 338 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 66 SER Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain b residue 266 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 113 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 126 optimal weight: 10.0000 chunk 148 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 37 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 115 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 284 GLN c 232 HIS b 32 HIS h 94 GLN g 94 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.222647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.182594 restraints weight = 23093.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.184910 restraints weight = 14920.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.187925 restraints weight = 11009.516| |-----------------------------------------------------------------------------| r_work (final): 0.3926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16986 Z= 0.166 Angle : 0.778 11.060 23283 Z= 0.381 Chirality : 0.046 0.288 2766 Planarity : 0.006 0.091 2903 Dihedral : 15.628 179.642 2718 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.81 % Favored : 84.19 % Rotamer: Outliers : 4.81 % Allowed : 19.92 % Favored : 75.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -2.21 (0.19), residues: 2005 helix: 0.97 (0.21), residues: 619 sheet: -1.17 (0.32), residues: 264 loop : -3.18 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP c 281 HIS 0.006 0.001 HIS f 159 PHE 0.012 0.001 PHE d 70 TYR 0.009 0.001 TYR i 47 ARG 0.006 0.000 ARG b 48 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 548) hydrogen bonds : angle 5.03279 ( 1608) covalent geometry : bond 0.00373 (16986) covalent geometry : angle 0.77771 (23283) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 354 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 33 ARG cc_start: 0.7620 (tpp80) cc_final: 0.7404 (ttm170) REVERT: e 127 PRO cc_start: 0.8480 (Cg_endo) cc_final: 0.8190 (Cg_exo) REVERT: d 70 PHE cc_start: 0.9021 (t80) cc_final: 0.8792 (t80) REVERT: d 141 MET cc_start: 0.7763 (mmm) cc_final: 0.7310 (mmm) REVERT: c 52 ILE cc_start: 0.8581 (OUTLIER) cc_final: 0.8322 (pt) REVERT: c 59 ILE cc_start: 0.9109 (mm) cc_final: 0.8791 (tt) REVERT: f 33 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7816 (mtm-85) REVERT: b 29 SER cc_start: 0.8475 (m) cc_final: 0.7917 (t) REVERT: b 231 GLU cc_start: 0.5800 (tm-30) cc_final: 0.5280 (tm-30) REVERT: b 232 HIS cc_start: 0.7694 (m-70) cc_final: 0.6874 (m-70) REVERT: b 254 SER cc_start: 0.8925 (p) cc_final: 0.8294 (t) REVERT: a 141 MET cc_start: 0.7891 (mmm) cc_final: 0.7342 (mmm) REVERT: h 8 GLN cc_start: 0.7337 (mm-40) cc_final: 0.6895 (mm-40) REVERT: h 33 ARG cc_start: 0.7645 (mpt180) cc_final: 0.7197 (mpt90) REVERT: h 44 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7872 (tt) REVERT: h 107 LEU cc_start: 0.8797 (tp) cc_final: 0.8514 (mp) REVERT: h 122 THR cc_start: 0.7550 (p) cc_final: 0.7258 (t) REVERT: g 104 ASP cc_start: 0.7086 (p0) cc_final: 0.6817 (p0) REVERT: g 106 ARG cc_start: 0.6865 (ttp-110) cc_final: 0.5919 (ttt90) outliers start: 80 outliers final: 55 residues processed: 390 average time/residue: 0.3018 time to fit residues: 168.2009 Evaluate side-chains 388 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 330 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 221 GLN Chi-restraints excluded: chain d residue 266 THR Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 35 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 131 optimal weight: 9.9990 chunk 135 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 137 optimal weight: 20.0000 chunk 167 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 61 GLN c 232 HIS f 228 ASN g 94 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.217276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.177147 restraints weight = 23194.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.178810 restraints weight = 14764.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.181481 restraints weight = 12138.462| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16986 Z= 0.219 Angle : 0.837 11.898 23283 Z= 0.414 Chirality : 0.048 0.302 2766 Planarity : 0.007 0.145 2903 Dihedral : 15.635 177.385 2718 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.96 % Favored : 84.04 % Rotamer: Outliers : 6.20 % Allowed : 21.42 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.31 (0.19), residues: 2005 helix: 0.87 (0.21), residues: 619 sheet: -1.12 (0.32), residues: 264 loop : -3.26 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP f 281 HIS 0.008 0.002 HIS f 159 PHE 0.012 0.002 PHE c 70 TYR 0.010 0.002 TYR j 47 ARG 0.007 0.001 ARG i 75 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 548) hydrogen bonds : angle 5.19323 ( 1608) covalent geometry : bond 0.00491 (16986) covalent geometry : angle 0.83719 (23283) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 324 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 19 ARG cc_start: 0.8546 (ttp80) cc_final: 0.8069 (ttp80) REVERT: e 127 PRO cc_start: 0.8593 (Cg_endo) cc_final: 0.8310 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7285 (m-10) cc_final: 0.6954 (m-10) REVERT: e 285 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6236 (tp) REVERT: d 76 ARG cc_start: 0.8128 (mmt90) cc_final: 0.7926 (mmt180) REVERT: d 141 MET cc_start: 0.7867 (mmm) cc_final: 0.7473 (mmm) REVERT: c 52 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8287 (pt) REVERT: f 33 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7885 (mtm-85) REVERT: b 29 SER cc_start: 0.8547 (m) cc_final: 0.7970 (t) REVERT: a 48 ARG cc_start: 0.6760 (tpt-90) cc_final: 0.6039 (tpt-90) REVERT: a 141 MET cc_start: 0.8008 (mmm) cc_final: 0.7434 (mmm) REVERT: h 33 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7195 (mpt90) REVERT: h 44 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8077 (tt) REVERT: h 122 THR cc_start: 0.7693 (p) cc_final: 0.7415 (t) REVERT: g 40 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7955 (mtp180) REVERT: g 73 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8094 (mmm-85) REVERT: g 94 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8173 (tm-30) REVERT: g 106 ARG cc_start: 0.6715 (ttp-110) cc_final: 0.5835 (ttt180) REVERT: g 108 GLU cc_start: 0.6678 (tp30) cc_final: 0.6393 (tp30) REVERT: g 118 LEU cc_start: 0.8418 (tp) cc_final: 0.8116 (tp) REVERT: i 16 GLU cc_start: 0.8375 (mp0) cc_final: 0.8157 (mp0) REVERT: i 80 ARG cc_start: 0.8452 (mpt180) cc_final: 0.8183 (mpt180) outliers start: 103 outliers final: 78 residues processed: 379 average time/residue: 0.3072 time to fit residues: 167.6618 Evaluate side-chains 401 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 319 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 28 SER Chi-restraints excluded: chain e residue 73 VAL Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain e residue 285 LEU Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 139 ARG Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 211 ILE Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 254 SER Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 33 ARG Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 64 LEU Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 9 VAL Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain h residue 70 LEU Chi-restraints excluded: chain h residue 123 VAL Chi-restraints excluded: chain h residue 133 LEU Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain j residue 13 THR Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain i residue 37 THR Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain i residue 133 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 205 random chunks: chunk 184 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 154 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.221298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.181494 restraints weight = 23012.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.182996 restraints weight = 15892.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.185809 restraints weight = 11887.976| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16986 Z= 0.228 Angle : 0.851 17.365 23283 Z= 0.419 Chirality : 0.048 0.199 2766 Planarity : 0.007 0.117 2903 Dihedral : 15.609 177.789 2718 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.16 % Favored : 83.84 % Rotamer: Outliers : 6.80 % Allowed : 22.32 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.26 % 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: -2.43 (0.18), residues: 2005 helix: 0.78 (0.21), residues: 620 sheet: -1.05 (0.33), residues: 264 loop : -3.39 (0.17), residues: 1121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP f 281 HIS 0.008 0.002 HIS f 159 PHE 0.013 0.002 PHE d 237 TYR 0.013 0.002 TYR j 47 ARG 0.010 0.001 ARG i 75 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 548) hydrogen bonds : angle 5.23171 ( 1608) covalent geometry : bond 0.00515 (16986) covalent geometry : angle 0.85097 (23283) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4010 Ramachandran restraints generated. 2005 Oldfield, 0 Emsley, 2005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 339 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: e 19 ARG cc_start: 0.8557 (ttp80) cc_final: 0.8121 (ttp80) REVERT: e 33 ARG cc_start: 0.7919 (ttm110) cc_final: 0.7659 (ttt180) REVERT: e 127 PRO cc_start: 0.8679 (Cg_endo) cc_final: 0.8387 (Cg_exo) REVERT: e 209 PHE cc_start: 0.7295 (m-10) cc_final: 0.6936 (m-10) REVERT: d 139 ARG cc_start: 0.7408 (OUTLIER) cc_final: 0.6496 (ptp90) REVERT: d 141 MET cc_start: 0.7910 (mmm) cc_final: 0.7480 (mmm) REVERT: d 281 TRP cc_start: 0.5422 (OUTLIER) cc_final: 0.4337 (p90) REVERT: d 285 LEU cc_start: 0.6328 (OUTLIER) cc_final: 0.5854 (tt) REVERT: c 52 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8360 (pt) REVERT: f 33 ARG cc_start: 0.8198 (OUTLIER) cc_final: 0.7665 (mtm180) REVERT: f 232 HIS cc_start: 0.6937 (m-70) cc_final: 0.6352 (m-70) REVERT: f 266 THR cc_start: 0.7199 (OUTLIER) cc_final: 0.6927 (p) REVERT: b 29 SER cc_start: 0.8565 (m) cc_final: 0.7968 (t) REVERT: b 91 VAL cc_start: 0.7925 (p) cc_final: 0.7691 (m) REVERT: b 232 HIS cc_start: 0.7705 (m-70) cc_final: 0.7478 (m90) REVERT: a 48 ARG cc_start: 0.6838 (tpt-90) cc_final: 0.6133 (tpt-90) REVERT: a 126 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6946 (tt) REVERT: a 141 MET cc_start: 0.7983 (mmm) cc_final: 0.7444 (mmm) REVERT: h 33 ARG cc_start: 0.7676 (mpt180) cc_final: 0.7116 (mpt180) REVERT: h 44 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8042 (tt) REVERT: h 122 THR cc_start: 0.7764 (p) cc_final: 0.7453 (t) REVERT: g 40 ARG cc_start: 0.8132 (mtp180) cc_final: 0.7919 (mtp180) REVERT: g 42 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6894 (tt) REVERT: g 87 TRP cc_start: 0.8105 (t-100) cc_final: 0.7893 (t60) REVERT: g 106 ARG cc_start: 0.6519 (ttp-110) cc_final: 0.5889 (tpt-90) REVERT: g 108 GLU cc_start: 0.6619 (tp30) cc_final: 0.6286 (tp30) REVERT: g 118 LEU cc_start: 0.8462 (tp) cc_final: 0.8174 (tp) REVERT: k 40 ARG cc_start: 0.7516 (ttm170) cc_final: 0.7193 (ttt180) REVERT: i 16 GLU cc_start: 0.8484 (mp0) cc_final: 0.8244 (mp0) REVERT: i 20 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8213 (mt) REVERT: i 80 ARG cc_start: 0.8468 (mpt180) cc_final: 0.8162 (mpt180) outliers start: 113 outliers final: 82 residues processed: 399 average time/residue: 0.2903 time to fit residues: 169.4817 Evaluate side-chains 425 residues out of total 1678 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 333 time to evaluate : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 18 ILE Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 28 SER Chi-restraints excluded: chain e residue 52 ILE Chi-restraints excluded: chain e residue 140 VAL Chi-restraints excluded: chain e residue 166 HIS Chi-restraints excluded: chain e residue 168 THR Chi-restraints excluded: chain e residue 177 VAL Chi-restraints excluded: chain e residue 226 LEU Chi-restraints excluded: chain e residue 247 HIS Chi-restraints excluded: chain e residue 264 THR Chi-restraints excluded: chain d residue 22 VAL Chi-restraints excluded: chain d residue 25 ILE Chi-restraints excluded: chain d residue 77 VAL Chi-restraints excluded: chain d residue 139 ARG Chi-restraints excluded: chain d residue 148 SER Chi-restraints excluded: chain d residue 160 LEU Chi-restraints excluded: chain d residue 168 THR Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 211 ILE Chi-restraints excluded: chain d residue 242 SER Chi-restraints excluded: chain d residue 281 TRP Chi-restraints excluded: chain d residue 285 LEU Chi-restraints excluded: chain c residue 22 VAL Chi-restraints excluded: chain c residue 25 ILE Chi-restraints excluded: chain c residue 46 LEU Chi-restraints excluded: chain c residue 52 ILE Chi-restraints excluded: chain c residue 58 GLN Chi-restraints excluded: chain c residue 75 ARG Chi-restraints excluded: chain c residue 85 VAL Chi-restraints excluded: chain c residue 129 ILE Chi-restraints excluded: chain c residue 145 LEU Chi-restraints excluded: chain c residue 148 SER Chi-restraints excluded: chain c residue 167 SER Chi-restraints excluded: chain c residue 168 THR Chi-restraints excluded: chain c residue 177 VAL Chi-restraints excluded: chain c residue 211 ILE Chi-restraints excluded: chain c residue 241 LEU Chi-restraints excluded: chain c residue 242 SER Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain f residue 25 ILE Chi-restraints excluded: chain f residue 29 SER Chi-restraints excluded: chain f residue 33 ARG Chi-restraints excluded: chain f residue 66 SER Chi-restraints excluded: chain f residue 149 LYS Chi-restraints excluded: chain f residue 166 HIS Chi-restraints excluded: chain f residue 167 SER Chi-restraints excluded: chain f residue 168 THR Chi-restraints excluded: chain f residue 264 THR Chi-restraints excluded: chain f residue 265 VAL Chi-restraints excluded: chain f residue 266 THR Chi-restraints excluded: chain b residue 23 ASP Chi-restraints excluded: chain b residue 24 ILE Chi-restraints excluded: chain b residue 31 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 247 HIS Chi-restraints excluded: chain b residue 264 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 126 LEU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 168 THR Chi-restraints excluded: chain h residue 5 THR Chi-restraints excluded: chain h residue 42 LEU Chi-restraints excluded: chain h residue 44 LEU Chi-restraints excluded: chain g residue 10 TRP Chi-restraints excluded: chain g residue 29 SER Chi-restraints excluded: chain g residue 31 THR Chi-restraints excluded: chain g residue 42 LEU Chi-restraints excluded: chain g residue 112 LEU Chi-restraints excluded: chain g residue 137 ILE Chi-restraints excluded: chain g residue 146 ARG Chi-restraints excluded: chain j residue 31 THR Chi-restraints excluded: chain j residue 66 TRP Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain j residue 113 LEU Chi-restraints excluded: chain j residue 124 LEU Chi-restraints excluded: chain j residue 128 LEU Chi-restraints excluded: chain j residue 142 VAL Chi-restraints excluded: chain k residue 29 SER Chi-restraints excluded: chain k residue 74 VAL Chi-restraints excluded: chain k residue 87 TRP Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain k residue 113 LEU Chi-restraints excluded: chain k residue 124 LEU Chi-restraints excluded: chain k residue 132 LEU Chi-restraints excluded: chain k residue 133 LEU Chi-restraints excluded: chain i residue 20 LEU Chi-restraints excluded: chain i residue 58 ASP Chi-restraints excluded: chain i residue 69 LEU Chi-restraints excluded: chain i residue 83 THR Chi-restraints excluded: chain i residue 133 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.1068 > 50: distance: 44 - 63: 21.743 distance: 61 - 63: 21.784 distance: 63 - 64: 8.736 distance: 64 - 65: 17.605 distance: 64 - 67: 12.102 distance: 65 - 66: 26.099 distance: 65 - 72: 15.532 distance: 68 - 69: 33.283 distance: 69 - 70: 3.714 distance: 69 - 71: 16.348 distance: 72 - 73: 17.728 distance: 73 - 74: 28.572 distance: 73 - 76: 28.601 distance: 74 - 75: 13.252 distance: 74 - 80: 45.690 distance: 76 - 77: 36.244 distance: 77 - 78: 22.783 distance: 77 - 79: 17.522 distance: 80 - 81: 50.220 distance: 81 - 82: 36.624 distance: 82 - 83: 27.662 distance: 82 - 84: 27.324 distance: 84 - 85: 41.327 distance: 85 - 86: 38.015 distance: 85 - 88: 46.296 distance: 86 - 89: 32.459 distance: 89 - 90: 7.198 distance: 89 - 95: 49.709 distance: 90 - 91: 22.013 distance: 90 - 93: 6.138 distance: 91 - 92: 45.836 distance: 91 - 96: 42.714 distance: 93 - 94: 5.104 distance: 94 - 95: 54.523 distance: 96 - 97: 15.503 distance: 97 - 98: 14.556 distance: 97 - 100: 15.804 distance: 98 - 99: 17.414 distance: 98 - 101: 8.436 distance: 101 - 102: 31.135 distance: 101 - 107: 11.719 distance: 102 - 103: 20.236 distance: 102 - 105: 47.605 distance: 103 - 104: 26.251 distance: 103 - 108: 29.123 distance: 105 - 106: 6.121 distance: 106 - 107: 63.563 distance: 109 - 110: 17.299 distance: 110 - 111: 23.290 distance: 110 - 119: 15.295 distance: 112 - 113: 51.120 distance: 113 - 114: 24.449 distance: 114 - 115: 19.620 distance: 115 - 116: 18.902 distance: 116 - 117: 7.363 distance: 116 - 118: 9.839 distance: 119 - 120: 24.208 distance: 120 - 121: 24.918 distance: 120 - 123: 20.552 distance: 121 - 122: 13.353 distance: 121 - 129: 31.486 distance: 122 - 157: 26.691 distance: 123 - 124: 11.843 distance: 124 - 125: 12.494 distance: 124 - 126: 27.202 distance: 125 - 127: 45.078 distance: 126 - 128: 41.638 distance: 127 - 128: 25.019 distance: 129 - 130: 32.138 distance: 130 - 131: 15.958 distance: 130 - 133: 24.160 distance: 131 - 132: 19.184 distance: 131 - 140: 22.655 distance: 132 - 168: 21.932 distance: 133 - 134: 50.030 distance: 135 - 136: 16.722 distance: 136 - 137: 26.312 distance: 137 - 138: 19.876 distance: 137 - 139: 34.145