Starting phenix.real_space_refine on Sat Oct 24 02:30:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.cif Found real_map, /net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.map" model { file = "/net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9svk_55261/10_2026/9svk_55261.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.000 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 47 5.49 5 S 36 5.16 5 C 7602 2.51 5 N 1947 2.21 5 O 2354 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11986 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "C" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1111 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "D" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "E" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "G" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "H" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "J" Number of atoms: 1118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1118 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 5, 'TRANS': 132} Chain: "K" Number of atoms: 1114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1114 Classifications: {'peptide': 138} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 132} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 3, 'TRANS': 59} Chain: "M" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 754 Classifications: {'RNA': 35} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p_pur': 18, 'rna3p_pyr': 8} Link IDs: {'rna2p': 9, 'rna3p': 25} Chain: "N" Number of atoms: 275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 275 Classifications: {'RNA': 13} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 6} Link IDs: {'rna2p': 2, 'rna3p': 10} Chain breaks: 1 Time building chain proxies: 2.74, per 1000 atoms: 0.23 Number of scatterers: 11986 At special positions: 0 Unit cell: (98.49, 104.52, 140.7, 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 36 16.00 P 47 15.00 O 2354 8.00 N 1947 7.00 C 7602 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: 0.77 Conformation dependent library (CDL) restraints added in 511.8 milliseconds 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2560 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 14 sheets defined 41.2% alpha, 19.8% beta 8 base pairs and 22 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'B' and resid 40 through 61 removed outlier: 3.655A pdb=" N GLY B 53 " --> pdb=" O ARG B 49 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LEU B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE B 59 " --> pdb=" O HIS B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 97 removed outlier: 3.538A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 119 Processing helix chain 'B' and resid 122 through 136 Processing helix chain 'C' and resid 40 through 63 Processing helix chain 'C' and resid 89 through 99 Processing helix chain 'C' and resid 110 through 120 removed outlier: 3.893A pdb=" N LEU C 115 " --> pdb=" O TRP C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 135 removed outlier: 3.561A pdb=" N ILE C 126 " --> pdb=" O ASN C 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.605A pdb=" N LEU A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 61 removed outlier: 3.537A pdb=" N GLY D 53 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N PHE D 59 " --> pdb=" O HIS D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 96 Processing helix chain 'D' and resid 110 through 120 Processing helix chain 'D' and resid 122 through 136 removed outlier: 3.534A pdb=" N ILE D 126 " --> pdb=" O ASN D 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 47 removed outlier: 4.332A pdb=" N ASN E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 63 removed outlier: 3.876A pdb=" N VAL E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 99 Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.759A pdb=" N LEU E 115 " --> pdb=" O TRP E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 135 removed outlier: 3.525A pdb=" N ILE E 126 " --> pdb=" O ASN E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.605A pdb=" N ARG F 12 " --> pdb=" O LYS F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 60 Processing helix chain 'G' and resid 40 through 61 removed outlier: 3.775A pdb=" N GLY G 53 " --> pdb=" O ARG G 49 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU G 54 " --> pdb=" O GLU G 50 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE G 59 " --> pdb=" O HIS G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 110 through 120 Processing helix chain 'G' and resid 122 through 135 Processing helix chain 'H' and resid 40 through 63 Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'H' and resid 122 through 135 Processing helix chain 'I' and resid 5 through 16 removed outlier: 3.521A pdb=" N ILE I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU I 16 " --> pdb=" O ARG I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 60 removed outlier: 3.642A pdb=" N LEU I 52 " --> pdb=" O PRO I 48 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG I 53 " --> pdb=" O VAL I 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 61 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 110 through 120 Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.972A pdb=" N ILE J 126 " --> pdb=" O ASN J 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 60 removed outlier: 4.075A pdb=" N ASN K 47 " --> pdb=" O GLU K 43 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG K 49 " --> pdb=" O VAL K 45 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU K 50 " --> pdb=" O SER K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 99 removed outlier: 3.506A pdb=" N VAL K 97 " --> pdb=" O GLU K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 110 through 120 Processing helix chain 'K' and resid 122 through 135 removed outlier: 3.569A pdb=" N ILE K 126 " --> pdb=" O ASN K 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.530A pdb=" N ILE L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU L 16 " --> pdb=" O ARG L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 60 removed outlier: 3.553A pdb=" N ARG L 53 " --> pdb=" O VAL L 49 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 99 removed outlier: 3.591A pdb=" N THR B 98 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 23 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N VAL A 20 " --> pdb=" O MET A 31 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N MET A 31 " --> pdb=" O VAL A 20 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 103 through 109 Processing sheet with id=AA4, first strand: chain 'C' and resid 3 through 4 Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 20 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 109 Processing sheet with id=AA7, first strand: chain 'D' and resid 36 through 38 removed outlier: 14.476A pdb=" N GLN D 81 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 11.517A pdb=" N LEU E 83 " --> pdb=" O GLN D 81 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU D 83 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE E 85 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE D 85 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N SER E 87 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N SER D 87 " --> pdb=" O SER E 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR E 36 " --> pdb=" O GLY E 18 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 98 through 99 removed outlier: 3.522A pdb=" N THR D 98 " --> pdb=" O ILE F 23 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL F 20 " --> pdb=" O MET F 31 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N MET F 31 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 36 through 38 removed outlier: 14.724A pdb=" N GLN G 81 " --> pdb=" O GLN H 81 " (cutoff:3.500A) removed outlier: 11.853A pdb=" N LEU H 83 " --> pdb=" O GLN G 81 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N LEU G 83 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N ILE H 85 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE G 85 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER H 87 " --> pdb=" O ILE G 85 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N SER G 87 " --> pdb=" O SER H 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 86 " --> pdb=" O TYR H 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL H 8 " --> pdb=" O CYS H 19 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 98 through 99 removed outlier: 3.563A pdb=" N THR G 98 " --> pdb=" O ILE I 23 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N VAL I 20 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N MET I 31 " --> pdb=" O VAL I 20 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 101 through 109 Processing sheet with id=AB3, first strand: chain 'H' and resid 101 through 109 Processing sheet with id=AB4, first strand: chain 'J' and resid 36 through 38 removed outlier: 14.439A pdb=" N GLN J 81 " --> pdb=" O GLN K 81 " (cutoff:3.500A) removed outlier: 11.787A pdb=" N LEU K 83 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N LEU J 83 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ILE K 85 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ILE J 85 " --> pdb=" O ILE K 85 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N SER K 87 " --> pdb=" O ILE J 85 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER J 87 " --> pdb=" O SER K 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 98 through 99 removed outlier: 6.065A pdb=" N VAL L 20 " --> pdb=" O MET L 31 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET L 31 " --> pdb=" O VAL L 20 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA L 22 " --> pdb=" O GLN L 29 " (cutoff:3.500A) 544 hydrogen bonds defined for protein. 1539 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 8 basepair parallelities 22 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3473 1.34 - 1.45: 2140 1.45 - 1.57: 6561 1.57 - 1.69: 92 1.69 - 1.81: 64 Bond restraints: 12330 Sorted by residual: bond pdb=" N VAL C 62 " pdb=" CA VAL C 62 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.49e+00 bond pdb=" N ASP C 61 " pdb=" CA ASP C 61 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.35e-02 5.49e+03 6.02e+00 bond pdb=" N9 A M 13 " pdb=" C4 A M 13 " ideal model delta sigma weight residual 1.374 1.389 -0.015 6.00e-03 2.78e+04 5.94e+00 bond pdb=" N LEU C 60 " pdb=" CA LEU C 60 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.28e-02 6.10e+03 4.26e+00 bond pdb=" N7 A M 26 " pdb=" C5 A M 26 " ideal model delta sigma weight residual 1.388 1.378 0.010 6.00e-03 2.78e+04 2.74e+00 ... (remaining 12325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.94: 16758 2.94 - 5.88: 108 5.88 - 8.82: 11 8.82 - 11.76: 1 11.76 - 14.70: 1 Bond angle restraints: 16879 Sorted by residual: angle pdb=" C3' A M 13 " pdb=" O3' A M 13 " pdb=" P A M 14 " ideal model delta sigma weight residual 119.70 125.11 -5.41 1.20e+00 6.94e-01 2.03e+01 angle pdb=" O5' A M 28 " pdb=" C5' A M 28 " pdb=" C4' A M 28 " ideal model delta sigma weight residual 109.40 112.94 -3.54 8.00e-01 1.56e+00 1.96e+01 angle pdb=" CA LEU K 60 " pdb=" CB LEU K 60 " pdb=" CG LEU K 60 " ideal model delta sigma weight residual 116.30 131.00 -14.70 3.50e+00 8.16e-02 1.76e+01 angle pdb=" O5' C M 7 " pdb=" C5' C M 7 " pdb=" C4' C M 7 " ideal model delta sigma weight residual 109.40 112.52 -3.12 8.00e-01 1.56e+00 1.52e+01 angle pdb=" O5' A M 29 " pdb=" C5' A M 29 " pdb=" C4' A M 29 " ideal model delta sigma weight residual 109.40 112.30 -2.90 8.00e-01 1.56e+00 1.32e+01 ... (remaining 16874 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 7131 35.76 - 71.52: 288 71.52 - 107.28: 34 107.28 - 143.04: 2 143.04 - 178.80: 3 Dihedral angle restraints: 7458 sinusoidal: 3478 harmonic: 3980 Sorted by residual: dihedral pdb=" O4' C N 4 " pdb=" C1' C N 4 " pdb=" N1 C N 4 " pdb=" C2 C N 4 " ideal model delta sinusoidal sigma weight residual 232.00 53.20 178.80 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C M 4 " pdb=" C1' C M 4 " pdb=" N1 C M 4 " pdb=" C2 C M 4 " ideal model delta sinusoidal sigma weight residual -128.00 35.46 -163.46 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" CA MET L 1 " pdb=" C MET L 1 " pdb=" N ILE L 2 " pdb=" CA ILE L 2 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1428 0.043 - 0.086: 350 0.086 - 0.129: 119 0.129 - 0.172: 38 0.172 - 0.215: 4 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CB THR H 15 " pdb=" CA THR H 15 " pdb=" OG1 THR H 15 " pdb=" CG2 THR H 15 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA PRO L 48 " pdb=" N PRO L 48 " pdb=" C PRO L 48 " pdb=" CB PRO L 48 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C3' A M 13 " pdb=" C4' A M 13 " pdb=" O3' A M 13 " pdb=" C2' A M 13 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.67e-01 ... (remaining 1936 not shown) Planarity restraints: 1939 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO L 48 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.30e+00 pdb=" C PRO L 48 " 0.031 2.00e-02 2.50e+03 pdb=" O PRO L 48 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL L 49 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU K 60 " -0.008 2.00e-02 2.50e+03 1.58e-02 2.51e+00 pdb=" C LEU K 60 " 0.027 2.00e-02 2.50e+03 pdb=" O LEU K 60 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP K 61 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 108 " 0.023 5.00e-02 4.00e+02 3.47e-02 1.92e+00 pdb=" N PRO H 109 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " 0.019 5.00e-02 4.00e+02 ... (remaining 1936 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 83 2.65 - 3.21: 10676 3.21 - 3.78: 17337 3.78 - 4.34: 22464 4.34 - 4.90: 37994 Nonbonded interactions: 88554 Sorted by model distance: nonbonded pdb=" O ASN C 39 " pdb=" OD1 ASN C 39 " model vdw 2.089 3.040 nonbonded pdb=" O GLU C 43 " pdb=" OD1 ASN C 47 " model vdw 2.394 3.040 nonbonded pdb=" CE2 TYR C 16 " pdb=" OD1 ASN C 39 " model vdw 2.399 3.340 nonbonded pdb=" O ILE L 47 " pdb=" O PRO L 48 " model vdw 2.428 3.040 nonbonded pdb=" N GLU A 36 " pdb=" OE1 GLU A 36 " model vdw 2.454 3.120 ... (remaining 88549 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 'F' selection = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'B' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 138)) selection = chain 'C' selection = (chain 'D' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 138)) selection = (chain 'E' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 138)) selection = (chain 'G' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 138)) selection = (chain 'H' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 138)) selection = (chain 'J' and (resid 1 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 60 or (resid 61 and (name N or name \ CA or name C or name O or name CB )) or resid 62 through 138)) selection = (chain 'K' and (resid 1 through 60 or (resid 61 and (name N or name CA or name C \ or name O or name CB )) or resid 62 through 138)) } 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: 2.330 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.100 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 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 0.040 12330 Z= 0.218 Angle : 0.687 14.696 16879 Z= 0.427 Chirality : 0.046 0.215 1939 Planarity : 0.004 0.037 1939 Dihedral : 18.948 178.803 4898 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.98 % Favored : 95.95 % Rotamer: Outliers : 2.73 % Allowed : 21.13 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.23), residues: 1332 helix: 1.44 (0.23), residues: 544 sheet: 0.29 (0.32), residues: 252 loop : -1.70 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 53 TYR 0.015 0.001 TYR F 43 PHE 0.014 0.001 PHE G 26 TRP 0.010 0.001 TRP I 30 HIS 0.002 0.001 HIS H 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (12330) covalent geometry : angle 0.68689 / 0.43 (16879) hydrogen bonds : bond 0.12809 / 8.39 ( 568) hydrogen bonds : angle 5.75824 / 3.91 ( 1587) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9220 (m-30) cc_final: 0.8847 (p0) REVERT: B 49 ARG cc_start: 0.8666 (tmm-80) cc_final: 0.8421 (tmm-80) REVERT: C 1 MET cc_start: 0.7859 (ppp) cc_final: 0.7652 (ppp) REVERT: C 32 ASN cc_start: 0.8490 (t0) cc_final: 0.8187 (t0) REVERT: C 80 ASN cc_start: 0.7061 (t0) cc_final: 0.6833 (t0) REVERT: C 81 GLN cc_start: 0.7566 (mp10) cc_final: 0.7216 (mp10) REVERT: C 120 ASN cc_start: 0.8341 (m-40) cc_final: 0.8024 (m-40) REVERT: A 7 ARG cc_start: 0.7467 (mmm-85) cc_final: 0.7244 (mmm-85) REVERT: D 2 ASP cc_start: 0.9156 (p0) cc_final: 0.8874 (p0) REVERT: D 30 GLU cc_start: 0.8386 (mp0) cc_final: 0.7576 (mp0) REVERT: E 59 PHE cc_start: 0.7361 (OUTLIER) cc_final: 0.6822 (t80) REVERT: E 80 ASN cc_start: 0.8774 (t0) cc_final: 0.8480 (t0) REVERT: E 134 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8148 (tm-30) REVERT: F 62 LYS cc_start: 0.9031 (tppt) cc_final: 0.8719 (tptp) REVERT: H 17 TYR cc_start: 0.8594 (m-80) cc_final: 0.8239 (m-10) REVERT: H 81 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8588 (mt0) REVERT: I 1 MET cc_start: 0.7444 (tmm) cc_final: 0.7169 (ppp) REVERT: J 117 GLN cc_start: 0.9054 (mt0) cc_final: 0.8651 (mt0) REVERT: K 3 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9023 (m) REVERT: K 24 ASP cc_start: 0.8327 (m-30) cc_final: 0.7813 (t0) REVERT: K 41 MET cc_start: 0.7005 (mtp) cc_final: 0.6641 (ttm) REVERT: L 4 MET cc_start: 0.7957 (tpt) cc_final: 0.7245 (mpp) REVERT: L 11 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8725 (mmtm) REVERT: L 53 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7521 (mtm-85) outliers start: 33 outliers final: 26 residues processed: 224 average time/residue: 0.1113 time to fit residues: 35.1460 Evaluate side-chains 222 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 193 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 44 SER Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 5 SER Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 8 LYS Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 117 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 7.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN G 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.115148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076752 restraints weight = 20601.059| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.00 r_work: 0.2851 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12330 Z= 0.120 Angle : 0.524 10.792 16879 Z= 0.283 Chirality : 0.041 0.352 1939 Planarity : 0.004 0.046 1939 Dihedral : 16.539 179.185 2204 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 2.73 % Allowed : 20.46 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.24), residues: 1332 helix: 1.56 (0.23), residues: 564 sheet: 0.58 (0.33), residues: 252 loop : -1.70 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 53 TYR 0.015 0.001 TYR K 16 PHE 0.008 0.001 PHE J 26 TRP 0.014 0.001 TRP I 30 HIS 0.001 0.000 HIS L 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (12330) covalent geometry : angle 0.52406 / 0.28 (16879) hydrogen bonds : bond 0.04442 / 2.92 ( 568) hydrogen bonds : angle 4.67458 / 3.16 ( 1587) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 196 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9216 (m-30) cc_final: 0.8852 (p0) REVERT: B 49 ARG cc_start: 0.8677 (tmm-80) cc_final: 0.7973 (ttt-90) REVERT: B 112 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8472 (mt) REVERT: C 1 MET cc_start: 0.7879 (ppp) cc_final: 0.7643 (ppp) REVERT: C 32 ASN cc_start: 0.8524 (t0) cc_final: 0.8232 (t0) REVERT: C 80 ASN cc_start: 0.7073 (t0) cc_final: 0.6746 (t0) REVERT: C 81 GLN cc_start: 0.7639 (mp10) cc_final: 0.7221 (mp10) REVERT: C 120 ASN cc_start: 0.8192 (m-40) cc_final: 0.7930 (m-40) REVERT: A 1 MET cc_start: 0.5966 (tpt) cc_final: 0.3366 (ppp) REVERT: A 15 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8260 (mmtt) REVERT: D 2 ASP cc_start: 0.9165 (p0) cc_final: 0.8867 (p0) REVERT: D 28 ASP cc_start: 0.8115 (t0) cc_final: 0.7785 (t0) REVERT: D 30 GLU cc_start: 0.8031 (mp0) cc_final: 0.7813 (mp0) REVERT: E 59 PHE cc_start: 0.7153 (OUTLIER) cc_final: 0.6603 (t80) REVERT: E 80 ASN cc_start: 0.8772 (t0) cc_final: 0.8477 (t0) REVERT: F 1 MET cc_start: 0.5413 (ptt) cc_final: 0.4862 (mtm) REVERT: F 62 LYS cc_start: 0.9000 (tppt) cc_final: 0.8744 (tptp) REVERT: H 17 TYR cc_start: 0.8546 (m-80) cc_final: 0.8273 (m-10) REVERT: H 24 ASP cc_start: 0.8274 (t70) cc_final: 0.7758 (t0) REVERT: I 1 MET cc_start: 0.7328 (tmm) cc_final: 0.7053 (ppp) REVERT: J 117 GLN cc_start: 0.9024 (mt0) cc_final: 0.8618 (mt0) REVERT: K 3 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.9030 (m) REVERT: K 24 ASP cc_start: 0.8339 (m-30) cc_final: 0.7810 (t0) REVERT: K 41 MET cc_start: 0.6775 (mtp) cc_final: 0.6445 (mtp) REVERT: L 4 MET cc_start: 0.7935 (tpt) cc_final: 0.7298 (mpp) REVERT: L 11 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8688 (mmtm) REVERT: L 53 ARG cc_start: 0.7735 (mtm-85) cc_final: 0.7512 (mtm-85) outliers start: 33 outliers final: 18 residues processed: 221 average time/residue: 0.1183 time to fit residues: 36.3720 Evaluate side-chains 212 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 19 CYS Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [115, 41, 70, 21, 82, 14, 42, 45, 109, 87, 85] chunk 115 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 87 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN G 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.113208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.074552 restraints weight = 20686.073| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.99 r_work: 0.2806 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 12330 Z= 0.194 Angle : 0.550 9.765 16879 Z= 0.293 Chirality : 0.043 0.349 1939 Planarity : 0.004 0.043 1939 Dihedral : 16.281 179.157 2172 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.73 % Allowed : 20.30 % Favored : 75.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.23), residues: 1332 helix: 1.50 (0.22), residues: 564 sheet: 0.54 (0.34), residues: 244 loop : -1.72 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.017 0.001 TYR K 17 PHE 0.012 0.001 PHE G 26 TRP 0.009 0.001 TRP J 111 HIS 0.002 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.19 (12330) covalent geometry : angle 0.54958 / 0.29 (16879) hydrogen bonds : bond 0.04871 / 3.24 ( 568) hydrogen bonds : angle 4.62587 / 3.14 ( 1587) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9214 (m-30) cc_final: 0.8848 (p0) REVERT: B 49 ARG cc_start: 0.8757 (tmm-80) cc_final: 0.8407 (tmm-80) REVERT: B 76 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8912 (mmmm) REVERT: C 24 ASP cc_start: 0.8236 (m-30) cc_final: 0.8018 (t70) REVERT: C 32 ASN cc_start: 0.8556 (t0) cc_final: 0.7824 (t0) REVERT: C 80 ASN cc_start: 0.7191 (t0) cc_final: 0.6819 (t0) REVERT: C 81 GLN cc_start: 0.7728 (mp10) cc_final: 0.7274 (mp10) REVERT: C 120 ASN cc_start: 0.8209 (m-40) cc_final: 0.7968 (m-40) REVERT: A 1 MET cc_start: 0.5995 (tpt) cc_final: 0.3376 (ppp) REVERT: A 7 ARG cc_start: 0.7078 (mmm-85) cc_final: 0.6676 (mmm-85) REVERT: A 10 GLU cc_start: 0.8371 (tt0) cc_final: 0.8074 (tt0) REVERT: D 2 ASP cc_start: 0.9183 (p0) cc_final: 0.8881 (p0) REVERT: D 28 ASP cc_start: 0.8306 (t0) cc_final: 0.7921 (t0) REVERT: D 30 GLU cc_start: 0.8121 (mp0) cc_final: 0.7874 (mp0) REVERT: F 1 MET cc_start: 0.5489 (ptt) cc_final: 0.4889 (mtm) REVERT: F 62 LYS cc_start: 0.9049 (tppt) cc_final: 0.8783 (tptp) REVERT: H 17 TYR cc_start: 0.8589 (m-80) cc_final: 0.8375 (m-10) REVERT: H 24 ASP cc_start: 0.8287 (t70) cc_final: 0.7717 (t0) REVERT: I 1 MET cc_start: 0.7306 (tmm) cc_final: 0.6997 (ppp) REVERT: J 117 GLN cc_start: 0.9036 (mt0) cc_final: 0.8629 (mt0) REVERT: K 3 VAL cc_start: 0.9300 (OUTLIER) cc_final: 0.9089 (m) REVERT: K 24 ASP cc_start: 0.8330 (m-30) cc_final: 0.7824 (t0) REVERT: K 61 ASP cc_start: 0.7205 (p0) cc_final: 0.6975 (p0) REVERT: L 4 MET cc_start: 0.7974 (tpt) cc_final: 0.7308 (mpp) REVERT: L 11 LYS cc_start: 0.8985 (mmmt) cc_final: 0.8694 (mmtm) outliers start: 45 outliers final: 31 residues processed: 229 average time/residue: 0.1204 time to fit residues: 38.1771 Evaluate side-chains 228 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 20 ILE Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 59 PHE Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain I residue 5 SER Chi-restraints excluded: chain J residue 13 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [16, 28, 97, 39, 113, 29, 25, 63, 115, 99, 52] chunk 16 optimal weight: 30.0000 chunk 28 optimal weight: 10.0000 chunk 97 optimal weight: 1.9990 chunk 39 optimal weight: 0.0270 chunk 113 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 115 optimal weight: 0.0050 chunk 99 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.0058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 39 ASN D 39 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.112716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.072387 restraints weight = 21148.989| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 3.58 r_work: 0.2754 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12330 Z= 0.110 Angle : 0.509 9.796 16879 Z= 0.271 Chirality : 0.041 0.349 1939 Planarity : 0.004 0.056 1939 Dihedral : 16.249 179.350 2172 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.93 % Favored : 97.00 % Rotamer: Outliers : 2.98 % Allowed : 21.54 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.24), residues: 1332 helix: 1.70 (0.22), residues: 564 sheet: 0.67 (0.34), residues: 244 loop : -1.66 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 53 TYR 0.013 0.001 TYR C 17 PHE 0.006 0.001 PHE J 123 TRP 0.014 0.001 TRP I 30 HIS 0.001 0.000 HIS L 27 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (12330) covalent geometry : angle 0.50856 / 0.27 (16879) hydrogen bonds : bond 0.03777 / 2.51 ( 568) hydrogen bonds : angle 4.38093 / 2.96 ( 1587) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 195 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9373 (m-30) cc_final: 0.8911 (p0) REVERT: B 49 ARG cc_start: 0.8543 (tmm-80) cc_final: 0.8209 (tmm-80) REVERT: B 76 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8747 (mmtt) REVERT: C 24 ASP cc_start: 0.8227 (m-30) cc_final: 0.7883 (t70) REVERT: C 32 ASN cc_start: 0.8397 (t0) cc_final: 0.7626 (t0) REVERT: C 80 ASN cc_start: 0.7122 (t0) cc_final: 0.6793 (t0) REVERT: C 81 GLN cc_start: 0.7530 (mp10) cc_final: 0.7104 (mp10) REVERT: C 107 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8929 (p) REVERT: A 1 MET cc_start: 0.6362 (tpt) cc_final: 0.3674 (ppp) REVERT: D 2 ASP cc_start: 0.9259 (p0) cc_final: 0.8973 (p0) REVERT: D 28 ASP cc_start: 0.8484 (t0) cc_final: 0.8022 (t0) REVERT: D 30 GLU cc_start: 0.8137 (mp0) cc_final: 0.7779 (mp0) REVERT: E 80 ASN cc_start: 0.8714 (t0) cc_final: 0.8322 (t0) REVERT: F 1 MET cc_start: 0.5726 (ptt) cc_final: 0.4964 (mtm) REVERT: F 62 LYS cc_start: 0.9188 (tppt) cc_final: 0.8815 (tptp) REVERT: H 24 ASP cc_start: 0.8304 (t70) cc_final: 0.7609 (t0) REVERT: H 81 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8561 (mt0) REVERT: I 1 MET cc_start: 0.7484 (tmm) cc_final: 0.7129 (ppp) REVERT: J 117 GLN cc_start: 0.9013 (mt0) cc_final: 0.8530 (mt0) REVERT: K 3 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9034 (m) REVERT: K 24 ASP cc_start: 0.8412 (m-30) cc_final: 0.7743 (t0) REVERT: K 78 LYS cc_start: 0.8777 (ptpp) cc_final: 0.8540 (pttm) REVERT: K 80 ASN cc_start: 0.8475 (t0) cc_final: 0.7490 (t0) REVERT: L 4 MET cc_start: 0.7948 (tpt) cc_final: 0.7132 (mpp) REVERT: L 11 LYS cc_start: 0.8832 (mmmt) cc_final: 0.8518 (mmtm) REVERT: L 53 ARG cc_start: 0.7662 (mtm-85) cc_final: 0.7422 (mtm-85) outliers start: 36 outliers final: 27 residues processed: 219 average time/residue: 0.1133 time to fit residues: 34.9191 Evaluate side-chains 222 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 192 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 15 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [102, 7, 53, 27, 109, 126, 56, 50, 64, 108, 43] chunk 102 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN G 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.069549 restraints weight = 21274.783| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.56 r_work: 0.2696 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12330 Z= 0.218 Angle : 0.556 8.955 16879 Z= 0.296 Chirality : 0.043 0.347 1939 Planarity : 0.004 0.042 1939 Dihedral : 16.222 179.178 2170 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 4.47 % Allowed : 20.46 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.23), residues: 1332 helix: 1.53 (0.22), residues: 564 sheet: 0.66 (0.34), residues: 244 loop : -1.74 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG J 49 TYR 0.020 0.001 TYR H 17 PHE 0.012 0.001 PHE G 26 TRP 0.012 0.002 TRP A 30 HIS 0.002 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (12330) covalent geometry : angle 0.55592 / 0.30 (16879) hydrogen bonds : bond 0.04850 / 3.23 ( 568) hydrogen bonds : angle 4.50910 / 3.06 ( 1587) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 192 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9368 (m-30) cc_final: 0.8911 (p0) REVERT: B 49 ARG cc_start: 0.8676 (tmm-80) cc_final: 0.8344 (tmm-80) REVERT: C 24 ASP cc_start: 0.8265 (m-30) cc_final: 0.7886 (t70) REVERT: C 32 ASN cc_start: 0.8430 (t0) cc_final: 0.7683 (t0) REVERT: C 80 ASN cc_start: 0.7194 (t0) cc_final: 0.6837 (t0) REVERT: C 81 GLN cc_start: 0.7635 (mp10) cc_final: 0.7174 (mp10) REVERT: C 107 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8914 (p) REVERT: A 1 MET cc_start: 0.6408 (tpt) cc_final: 0.3714 (ppp) REVERT: A 7 ARG cc_start: 0.6877 (mmm-85) cc_final: 0.6247 (mmm-85) REVERT: A 10 GLU cc_start: 0.8060 (tt0) cc_final: 0.7800 (tt0) REVERT: D 2 ASP cc_start: 0.9288 (p0) cc_final: 0.9005 (p0) REVERT: D 28 ASP cc_start: 0.8622 (t0) cc_final: 0.8111 (t0) REVERT: D 30 GLU cc_start: 0.8189 (mp0) cc_final: 0.7657 (mp0) REVERT: E 48 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7716 (mp) REVERT: E 80 ASN cc_start: 0.8773 (t0) cc_final: 0.8334 (t0) REVERT: F 1 MET cc_start: 0.5820 (ptt) cc_final: 0.5028 (mtm) REVERT: F 62 LYS cc_start: 0.9217 (tppt) cc_final: 0.8741 (tptp) REVERT: H 24 ASP cc_start: 0.8340 (t70) cc_final: 0.7612 (t0) REVERT: H 60 LEU cc_start: 0.8828 (tp) cc_final: 0.8628 (tt) REVERT: H 81 GLN cc_start: 0.9234 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: I 1 MET cc_start: 0.7506 (tmm) cc_final: 0.7141 (ppp) REVERT: J 117 GLN cc_start: 0.9026 (mt0) cc_final: 0.8559 (mt0) REVERT: K 3 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9049 (m) REVERT: K 24 ASP cc_start: 0.8445 (m-30) cc_final: 0.7689 (t0) REVERT: K 41 MET cc_start: 0.7184 (mtp) cc_final: 0.6837 (ttm) REVERT: K 78 LYS cc_start: 0.8796 (ptpp) cc_final: 0.8553 (pttm) REVERT: K 80 ASN cc_start: 0.8619 (OUTLIER) cc_final: 0.7716 (t0) REVERT: L 4 MET cc_start: 0.7959 (tpt) cc_final: 0.7121 (mpp) REVERT: L 11 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8536 (mmtm) REVERT: L 43 TYR cc_start: 0.8777 (t80) cc_final: 0.8573 (t80) REVERT: L 53 ARG cc_start: 0.7687 (mtm-85) cc_final: 0.7357 (mtm-85) outliers start: 54 outliers final: 39 residues processed: 232 average time/residue: 0.1155 time to fit residues: 37.6525 Evaluate side-chains 235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 15 THR Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 105 THR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 31 ILE Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 81 GLN Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 87 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 20 ILE Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [26, 51, 63, 47, 75, 79, 92, 109, 105, 17, 61] chunk 26 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 92 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 0.1980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.112850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072516 restraints weight = 21104.906| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.58 r_work: 0.2757 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12330 Z= 0.104 Angle : 0.497 7.304 16879 Z= 0.265 Chirality : 0.040 0.347 1939 Planarity : 0.004 0.052 1939 Dihedral : 16.183 179.428 2170 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.08 % Favored : 96.85 % Rotamer: Outliers : 3.23 % Allowed : 21.62 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1332 helix: 1.77 (0.22), residues: 568 sheet: 0.81 (0.34), residues: 244 loop : -1.73 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 63 TYR 0.018 0.001 TYR H 17 PHE 0.007 0.001 PHE J 123 TRP 0.015 0.001 TRP I 30 HIS 0.001 0.000 HIS B 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (12330) covalent geometry : angle 0.49663 / 0.27 (16879) hydrogen bonds : bond 0.03518 / 2.33 ( 568) hydrogen bonds : angle 4.23460 / 2.86 ( 1587) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9378 (m-30) cc_final: 0.8893 (p0) REVERT: B 49 ARG cc_start: 0.8599 (tmm-80) cc_final: 0.8261 (tmm-80) REVERT: C 24 ASP cc_start: 0.8239 (m-30) cc_final: 0.7718 (t70) REVERT: C 32 ASN cc_start: 0.8417 (t0) cc_final: 0.7517 (t0) REVERT: C 80 ASN cc_start: 0.7140 (t0) cc_final: 0.6809 (t0) REVERT: C 81 GLN cc_start: 0.7517 (mp10) cc_final: 0.7121 (mp10) REVERT: A 1 MET cc_start: 0.6454 (tpt) cc_final: 0.3688 (ppp) REVERT: D 2 ASP cc_start: 0.9262 (p0) cc_final: 0.8976 (p0) REVERT: D 28 ASP cc_start: 0.8613 (t0) cc_final: 0.8057 (t0) REVERT: D 30 GLU cc_start: 0.8152 (mp0) cc_final: 0.7597 (mp0) REVERT: E 63 ARG cc_start: 0.6875 (ttm110) cc_final: 0.6667 (ttm110) REVERT: E 80 ASN cc_start: 0.8777 (t0) cc_final: 0.8339 (t0) REVERT: F 1 MET cc_start: 0.5811 (ptt) cc_final: 0.5051 (mtm) REVERT: F 14 ARG cc_start: 0.9120 (tpp80) cc_final: 0.8873 (ttm-80) REVERT: F 62 LYS cc_start: 0.9185 (tppt) cc_final: 0.8804 (tptp) REVERT: H 24 ASP cc_start: 0.8306 (t70) cc_final: 0.7546 (t0) REVERT: I 1 MET cc_start: 0.7442 (tmm) cc_final: 0.7091 (ppp) REVERT: I 46 ASP cc_start: 0.8698 (t70) cc_final: 0.8377 (t70) REVERT: J 28 ASP cc_start: 0.9224 (OUTLIER) cc_final: 0.8678 (p0) REVERT: J 39 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.7992 (p0) REVERT: J 117 GLN cc_start: 0.8998 (mt0) cc_final: 0.8502 (mt0) REVERT: K 24 ASP cc_start: 0.8356 (m-30) cc_final: 0.7683 (t0) REVERT: K 41 MET cc_start: 0.7039 (mtp) cc_final: 0.6670 (ttm) REVERT: K 78 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8455 (pttm) REVERT: K 80 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.7744 (t0) REVERT: L 4 MET cc_start: 0.7940 (tpt) cc_final: 0.7083 (mpp) REVERT: L 11 LYS cc_start: 0.8802 (mmmt) cc_final: 0.8485 (mmtm) outliers start: 39 outliers final: 27 residues processed: 228 average time/residue: 0.1157 time to fit residues: 36.9203 Evaluate side-chains 221 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [92, 48, 3, 119, 25, 99, 57, 118, 54, 13, 70] chunk 92 optimal weight: 0.2980 chunk 48 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN G 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.072144 restraints weight = 21065.670| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.57 r_work: 0.2748 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12330 Z= 0.123 Angle : 0.514 9.305 16879 Z= 0.270 Chirality : 0.041 0.346 1939 Planarity : 0.004 0.064 1939 Dihedral : 16.145 179.541 2169 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 3.15 % Allowed : 22.37 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.24), residues: 1332 helix: 1.81 (0.22), residues: 568 sheet: 0.86 (0.34), residues: 244 loop : -1.74 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 53 TYR 0.019 0.001 TYR H 17 PHE 0.007 0.001 PHE J 123 TRP 0.011 0.001 TRP I 30 HIS 0.001 0.000 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (12330) covalent geometry : angle 0.51367 / 0.27 (16879) hydrogen bonds : bond 0.03693 / 2.46 ( 568) hydrogen bonds : angle 4.18422 / 2.83 ( 1587) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.8619 (tmm-80) cc_final: 0.8293 (tmm-80) REVERT: C 24 ASP cc_start: 0.8267 (m-30) cc_final: 0.7742 (t70) REVERT: C 32 ASN cc_start: 0.8448 (t0) cc_final: 0.7574 (t0) REVERT: C 80 ASN cc_start: 0.7168 (t0) cc_final: 0.6863 (t0) REVERT: C 81 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7162 (mp10) REVERT: A 1 MET cc_start: 0.6479 (tpt) cc_final: 0.3879 (ppp) REVERT: A 11 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7833 (mmtm) REVERT: D 2 ASP cc_start: 0.9260 (p0) cc_final: 0.8970 (p0) REVERT: D 28 ASP cc_start: 0.8668 (t0) cc_final: 0.8111 (t0) REVERT: D 30 GLU cc_start: 0.8191 (mp0) cc_final: 0.7647 (mp0) REVERT: E 11 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7707 (tttp) REVERT: E 63 ARG cc_start: 0.6920 (ttm110) cc_final: 0.6519 (ttm170) REVERT: E 80 ASN cc_start: 0.8788 (t0) cc_final: 0.8362 (t0) REVERT: E 134 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7991 (tm-30) REVERT: F 1 MET cc_start: 0.5831 (ptt) cc_final: 0.5055 (mtm) REVERT: F 62 LYS cc_start: 0.9179 (tppt) cc_final: 0.8692 (tptp) REVERT: H 24 ASP cc_start: 0.8331 (t70) cc_final: 0.7564 (t0) REVERT: I 1 MET cc_start: 0.7406 (tmm) cc_final: 0.7041 (ppp) REVERT: I 46 ASP cc_start: 0.8701 (t70) cc_final: 0.8375 (t70) REVERT: J 28 ASP cc_start: 0.9228 (OUTLIER) cc_final: 0.8690 (p0) REVERT: J 117 GLN cc_start: 0.8999 (mt0) cc_final: 0.8489 (mt0) REVERT: K 24 ASP cc_start: 0.8380 (m-30) cc_final: 0.7703 (t0) REVERT: K 41 MET cc_start: 0.7133 (mtp) cc_final: 0.6768 (ttm) REVERT: K 80 ASN cc_start: 0.8620 (OUTLIER) cc_final: 0.7957 (t0) REVERT: L 4 MET cc_start: 0.7948 (tpt) cc_final: 0.7096 (mpp) REVERT: L 11 LYS cc_start: 0.8828 (mmmt) cc_final: 0.8498 (mmtm) REVERT: L 53 ARG cc_start: 0.7521 (mtm-85) cc_final: 0.7231 (mtm-85) outliers start: 38 outliers final: 32 residues processed: 220 average time/residue: 0.1164 time to fit residues: 36.0906 Evaluate side-chains 225 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 2 ASP Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [101, 73, 113, 24, 26, 35, 98, 44, 84, 48, 85] chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN G 125 GLN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.110623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.070287 restraints weight = 21189.292| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 3.57 r_work: 0.2714 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12330 Z= 0.180 Angle : 0.555 9.858 16879 Z= 0.290 Chirality : 0.042 0.345 1939 Planarity : 0.004 0.056 1939 Dihedral : 16.162 179.396 2169 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.90 % Favored : 96.02 % Rotamer: Outliers : 3.31 % Allowed : 22.78 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.24), residues: 1332 helix: 1.70 (0.22), residues: 568 sheet: 0.84 (0.34), residues: 244 loop : -1.80 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 14 TYR 0.033 0.001 TYR L 43 PHE 0.010 0.001 PHE G 26 TRP 0.034 0.002 TRP A 30 HIS 0.002 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (12330) covalent geometry : angle 0.55469 / 0.29 (16879) hydrogen bonds : bond 0.04358 / 2.91 ( 568) hydrogen bonds : angle 4.29425 / 2.91 ( 1587) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.8706 (tmm-80) cc_final: 0.8363 (tmm-80) REVERT: C 24 ASP cc_start: 0.8292 (m-30) cc_final: 0.7732 (t70) REVERT: C 32 ASN cc_start: 0.8469 (t0) cc_final: 0.7620 (t0) REVERT: C 80 ASN cc_start: 0.7242 (t0) cc_final: 0.6940 (t0) REVERT: C 81 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7192 (mp10) REVERT: A 1 MET cc_start: 0.6517 (tpt) cc_final: 0.3892 (ppp) REVERT: A 11 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7900 (mmtm) REVERT: A 62 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8312 (tptt) REVERT: D 2 ASP cc_start: 0.9272 (p0) cc_final: 0.8990 (p0) REVERT: D 28 ASP cc_start: 0.8744 (t0) cc_final: 0.8167 (t0) REVERT: D 30 GLU cc_start: 0.8220 (mp0) cc_final: 0.7725 (mp0) REVERT: E 11 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.7685 (tttp) REVERT: E 37 PHE cc_start: 0.8437 (p90) cc_final: 0.8234 (p90) REVERT: E 63 ARG cc_start: 0.7021 (ttm110) cc_final: 0.6624 (ttm170) REVERT: E 80 ASN cc_start: 0.8841 (t0) cc_final: 0.8437 (t0) REVERT: F 1 MET cc_start: 0.5814 (ptt) cc_final: 0.5030 (mtm) REVERT: F 62 LYS cc_start: 0.9227 (tppt) cc_final: 0.8759 (tptp) REVERT: H 24 ASP cc_start: 0.8333 (t70) cc_final: 0.7542 (t0) REVERT: J 117 GLN cc_start: 0.8999 (mt0) cc_final: 0.8498 (mt0) REVERT: K 24 ASP cc_start: 0.8383 (m-30) cc_final: 0.7703 (t0) REVERT: K 78 LYS cc_start: 0.8761 (ptpp) cc_final: 0.8445 (pttm) REVERT: K 80 ASN cc_start: 0.8692 (OUTLIER) cc_final: 0.7864 (t0) REVERT: K 84 TYR cc_start: 0.8877 (m-80) cc_final: 0.8620 (m-80) REVERT: L 4 MET cc_start: 0.7928 (tpt) cc_final: 0.7083 (mpp) REVERT: L 11 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8516 (mmtm) REVERT: L 53 ARG cc_start: 0.7589 (mtm-85) cc_final: 0.7254 (mtm-85) outliers start: 40 outliers final: 35 residues processed: 222 average time/residue: 0.1141 time to fit residues: 35.2856 Evaluate side-chains 231 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 2 ASP Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [27, 124, 13, 75, 63, 78, 72, 47, 111, 57, 36] chunk 27 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN G 125 GLN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.110968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.070599 restraints weight = 21115.694| |-----------------------------------------------------------------------------| r_work (start): 0.2910 rms_B_bonded: 3.56 r_work: 0.2722 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12330 Z= 0.159 Angle : 0.548 8.786 16879 Z= 0.287 Chirality : 0.041 0.344 1939 Planarity : 0.004 0.051 1939 Dihedral : 16.154 179.409 2169 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.23 % Favored : 96.70 % Rotamer: Outliers : 3.31 % Allowed : 22.87 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1332 helix: 1.73 (0.22), residues: 568 sheet: 0.87 (0.34), residues: 244 loop : -1.79 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 53 TYR 0.024 0.001 TYR L 43 PHE 0.014 0.001 PHE L 3 TRP 0.033 0.002 TRP A 30 HIS 0.002 0.000 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.16 (12330) covalent geometry : angle 0.54772 / 0.29 (16879) hydrogen bonds : bond 0.04106 / 2.73 ( 568) hydrogen bonds : angle 4.24378 / 2.87 ( 1587) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 ARG cc_start: 0.8686 (tmm-80) cc_final: 0.8343 (tmm-80) REVERT: C 24 ASP cc_start: 0.8302 (m-30) cc_final: 0.7746 (t70) REVERT: C 32 ASN cc_start: 0.8490 (t0) cc_final: 0.7668 (t0) REVERT: C 80 ASN cc_start: 0.7283 (t0) cc_final: 0.7003 (t0) REVERT: C 81 GLN cc_start: 0.7615 (OUTLIER) cc_final: 0.7198 (mp10) REVERT: A 1 MET cc_start: 0.6498 (tpt) cc_final: 0.3835 (ppp) REVERT: A 11 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7852 (mmtm) REVERT: A 62 LYS cc_start: 0.8774 (mmmt) cc_final: 0.8316 (tptt) REVERT: D 2 ASP cc_start: 0.9266 (p0) cc_final: 0.8982 (p0) REVERT: D 28 ASP cc_start: 0.8762 (t0) cc_final: 0.8192 (t0) REVERT: D 30 GLU cc_start: 0.8214 (mp0) cc_final: 0.7717 (mp0) REVERT: E 11 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7685 (tttp) REVERT: E 80 ASN cc_start: 0.8857 (t0) cc_final: 0.8458 (t0) REVERT: F 1 MET cc_start: 0.5718 (ptt) cc_final: 0.4970 (mtm) REVERT: F 62 LYS cc_start: 0.9217 (tppt) cc_final: 0.8722 (tptp) REVERT: H 24 ASP cc_start: 0.8310 (t70) cc_final: 0.7519 (t0) REVERT: I 1 MET cc_start: 0.7465 (tmm) cc_final: 0.7239 (ppp) REVERT: I 46 ASP cc_start: 0.8720 (t0) cc_final: 0.8471 (t0) REVERT: J 39 ASN cc_start: 0.8493 (OUTLIER) cc_final: 0.7900 (p0) REVERT: J 117 GLN cc_start: 0.9001 (mt0) cc_final: 0.8497 (mt0) REVERT: K 24 ASP cc_start: 0.8375 (m-30) cc_final: 0.7706 (t0) REVERT: K 78 LYS cc_start: 0.8766 (ptpp) cc_final: 0.8450 (pttm) REVERT: K 80 ASN cc_start: 0.8713 (OUTLIER) cc_final: 0.7939 (t0) REVERT: K 84 TYR cc_start: 0.8870 (m-80) cc_final: 0.8631 (m-80) REVERT: L 1 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.5082 (tmm) REVERT: L 4 MET cc_start: 0.7967 (tpt) cc_final: 0.7168 (mpp) REVERT: L 11 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8518 (mmtm) outliers start: 40 outliers final: 32 residues processed: 222 average time/residue: 0.1177 time to fit residues: 36.6864 Evaluate side-chains 225 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 59 PHE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [130, 19, 25, 16, 112, 28, 101, 122, 29, 49, 18] chunk 130 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 128 GLN D 39 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN J 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.109967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.069572 restraints weight = 21320.449| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.56 r_work: 0.2699 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12330 Z= 0.207 Angle : 0.588 9.869 16879 Z= 0.308 Chirality : 0.043 0.343 1939 Planarity : 0.004 0.043 1939 Dihedral : 16.172 179.319 2169 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.20 % Favored : 95.72 % Rotamer: Outliers : 2.90 % Allowed : 23.53 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1332 helix: 1.62 (0.22), residues: 568 sheet: 0.82 (0.34), residues: 244 loop : -1.85 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 14 TYR 0.025 0.001 TYR L 43 PHE 0.012 0.001 PHE K 37 TRP 0.024 0.002 TRP A 30 HIS 0.002 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.21 (12330) covalent geometry : angle 0.58838 / 0.31 (16879) hydrogen bonds : bond 0.04612 / 3.08 ( 568) hydrogen bonds : angle 4.33910 / 2.94 ( 1587) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2664 Ramachandran restraints generated. 1332 Oldfield, 0 Emsley, 1332 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 28 ASP cc_start: 0.9374 (m-30) cc_final: 0.8882 (p0) REVERT: B 49 ARG cc_start: 0.8720 (tmm-80) cc_final: 0.8384 (tmm-80) REVERT: C 24 ASP cc_start: 0.8314 (m-30) cc_final: 0.7743 (t70) REVERT: C 32 ASN cc_start: 0.8497 (t0) cc_final: 0.7717 (t0) REVERT: C 80 ASN cc_start: 0.7410 (t0) cc_final: 0.7105 (t0) REVERT: C 81 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7234 (mp10) REVERT: A 1 MET cc_start: 0.6501 (tpt) cc_final: 0.3598 (ppp) REVERT: A 62 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8328 (tptt) REVERT: D 2 ASP cc_start: 0.9290 (p0) cc_final: 0.9009 (p0) REVERT: D 28 ASP cc_start: 0.8826 (t0) cc_final: 0.8264 (t0) REVERT: D 30 GLU cc_start: 0.8240 (mp0) cc_final: 0.7769 (mp0) REVERT: E 11 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7696 (tttp) REVERT: E 80 ASN cc_start: 0.8867 (t0) cc_final: 0.8426 (t0) REVERT: E 134 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7961 (tm-30) REVERT: F 1 MET cc_start: 0.5728 (ptt) cc_final: 0.4996 (mtm) REVERT: F 62 LYS cc_start: 0.9246 (tppt) cc_final: 0.8792 (tptp) REVERT: H 24 ASP cc_start: 0.8291 (t70) cc_final: 0.7468 (t0) REVERT: I 1 MET cc_start: 0.7519 (tmm) cc_final: 0.7197 (ppp) REVERT: J 39 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8051 (p0) REVERT: J 117 GLN cc_start: 0.9018 (mt0) cc_final: 0.8542 (mt0) REVERT: K 24 ASP cc_start: 0.8386 (m-30) cc_final: 0.7718 (t0) REVERT: K 78 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8478 (pttm) REVERT: K 80 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8059 (t0) REVERT: K 84 TYR cc_start: 0.8902 (m-80) cc_final: 0.8656 (m-80) REVERT: L 1 MET cc_start: 0.6804 (tpt) cc_final: 0.5237 (tmm) REVERT: L 4 MET cc_start: 0.7937 (tpt) cc_final: 0.7179 (mpp) REVERT: L 11 LYS cc_start: 0.8851 (mmmt) cc_final: 0.8523 (mmtm) REVERT: L 53 ARG cc_start: 0.7648 (mtm-85) cc_final: 0.7359 (mtm-85) outliers start: 35 outliers final: 31 residues processed: 218 average time/residue: 0.1163 time to fit residues: 34.9157 Evaluate side-chains 225 residues out of total 1212 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 98 THR Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain C residue 81 GLN Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain E residue 47 ASN Chi-restraints excluded: chain E residue 77 LEU Chi-restraints excluded: chain E residue 84 TYR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain G residue 13 ASP Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 72 VAL Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 108 ILE Chi-restraints excluded: chain H residue 115 LEU Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 39 ASN Chi-restraints excluded: chain J residue 40 SER Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain K residue 30 GLU Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain K residue 80 ASN Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain L residue 3 PHE Chi-restraints excluded: chain L residue 5 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: [70, 67, 57, 109, 11, 72, 122, 79, 123, 59, 52] chunk 70 optimal weight: 0.7980 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 39 ASN ** D 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 125 GLN J 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.069888 restraints weight = 21040.672| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.53 r_work: 0.2704 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 12330 Z= 0.190 Angle : 0.579 9.576 16879 Z= 0.304 Chirality : 0.043 0.343 1939 Planarity : 0.004 0.042 1939 Dihedral : 16.174 179.303 2169 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.45 % Favored : 96.47 % Rotamer: Outliers : 3.07 % Allowed : 23.12 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.92 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.24), residues: 1332 helix: 1.63 (0.22), residues: 568 sheet: 0.81 (0.34), residues: 244 loop : -1.85 (0.26), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 53 TYR 0.025 0.001 TYR L 43 PHE 0.011 0.001 PHE K 37 TRP 0.017 0.002 TRP A 30 HIS 0.002 0.001 HIS J 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (12330) covalent geometry : angle 0.57867 / 0.30 (16879) hydrogen bonds : bond 0.04465 / 2.98 ( 568) hydrogen bonds : angle 4.32338 / 2.93 ( 1587) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2607.19 seconds wall clock time: 45 minutes 28.00 seconds (2728.00 seconds total)