Starting phenix.real_space_refine on Sat Sep 12 01:00:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.map" model { file = "/net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9s6e_54625/09_2026/9s6e_54625.cif" } resolution = 3.5 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= 0.002 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7680 2.51 5 N 2480 2.21 5 O 2368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 104 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12608 Number of models: 1 Model: "" Number of chains: 16 Chain: "B" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "A" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "C" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "F" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "G" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "H" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "K" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "M" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "N" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "O" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "P" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 788 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Time building chain proxies: 3.14, per 1000 atoms: 0.25 Number of scatterers: 12608 At special positions: 0 Unit cell: (105.45, 105.45, 107.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2368 8.00 N 2480 7.00 C 7680 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: 0.99 Conformation dependent library (CDL) restraints added in 598.2 milliseconds 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2944 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 0 sheets defined 83.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 12 through 19 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.206A pdb=" N ALA B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 45 Processing helix chain 'B' and resid 50 through 63 removed outlier: 4.008A pdb=" N GLU B 63 " --> pdb=" O ILE B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 81 Processing helix chain 'B' and resid 82 through 95 removed outlier: 3.631A pdb=" N ALA B 86 " --> pdb=" O GLN B 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA B 95 " --> pdb=" O THR B 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 12 through 19 Processing helix chain 'A' and resid 24 through 32 removed outlier: 4.061A pdb=" N ALA A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 45 Processing helix chain 'A' and resid 50 through 63 removed outlier: 3.935A pdb=" N GLU A 63 " --> pdb=" O ILE A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 81 Processing helix chain 'A' and resid 82 through 95 removed outlier: 3.549A pdb=" N ALA A 86 " --> pdb=" O GLN A 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN A 94 " --> pdb=" O ARG A 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 95 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 12 Processing helix chain 'C' and resid 12 through 19 Processing helix chain 'C' and resid 24 through 32 removed outlier: 4.215A pdb=" N ALA C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 45 Processing helix chain 'C' and resid 50 through 62 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 68 through 81 Processing helix chain 'C' and resid 82 through 95 removed outlier: 3.528A pdb=" N ALA C 86 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA C 95 " --> pdb=" O THR C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 Processing helix chain 'D' and resid 12 through 19 Processing helix chain 'D' and resid 24 through 32 removed outlier: 4.000A pdb=" N ALA D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 45 Processing helix chain 'D' and resid 50 through 62 Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 68 through 81 Processing helix chain 'D' and resid 82 through 95 removed outlier: 3.798A pdb=" N ALA D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 12 through 19 Processing helix chain 'E' and resid 24 through 32 removed outlier: 4.153A pdb=" N ALA E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 Processing helix chain 'E' and resid 50 through 63 removed outlier: 4.050A pdb=" N GLU E 63 " --> pdb=" O ILE E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 81 Processing helix chain 'E' and resid 82 through 95 removed outlier: 3.655A pdb=" N ALA E 86 " --> pdb=" O GLN E 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER E 87 " --> pdb=" O ASP E 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 12 Processing helix chain 'F' and resid 12 through 19 Processing helix chain 'F' and resid 24 through 32 removed outlier: 4.064A pdb=" N ALA F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 45 removed outlier: 3.508A pdb=" N ARG F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 63 removed outlier: 4.064A pdb=" N GLU F 63 " --> pdb=" O ILE F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 81 Processing helix chain 'F' and resid 82 through 95 removed outlier: 3.594A pdb=" N ALA F 86 " --> pdb=" O GLN F 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA F 95 " --> pdb=" O THR F 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 12 Processing helix chain 'G' and resid 12 through 19 Processing helix chain 'G' and resid 24 through 32 removed outlier: 3.818A pdb=" N ALA G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 45 removed outlier: 3.558A pdb=" N ARG G 45 " --> pdb=" O GLU G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 63 removed outlier: 3.944A pdb=" N GLU G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 81 Processing helix chain 'G' and resid 82 through 95 removed outlier: 3.595A pdb=" N ALA G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA G 95 " --> pdb=" O THR G 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 12 Processing helix chain 'H' and resid 12 through 19 Processing helix chain 'H' and resid 24 through 32 removed outlier: 4.112A pdb=" N ALA H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 45 removed outlier: 3.602A pdb=" N ARG H 45 " --> pdb=" O GLU H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 63 removed outlier: 3.955A pdb=" N GLU H 63 " --> pdb=" O ILE H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 81 Processing helix chain 'H' and resid 82 through 95 removed outlier: 3.584A pdb=" N ALA H 86 " --> pdb=" O GLN H 82 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA H 95 " --> pdb=" O THR H 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 Processing helix chain 'I' and resid 12 through 19 Processing helix chain 'I' and resid 24 through 32 removed outlier: 4.061A pdb=" N ALA I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 45 Processing helix chain 'I' and resid 50 through 63 removed outlier: 3.935A pdb=" N GLU I 63 " --> pdb=" O ILE I 59 " (cutoff:3.500A) Processing helix chain 'I' and resid 68 through 81 Processing helix chain 'I' and resid 82 through 95 removed outlier: 3.549A pdb=" N ALA I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN I 94 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA I 95 " --> pdb=" O THR I 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 12 Processing helix chain 'J' and resid 12 through 19 Processing helix chain 'J' and resid 24 through 32 removed outlier: 4.215A pdb=" N ALA J 28 " --> pdb=" O GLN J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 45 Processing helix chain 'J' and resid 50 through 62 Processing helix chain 'J' and resid 63 through 65 No H-bonds generated for 'chain 'J' and resid 63 through 65' Processing helix chain 'J' and resid 68 through 81 Processing helix chain 'J' and resid 82 through 95 removed outlier: 3.528A pdb=" N ALA J 86 " --> pdb=" O GLN J 82 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLN J 94 " --> pdb=" O ARG J 90 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA J 95 " --> pdb=" O THR J 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 12 Processing helix chain 'K' and resid 12 through 19 Processing helix chain 'K' and resid 24 through 32 removed outlier: 4.000A pdb=" N ALA K 28 " --> pdb=" O GLN K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 45 Processing helix chain 'K' and resid 50 through 62 Processing helix chain 'K' and resid 63 through 65 No H-bonds generated for 'chain 'K' and resid 63 through 65' Processing helix chain 'K' and resid 68 through 81 Processing helix chain 'K' and resid 82 through 95 removed outlier: 3.798A pdb=" N ALA K 95 " --> pdb=" O THR K 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 12 Processing helix chain 'L' and resid 12 through 19 Processing helix chain 'L' and resid 24 through 32 removed outlier: 4.153A pdb=" N ALA L 28 " --> pdb=" O GLN L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 45 Processing helix chain 'L' and resid 50 through 63 removed outlier: 4.051A pdb=" N GLU L 63 " --> pdb=" O ILE L 59 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 81 Processing helix chain 'L' and resid 82 through 95 removed outlier: 3.654A pdb=" N ALA L 86 " --> pdb=" O GLN L 82 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER L 87 " --> pdb=" O ASP L 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA L 95 " --> pdb=" O THR L 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 12 Processing helix chain 'M' and resid 12 through 19 Processing helix chain 'M' and resid 24 through 32 removed outlier: 4.206A pdb=" N ALA M 28 " --> pdb=" O GLN M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 45 Processing helix chain 'M' and resid 50 through 63 removed outlier: 4.008A pdb=" N GLU M 63 " --> pdb=" O ILE M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 68 through 81 Processing helix chain 'M' and resid 82 through 95 removed outlier: 3.631A pdb=" N ALA M 86 " --> pdb=" O GLN M 82 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA M 95 " --> pdb=" O THR M 91 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 12 Processing helix chain 'N' and resid 12 through 19 Processing helix chain 'N' and resid 24 through 32 removed outlier: 4.064A pdb=" N ALA N 28 " --> pdb=" O GLN N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 36 through 45 removed outlier: 3.508A pdb=" N ARG N 45 " --> pdb=" O GLU N 41 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 63 removed outlier: 4.064A pdb=" N GLU N 63 " --> pdb=" O ILE N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 68 through 81 Processing helix chain 'N' and resid 82 through 95 removed outlier: 3.594A pdb=" N ALA N 86 " --> pdb=" O GLN N 82 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA N 95 " --> pdb=" O THR N 91 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 12 Processing helix chain 'O' and resid 12 through 19 Processing helix chain 'O' and resid 24 through 32 removed outlier: 3.818A pdb=" N ALA O 28 " --> pdb=" O GLN O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 45 removed outlier: 3.558A pdb=" N ARG O 45 " --> pdb=" O GLU O 41 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 63 removed outlier: 3.944A pdb=" N GLU O 63 " --> pdb=" O ILE O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 68 through 81 Processing helix chain 'O' and resid 82 through 95 removed outlier: 3.595A pdb=" N ALA O 86 " --> pdb=" O GLN O 82 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA O 95 " --> pdb=" O THR O 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 12 Processing helix chain 'P' and resid 12 through 19 Processing helix chain 'P' and resid 24 through 32 removed outlier: 4.112A pdb=" N ALA P 28 " --> pdb=" O GLN P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 45 removed outlier: 3.602A pdb=" N ARG P 45 " --> pdb=" O GLU P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 63 removed outlier: 3.955A pdb=" N GLU P 63 " --> pdb=" O ILE P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 68 through 81 Processing helix chain 'P' and resid 82 through 95 removed outlier: 3.584A pdb=" N ALA P 86 " --> pdb=" O GLN P 82 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA P 95 " --> pdb=" O THR P 91 " (cutoff:3.500A) 756 hydrogen bonds defined for protein. 2268 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.87 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4647 1.34 - 1.46: 1516 1.46 - 1.58: 6413 1.58 - 1.69: 0 1.69 - 1.81: 128 Bond restraints: 12704 Sorted by residual: bond pdb=" CA GLU P 19 " pdb=" CB GLU P 19 " ideal model delta sigma weight residual 1.526 1.544 -0.018 1.68e-02 3.54e+03 1.13e+00 bond pdb=" CA GLU H 19 " pdb=" CB GLU H 19 " ideal model delta sigma weight residual 1.526 1.544 -0.018 1.68e-02 3.54e+03 1.13e+00 bond pdb=" CA GLU H 19 " pdb=" C GLU H 19 " ideal model delta sigma weight residual 1.523 1.539 -0.017 1.61e-02 3.86e+03 1.08e+00 bond pdb=" CA GLU P 19 " pdb=" C GLU P 19 " ideal model delta sigma weight residual 1.523 1.539 -0.017 1.61e-02 3.86e+03 1.08e+00 bond pdb=" C VAL C 22 " pdb=" O VAL C 22 " ideal model delta sigma weight residual 1.236 1.224 0.012 1.47e-02 4.63e+03 6.12e-01 ... (remaining 12699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 16852 1.42 - 2.85: 112 2.85 - 4.27: 20 4.27 - 5.70: 20 5.70 - 7.12: 4 Bond angle restraints: 17008 Sorted by residual: angle pdb=" CA GLU P 19 " pdb=" CB GLU P 19 " pdb=" CG GLU P 19 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" CA GLU H 19 " pdb=" CB GLU H 19 " pdb=" CG GLU H 19 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C GLU H 19 " pdb=" CA GLU H 19 " pdb=" CB GLU H 19 " ideal model delta sigma weight residual 111.77 117.40 -5.63 2.28e+00 1.92e-01 6.10e+00 angle pdb=" C GLU P 19 " pdb=" CA GLU P 19 " pdb=" CB GLU P 19 " ideal model delta sigma weight residual 111.77 117.40 -5.63 2.28e+00 1.92e-01 6.10e+00 angle pdb=" CB MET M 84 " pdb=" CG MET M 84 " pdb=" SD MET M 84 " ideal model delta sigma weight residual 112.70 119.64 -6.94 3.00e+00 1.11e-01 5.35e+00 ... (remaining 17003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 6836 17.99 - 35.98: 944 35.98 - 53.97: 218 53.97 - 71.95: 42 71.95 - 89.94: 24 Dihedral angle restraints: 8064 sinusoidal: 3584 harmonic: 4480 Sorted by residual: dihedral pdb=" CA ASP I 23 " pdb=" CB ASP I 23 " pdb=" CG ASP I 23 " pdb=" OD1 ASP I 23 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP A 23 " pdb=" CB ASP A 23 " pdb=" CG ASP A 23 " pdb=" OD1 ASP A 23 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CB GLU G 3 " pdb=" CG GLU G 3 " pdb=" CD GLU G 3 " pdb=" OE1 GLU G 3 " ideal model delta sinusoidal sigma weight residual 0.00 89.94 -89.94 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 8061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 1110 0.021 - 0.042: 439 0.042 - 0.063: 247 0.063 - 0.084: 44 0.084 - 0.105: 48 Chirality restraints: 1888 Sorted by residual: chirality pdb=" CA LEU H 70 " pdb=" N LEU H 70 " pdb=" C LEU H 70 " pdb=" CB LEU H 70 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.11 2.00e-01 2.50e+01 2.77e-01 chirality pdb=" CA LEU P 70 " pdb=" N LEU P 70 " pdb=" C LEU P 70 " pdb=" CB LEU P 70 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.11 2.00e-01 2.50e+01 2.77e-01 chirality pdb=" CA LEU O 70 " pdb=" N LEU O 70 " pdb=" C LEU O 70 " pdb=" CB LEU O 70 " both_signs ideal model delta sigma weight residual False 2.51 2.41 0.10 2.00e-01 2.50e+01 2.63e-01 ... (remaining 1885 not shown) Planarity restraints: 2288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU K 19 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C GLU K 19 " 0.018 2.00e-02 2.50e+03 pdb=" O GLU K 19 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU K 20 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 19 " -0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C GLU D 19 " 0.018 2.00e-02 2.50e+03 pdb=" O GLU D 19 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU D 20 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 88 " 0.005 2.00e-02 2.50e+03 7.19e-03 9.04e-01 pdb=" CG PHE L 88 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE L 88 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE L 88 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE L 88 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 88 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE L 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 2285 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3109 2.80 - 3.33: 11740 3.33 - 3.85: 18492 3.85 - 4.38: 22947 4.38 - 4.90: 39901 Nonbonded interactions: 96189 Sorted by model distance: nonbonded pdb=" OE2 GLU P 41 " pdb=" NH2 ARG P 45 " model vdw 2.277 3.120 nonbonded pdb=" OE2 GLU H 41 " pdb=" NH2 ARG H 45 " model vdw 2.277 3.120 nonbonded pdb=" O ASP O 27 " pdb=" OG SER O 31 " model vdw 2.284 3.040 nonbonded pdb=" O ASP G 27 " pdb=" OG SER G 31 " model vdw 2.284 3.040 nonbonded pdb=" OE2 GLU O 78 " pdb=" NH2 ARG O 90 " model vdw 2.301 3.120 ... (remaining 96184 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.550 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 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 : 0.002 0.019 12704 Z= 0.087 Angle : 0.410 7.121 17008 Z= 0.228 Chirality : 0.031 0.105 1888 Planarity : 0.003 0.029 2288 Dihedral : 17.868 89.943 5120 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.00 % Allowed : 21.18 % Favored : 78.82 % 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: 1.40 (0.21), residues: 1520 helix: 1.42 (0.14), residues: 1168 sheet: None (None), residues: 0 loop : -0.61 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 45 PHE 0.016 0.001 PHE L 88 TRP 0.003 0.001 TRP G 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00173 / 0.09 (12704) covalent geometry : angle 0.40978 / 0.23 (17008) hydrogen bonds : bond 0.26326 / 17.46 ( 756) hydrogen bonds : angle 5.31131 / 3.80 ( 2268) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.510 Fit side-chains REVERT: A 7 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7360 (ttt-90) REVERT: G 41 GLU cc_start: 0.7812 (tt0) cc_final: 0.7239 (tt0) REVERT: H 45 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7459 (mtt90) REVERT: I 7 ARG cc_start: 0.7738 (mtp85) cc_final: 0.7359 (ttt-90) REVERT: O 41 GLU cc_start: 0.7805 (tt0) cc_final: 0.7229 (tt0) REVERT: P 45 ARG cc_start: 0.7709 (mtt90) cc_final: 0.7453 (mtt90) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1355 time to fit residues: 59.8798 Evaluate side-chains 318 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 24 GLN G 44 GLN K 54 GLN L 57 GLN N 24 GLN O 44 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.097853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.087952 restraints weight = 16749.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.090345 restraints weight = 10698.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.092041 restraints weight = 7408.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.093286 restraints weight = 5418.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.094164 restraints weight = 4105.945| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 12704 Z= 0.144 Angle : 0.476 4.822 17008 Z= 0.258 Chirality : 0.036 0.112 1888 Planarity : 0.004 0.025 2288 Dihedral : 3.053 14.695 1792 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 1.76 % Allowed : 16.91 % Favored : 81.32 % 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: 1.95 (0.21), residues: 1520 helix: 1.77 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : -0.74 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 45 PHE 0.005 0.001 PHE I 73 TRP 0.005 0.001 TRP O 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.14 (12704) covalent geometry : angle 0.47583 / 0.26 (17008) hydrogen bonds : bond 0.04880 / 3.27 ( 756) hydrogen bonds : angle 3.31760 / 2.36 ( 2268) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 324 time to evaluate : 0.520 Fit side-chains REVERT: A 42 ASP cc_start: 0.9093 (m-30) cc_final: 0.8860 (m-30) REVERT: C 92 ASN cc_start: 0.8991 (m-40) cc_final: 0.8747 (m110) REVERT: E 92 ASN cc_start: 0.8748 (m-40) cc_final: 0.8393 (m110) REVERT: F 18 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7614 (mt-10) REVERT: F 92 ASN cc_start: 0.8820 (m-40) cc_final: 0.8268 (m110) REVERT: G 41 GLU cc_start: 0.7846 (tt0) cc_final: 0.7408 (tt0) REVERT: G 45 ARG cc_start: 0.7895 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: H 87 SER cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (p) REVERT: I 42 ASP cc_start: 0.9103 (m-30) cc_final: 0.8870 (m-30) REVERT: J 92 ASN cc_start: 0.8987 (m-40) cc_final: 0.8741 (m110) REVERT: L 92 ASN cc_start: 0.8746 (m-40) cc_final: 0.8392 (m110) REVERT: N 92 ASN cc_start: 0.8822 (m-40) cc_final: 0.8267 (m110) REVERT: O 41 GLU cc_start: 0.7841 (tt0) cc_final: 0.7389 (tt0) REVERT: O 45 ARG cc_start: 0.7896 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: P 87 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8744 (p) outliers start: 24 outliers final: 12 residues processed: 334 average time/residue: 0.1390 time to fit residues: 63.2027 Evaluate side-chains 330 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 316 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 63 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain K residue 23 ASP Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 63 GLU Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 65 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 103 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 44 GLN F 24 GLN K 44 GLN N 24 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.094272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.083413 restraints weight = 17167.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.086151 restraints weight = 10271.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.088055 restraints weight = 6806.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.089419 restraints weight = 4801.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.090405 restraints weight = 3547.431| |-----------------------------------------------------------------------------| r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 12704 Z= 0.089 Angle : 0.403 4.799 17008 Z= 0.217 Chirality : 0.033 0.103 1888 Planarity : 0.003 0.022 2288 Dihedral : 2.992 15.651 1792 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Rotamer: Outliers : 1.03 % Allowed : 16.99 % Favored : 81.99 % 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: 2.54 (0.22), residues: 1520 helix: 2.24 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.82 (0.36), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 45 PHE 0.003 0.001 PHE L 73 TRP 0.004 0.001 TRP F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (12704) covalent geometry : angle 0.40294 / 0.22 (17008) hydrogen bonds : bond 0.03448 / 2.30 ( 756) hydrogen bonds : angle 2.94825 / 2.09 ( 2268) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 328 time to evaluate : 0.437 Fit side-chains REVERT: A 42 ASP cc_start: 0.9085 (m-30) cc_final: 0.8817 (m-30) REVERT: C 92 ASN cc_start: 0.8956 (m-40) cc_final: 0.8645 (m110) REVERT: E 92 ASN cc_start: 0.8748 (m-40) cc_final: 0.8293 (m-40) REVERT: F 33 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8289 (mm-30) REVERT: F 41 GLU cc_start: 0.7936 (tt0) cc_final: 0.7507 (tt0) REVERT: F 92 ASN cc_start: 0.8781 (m-40) cc_final: 0.8363 (m-40) REVERT: G 41 GLU cc_start: 0.7840 (tt0) cc_final: 0.7300 (tt0) REVERT: G 45 ARG cc_start: 0.7882 (mtm-85) cc_final: 0.7603 (mtm-85) REVERT: I 42 ASP cc_start: 0.9096 (m-30) cc_final: 0.8823 (m-30) REVERT: J 92 ASN cc_start: 0.8955 (m-40) cc_final: 0.8642 (m110) REVERT: L 92 ASN cc_start: 0.8744 (m-40) cc_final: 0.8286 (m-40) REVERT: N 33 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8284 (mm-30) REVERT: N 41 GLU cc_start: 0.7957 (tt0) cc_final: 0.7524 (tt0) REVERT: N 92 ASN cc_start: 0.8780 (m-40) cc_final: 0.8360 (m-40) REVERT: O 41 GLU cc_start: 0.7832 (tt0) cc_final: 0.7279 (tt0) REVERT: O 45 ARG cc_start: 0.7876 (mtm-85) cc_final: 0.7588 (mtm-85) outliers start: 14 outliers final: 12 residues processed: 332 average time/residue: 0.1363 time to fit residues: 61.1853 Evaluate side-chains 322 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 310 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 95 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 92 ASN D 44 GLN F 24 GLN G 57 GLN I 24 GLN I 92 ASN K 44 GLN N 24 GLN O 57 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.091858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.081211 restraints weight = 17125.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.083811 restraints weight = 10326.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.085687 restraints weight = 6909.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.087049 restraints weight = 4894.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.088030 restraints weight = 3619.724| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 12704 Z= 0.131 Angle : 0.453 6.750 17008 Z= 0.237 Chirality : 0.036 0.111 1888 Planarity : 0.003 0.023 2288 Dihedral : 3.068 15.804 1792 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.40 % Allowed : 16.84 % Favored : 81.76 % 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: 2.58 (0.21), residues: 1520 helix: 2.25 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.75 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 90 PHE 0.005 0.001 PHE C 73 TRP 0.005 0.001 TRP F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (12704) covalent geometry : angle 0.45266 / 0.24 (17008) hydrogen bonds : bond 0.03807 / 2.55 ( 756) hydrogen bonds : angle 2.96291 / 2.11 ( 2268) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 319 time to evaluate : 0.520 Fit side-chains REVERT: A 42 ASP cc_start: 0.9069 (m-30) cc_final: 0.8798 (m-30) REVERT: C 92 ASN cc_start: 0.8975 (m-40) cc_final: 0.8631 (m110) REVERT: D 33 GLU cc_start: 0.8348 (mt-10) cc_final: 0.8111 (mt-10) REVERT: E 1 MET cc_start: 0.8791 (mtp) cc_final: 0.8455 (mtm) REVERT: E 92 ASN cc_start: 0.8768 (m-40) cc_final: 0.8230 (m-40) REVERT: F 41 GLU cc_start: 0.7995 (tt0) cc_final: 0.7631 (tt0) REVERT: F 92 ASN cc_start: 0.8825 (m-40) cc_final: 0.8368 (m110) REVERT: G 41 GLU cc_start: 0.7854 (tt0) cc_final: 0.7290 (tt0) REVERT: G 45 ARG cc_start: 0.7949 (mtm-85) cc_final: 0.7580 (mtm-85) REVERT: H 87 SER cc_start: 0.8960 (OUTLIER) cc_final: 0.8747 (p) REVERT: I 42 ASP cc_start: 0.9073 (m-30) cc_final: 0.8804 (m-30) REVERT: J 92 ASN cc_start: 0.8974 (m-40) cc_final: 0.8629 (m110) REVERT: K 33 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8121 (mt-10) REVERT: L 1 MET cc_start: 0.8790 (mtp) cc_final: 0.8460 (mtm) REVERT: L 92 ASN cc_start: 0.8767 (m-40) cc_final: 0.8228 (m-40) REVERT: N 41 GLU cc_start: 0.7998 (tt0) cc_final: 0.7635 (tt0) REVERT: N 92 ASN cc_start: 0.8825 (m-40) cc_final: 0.8363 (m110) REVERT: O 41 GLU cc_start: 0.7846 (tt0) cc_final: 0.7270 (tt0) REVERT: O 45 ARG cc_start: 0.7941 (mtm-85) cc_final: 0.7558 (mtm-85) REVERT: P 87 SER cc_start: 0.8963 (OUTLIER) cc_final: 0.8755 (p) outliers start: 19 outliers final: 17 residues processed: 325 average time/residue: 0.1346 time to fit residues: 59.3762 Evaluate side-chains 334 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 315 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 1 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 111 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 92 ASN D 44 GLN F 24 GLN I 24 GLN I 92 ASN K 44 GLN N 24 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.082229 restraints weight = 17141.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.084960 restraints weight = 10281.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.086891 restraints weight = 6833.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.088249 restraints weight = 4810.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.089262 restraints weight = 3564.176| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 12704 Z= 0.102 Angle : 0.410 4.786 17008 Z= 0.218 Chirality : 0.034 0.108 1888 Planarity : 0.003 0.022 2288 Dihedral : 3.041 15.750 1792 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.69 % Allowed : 16.69 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.78 (0.22), residues: 1520 helix: 2.42 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.81 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 90 PHE 0.003 0.001 PHE I 88 TRP 0.005 0.001 TRP N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (12704) covalent geometry : angle 0.40968 / 0.22 (17008) hydrogen bonds : bond 0.03351 / 2.24 ( 756) hydrogen bonds : angle 2.84518 / 2.02 ( 2268) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 312 time to evaluate : 0.523 Fit side-chains REVERT: A 42 ASP cc_start: 0.9065 (m-30) cc_final: 0.8854 (m-30) REVERT: C 92 ASN cc_start: 0.8967 (m-40) cc_final: 0.8622 (m110) REVERT: D 33 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8116 (mt-10) REVERT: D 88 PHE cc_start: 0.9194 (t80) cc_final: 0.8867 (t80) REVERT: E 1 MET cc_start: 0.8780 (mtp) cc_final: 0.8374 (mtm) REVERT: E 92 ASN cc_start: 0.8750 (m-40) cc_final: 0.8199 (m-40) REVERT: F 41 GLU cc_start: 0.7991 (tt0) cc_final: 0.7633 (tt0) REVERT: F 92 ASN cc_start: 0.8807 (m-40) cc_final: 0.8310 (m110) REVERT: G 41 GLU cc_start: 0.7877 (tt0) cc_final: 0.7174 (tt0) REVERT: G 45 ARG cc_start: 0.7913 (mtm-85) cc_final: 0.7526 (mtm-85) REVERT: H 45 ARG cc_start: 0.7895 (mtt90) cc_final: 0.7364 (mtt90) REVERT: I 42 ASP cc_start: 0.9072 (m-30) cc_final: 0.8862 (m-30) REVERT: J 92 ASN cc_start: 0.8964 (m-40) cc_final: 0.8621 (m110) REVERT: K 33 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8127 (mt-10) REVERT: K 88 PHE cc_start: 0.9196 (t80) cc_final: 0.8868 (t80) REVERT: L 1 MET cc_start: 0.8780 (mtp) cc_final: 0.8379 (mtm) REVERT: L 92 ASN cc_start: 0.8744 (m-40) cc_final: 0.8191 (m-40) REVERT: N 33 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8411 (mm-30) REVERT: N 41 GLU cc_start: 0.7997 (tt0) cc_final: 0.7646 (tt0) REVERT: N 92 ASN cc_start: 0.8804 (m-40) cc_final: 0.8307 (m110) REVERT: O 41 GLU cc_start: 0.7873 (tt0) cc_final: 0.7166 (tt0) REVERT: O 45 ARG cc_start: 0.7905 (mtm-85) cc_final: 0.7519 (mtm-85) REVERT: P 45 ARG cc_start: 0.7889 (mtt90) cc_final: 0.7366 (mtt90) outliers start: 23 outliers final: 17 residues processed: 322 average time/residue: 0.1390 time to fit residues: 60.7586 Evaluate side-chains 321 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 304 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 3 optimal weight: 0.7980 chunk 52 optimal weight: 0.0270 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 134 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 97 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN D 44 GLN F 24 GLN I 24 GLN K 44 GLN N 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.095400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.084671 restraints weight = 16962.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.087428 restraints weight = 10111.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.089332 restraints weight = 6665.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.090703 restraints weight = 4687.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.091683 restraints weight = 3438.178| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 12704 Z= 0.077 Angle : 0.382 4.777 17008 Z= 0.203 Chirality : 0.033 0.104 1888 Planarity : 0.003 0.022 2288 Dihedral : 2.948 15.675 1792 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.69 % Allowed : 17.06 % Favored : 81.25 % 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: 3.09 (0.22), residues: 1520 helix: 2.66 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.82 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 90 PHE 0.002 0.001 PHE I 73 TRP 0.005 0.001 TRP G 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00163 / 0.08 (12704) covalent geometry : angle 0.38202 / 0.20 (17008) hydrogen bonds : bond 0.02825 / 1.88 ( 756) hydrogen bonds : angle 2.70421 / 1.92 ( 2268) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 314 time to evaluate : 0.420 Fit side-chains REVERT: A 42 ASP cc_start: 0.9080 (m-30) cc_final: 0.8752 (m-30) REVERT: A 44 GLN cc_start: 0.9386 (mt0) cc_final: 0.9173 (mt0) REVERT: C 92 ASN cc_start: 0.8963 (m-40) cc_final: 0.8603 (m110) REVERT: D 33 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 88 PHE cc_start: 0.9137 (t80) cc_final: 0.8857 (t80) REVERT: E 92 ASN cc_start: 0.8764 (m-40) cc_final: 0.8206 (m-40) REVERT: F 33 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8330 (mm-30) REVERT: F 41 GLU cc_start: 0.7935 (tt0) cc_final: 0.7672 (tt0) REVERT: F 44 GLN cc_start: 0.9254 (mt0) cc_final: 0.9044 (mt0) REVERT: F 92 ASN cc_start: 0.8743 (m-40) cc_final: 0.8161 (m110) REVERT: G 41 GLU cc_start: 0.7805 (tt0) cc_final: 0.7141 (tt0) REVERT: G 45 ARG cc_start: 0.7833 (mtm-85) cc_final: 0.7476 (mtm-85) REVERT: G 79 ASP cc_start: 0.8422 (m-30) cc_final: 0.8085 (m-30) REVERT: H 41 GLU cc_start: 0.7824 (tt0) cc_final: 0.7399 (tt0) REVERT: H 45 ARG cc_start: 0.7881 (mtt90) cc_final: 0.7307 (mtt90) REVERT: I 42 ASP cc_start: 0.9087 (m-30) cc_final: 0.8764 (m-30) REVERT: I 44 GLN cc_start: 0.9384 (mt0) cc_final: 0.9172 (mt0) REVERT: J 92 ASN cc_start: 0.8959 (m-40) cc_final: 0.8601 (m110) REVERT: K 33 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8032 (mt-10) REVERT: K 88 PHE cc_start: 0.9136 (t80) cc_final: 0.8855 (t80) REVERT: L 92 ASN cc_start: 0.8764 (m-40) cc_final: 0.8204 (m-40) REVERT: N 41 GLU cc_start: 0.7954 (tt0) cc_final: 0.7685 (tt0) REVERT: N 44 GLN cc_start: 0.9252 (mt0) cc_final: 0.9039 (mt0) REVERT: N 92 ASN cc_start: 0.8738 (m-40) cc_final: 0.8155 (m110) REVERT: O 41 GLU cc_start: 0.7797 (tt0) cc_final: 0.7134 (tt0) REVERT: O 45 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7471 (mtm-85) REVERT: O 79 ASP cc_start: 0.8416 (m-30) cc_final: 0.8077 (m-30) REVERT: P 41 GLU cc_start: 0.7818 (tt0) cc_final: 0.7406 (tt0) REVERT: P 45 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7326 (mtt90) outliers start: 23 outliers final: 15 residues processed: 324 average time/residue: 0.1256 time to fit residues: 55.3649 Evaluate side-chains 325 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 310 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 53 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN D 44 GLN F 24 GLN I 24 GLN K 44 GLN N 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.092376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.081647 restraints weight = 17469.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.084297 restraints weight = 10594.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.086215 restraints weight = 7091.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.087507 restraints weight = 5020.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.088485 restraints weight = 3739.971| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 12704 Z= 0.115 Angle : 0.415 4.797 17008 Z= 0.219 Chirality : 0.035 0.109 1888 Planarity : 0.003 0.023 2288 Dihedral : 3.019 15.990 1792 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 1.40 % Allowed : 18.01 % Favored : 80.59 % 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: 2.96 (0.22), residues: 1520 helix: 2.54 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.75 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 7 PHE 0.004 0.001 PHE N 35 TRP 0.005 0.001 TRP G 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (12704) covalent geometry : angle 0.41450 / 0.22 (17008) hydrogen bonds : bond 0.03364 / 2.24 ( 756) hydrogen bonds : angle 2.80476 / 2.00 ( 2268) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 312 time to evaluate : 0.522 Fit side-chains REVERT: A 42 ASP cc_start: 0.9078 (m-30) cc_final: 0.8754 (m-30) REVERT: C 92 ASN cc_start: 0.8983 (m-40) cc_final: 0.8616 (m110) REVERT: D 88 PHE cc_start: 0.9159 (t80) cc_final: 0.8871 (t80) REVERT: E 92 ASN cc_start: 0.8726 (m-40) cc_final: 0.8170 (m-40) REVERT: F 33 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8340 (mm-30) REVERT: F 41 GLU cc_start: 0.7959 (tt0) cc_final: 0.7674 (tt0) REVERT: F 44 GLN cc_start: 0.9257 (mt0) cc_final: 0.9004 (mt0) REVERT: F 92 ASN cc_start: 0.8768 (m-40) cc_final: 0.8227 (m110) REVERT: G 41 GLU cc_start: 0.7813 (tt0) cc_final: 0.7111 (tt0) REVERT: G 45 ARG cc_start: 0.7863 (mtm-85) cc_final: 0.7477 (mtm-85) REVERT: G 79 ASP cc_start: 0.8404 (m-30) cc_final: 0.8070 (m-30) REVERT: H 41 GLU cc_start: 0.7798 (tt0) cc_final: 0.7590 (tt0) REVERT: I 42 ASP cc_start: 0.9085 (m-30) cc_final: 0.8765 (m-30) REVERT: J 92 ASN cc_start: 0.8980 (m-40) cc_final: 0.8612 (m110) REVERT: K 88 PHE cc_start: 0.9161 (t80) cc_final: 0.8875 (t80) REVERT: L 92 ASN cc_start: 0.8729 (m-40) cc_final: 0.8172 (m-40) REVERT: N 41 GLU cc_start: 0.7960 (tt0) cc_final: 0.7687 (tt0) REVERT: N 44 GLN cc_start: 0.9253 (mt0) cc_final: 0.9000 (mt0) REVERT: N 92 ASN cc_start: 0.8765 (m-40) cc_final: 0.8223 (m110) REVERT: O 41 GLU cc_start: 0.7806 (tt0) cc_final: 0.7109 (tt0) REVERT: O 45 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: O 79 ASP cc_start: 0.8396 (m-30) cc_final: 0.8064 (m-30) outliers start: 19 outliers final: 19 residues processed: 320 average time/residue: 0.1341 time to fit residues: 58.6252 Evaluate side-chains 325 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 70 optimal weight: 0.8980 chunk 128 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN D 44 GLN F 24 GLN I 24 GLN K 44 GLN N 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.104018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.093466 restraints weight = 16598.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.096226 restraints weight = 9825.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098098 restraints weight = 6467.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.099430 restraints weight = 4555.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100358 restraints weight = 3357.896| |-----------------------------------------------------------------------------| r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12704 Z= 0.103 Angle : 0.415 5.259 17008 Z= 0.217 Chirality : 0.034 0.107 1888 Planarity : 0.003 0.022 2288 Dihedral : 3.014 16.083 1792 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.69 % Allowed : 17.72 % Favored : 80.59 % 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: 2.97 (0.22), residues: 1520 helix: 2.56 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG N 7 PHE 0.003 0.001 PHE C 73 TRP 0.005 0.001 TRP N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.10 (12704) covalent geometry : angle 0.41498 / 0.22 (17008) hydrogen bonds : bond 0.03200 / 2.13 ( 756) hydrogen bonds : angle 2.80527 / 1.99 ( 2268) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 310 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9085 (m-30) cc_final: 0.8764 (m-30) REVERT: C 92 ASN cc_start: 0.8985 (m-40) cc_final: 0.8623 (m110) REVERT: D 88 PHE cc_start: 0.9104 (t80) cc_final: 0.8805 (t80) REVERT: E 92 ASN cc_start: 0.8714 (m-40) cc_final: 0.8153 (m-40) REVERT: F 33 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8357 (mm-30) REVERT: F 41 GLU cc_start: 0.7977 (tt0) cc_final: 0.7669 (tt0) REVERT: F 44 GLN cc_start: 0.9234 (mt0) cc_final: 0.8988 (mt0) REVERT: F 92 ASN cc_start: 0.8764 (m-40) cc_final: 0.8215 (m110) REVERT: G 41 GLU cc_start: 0.7818 (tt0) cc_final: 0.7120 (tt0) REVERT: G 45 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: H 45 ARG cc_start: 0.7937 (mtt90) cc_final: 0.7486 (mtt90) REVERT: I 42 ASP cc_start: 0.9091 (m-30) cc_final: 0.8776 (m-30) REVERT: J 92 ASN cc_start: 0.8984 (m-40) cc_final: 0.8621 (m110) REVERT: K 88 PHE cc_start: 0.9104 (t80) cc_final: 0.8807 (t80) REVERT: L 92 ASN cc_start: 0.8708 (m-40) cc_final: 0.8147 (m-40) REVERT: N 33 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8363 (mm-30) REVERT: N 41 GLU cc_start: 0.7978 (tt0) cc_final: 0.7689 (tt0) REVERT: N 44 GLN cc_start: 0.9230 (mt0) cc_final: 0.8982 (mt0) REVERT: N 92 ASN cc_start: 0.8764 (m-40) cc_final: 0.8215 (m110) REVERT: O 41 GLU cc_start: 0.7815 (tt0) cc_final: 0.7104 (tt0) REVERT: O 45 ARG cc_start: 0.7871 (mtm-85) cc_final: 0.7468 (mtm-85) REVERT: P 41 GLU cc_start: 0.7862 (tt0) cc_final: 0.7625 (tt0) REVERT: P 45 ARG cc_start: 0.7921 (mtt90) cc_final: 0.7564 (mtt90) outliers start: 23 outliers final: 19 residues processed: 317 average time/residue: 0.1315 time to fit residues: 56.9548 Evaluate side-chains 325 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 306 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain F residue 31 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 3 GLU Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain M residue 23 ASP Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 139 optimal weight: 0.0270 chunk 86 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 0.0370 chunk 134 optimal weight: 0.0040 chunk 88 optimal weight: 0.6980 chunk 133 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.2928 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN D 44 GLN I 24 GLN K 44 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.096014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.085590 restraints weight = 17318.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.088192 restraints weight = 10570.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.090078 restraints weight = 7092.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.091388 restraints weight = 5021.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.092349 restraints weight = 3719.932| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 12704 Z= 0.071 Angle : 0.379 4.762 17008 Z= 0.200 Chirality : 0.032 0.101 1888 Planarity : 0.003 0.021 2288 Dihedral : 2.935 17.293 1792 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.10 % Allowed : 18.01 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.22 (0.22), residues: 1520 helix: 2.76 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.84 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 7 PHE 0.003 0.001 PHE M 88 TRP 0.005 0.001 TRP N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00141 / 0.07 (12704) covalent geometry : angle 0.37943 / 0.20 (17008) hydrogen bonds : bond 0.02597 / 1.73 ( 756) hydrogen bonds : angle 2.65114 / 1.87 ( 2268) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 309 time to evaluate : 0.436 Fit side-chains REVERT: A 44 GLN cc_start: 0.9335 (mt0) cc_final: 0.9111 (mt0) REVERT: C 92 ASN cc_start: 0.8992 (m-40) cc_final: 0.8640 (m110) REVERT: D 88 PHE cc_start: 0.9041 (t80) cc_final: 0.8610 (t80) REVERT: D 92 ASN cc_start: 0.8727 (m-40) cc_final: 0.8148 (m-40) REVERT: E 84 MET cc_start: 0.6767 (mmt) cc_final: 0.6508 (mpp) REVERT: E 92 ASN cc_start: 0.8780 (m-40) cc_final: 0.8188 (m-40) REVERT: F 41 GLU cc_start: 0.7947 (tt0) cc_final: 0.7662 (tt0) REVERT: F 44 GLN cc_start: 0.9223 (mt0) cc_final: 0.8990 (mt0) REVERT: F 78 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: F 92 ASN cc_start: 0.8712 (m-40) cc_final: 0.8093 (m110) REVERT: G 41 GLU cc_start: 0.7808 (tt0) cc_final: 0.7148 (tt0) REVERT: G 45 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7660 (mtm-85) REVERT: H 41 GLU cc_start: 0.7829 (tt0) cc_final: 0.7439 (tt0) REVERT: H 45 ARG cc_start: 0.7908 (mtt90) cc_final: 0.7493 (mtt90) REVERT: I 44 GLN cc_start: 0.9329 (mt0) cc_final: 0.9103 (mt0) REVERT: J 92 ASN cc_start: 0.8992 (m-40) cc_final: 0.8641 (m110) REVERT: K 88 PHE cc_start: 0.9047 (t80) cc_final: 0.8614 (t80) REVERT: K 92 ASN cc_start: 0.8726 (m-40) cc_final: 0.8145 (m-40) REVERT: L 84 MET cc_start: 0.6775 (mmt) cc_final: 0.6500 (mpp) REVERT: L 92 ASN cc_start: 0.8772 (m-40) cc_final: 0.8181 (m-40) REVERT: N 33 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8327 (mm-30) REVERT: N 41 GLU cc_start: 0.7967 (tt0) cc_final: 0.7687 (tt0) REVERT: N 44 GLN cc_start: 0.9242 (mt0) cc_final: 0.9001 (mt0) REVERT: N 78 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: N 92 ASN cc_start: 0.8709 (m-40) cc_final: 0.8089 (m110) REVERT: O 41 GLU cc_start: 0.7806 (tt0) cc_final: 0.7148 (tt0) REVERT: O 45 ARG cc_start: 0.7897 (mtm-85) cc_final: 0.7669 (mtm-85) REVERT: P 41 GLU cc_start: 0.7858 (tt0) cc_final: 0.6909 (tt0) REVERT: P 45 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7224 (mtt180) outliers start: 15 outliers final: 13 residues processed: 316 average time/residue: 0.1340 time to fit residues: 57.5061 Evaluate side-chains 316 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 301 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain F residue 78 GLU Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain K residue 45 ARG Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 78 GLU Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 88 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN C 44 GLN I 24 GLN J 44 GLN N 24 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.089550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.079429 restraints weight = 17736.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.081918 restraints weight = 10902.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.083691 restraints weight = 7345.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.084926 restraints weight = 5249.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.085862 restraints weight = 3930.816| |-----------------------------------------------------------------------------| r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 12704 Z= 0.180 Angle : 0.490 4.854 17008 Z= 0.256 Chirality : 0.038 0.117 1888 Planarity : 0.004 0.025 2288 Dihedral : 3.221 16.201 1792 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Rotamer: Outliers : 1.54 % Allowed : 17.79 % Favored : 80.66 % 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: 2.71 (0.21), residues: 1520 helix: 2.35 (0.14), residues: 1232 sheet: None (None), residues: 0 loop : -0.73 (0.35), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 93 PHE 0.006 0.001 PHE C 73 TRP 0.006 0.001 TRP G 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.18 (12704) covalent geometry : angle 0.48958 / 0.26 (17008) hydrogen bonds : bond 0.04072 / 2.71 ( 756) hydrogen bonds : angle 2.99882 / 2.14 ( 2268) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 322 time to evaluate : 0.500 Fit side-chains REVERT: A 42 ASP cc_start: 0.9110 (m-30) cc_final: 0.8807 (m-30) REVERT: C 92 ASN cc_start: 0.8994 (m-40) cc_final: 0.8682 (m110) REVERT: D 88 PHE cc_start: 0.9162 (t80) cc_final: 0.8856 (t80) REVERT: E 92 ASN cc_start: 0.8785 (m-40) cc_final: 0.8206 (m-40) REVERT: F 44 GLN cc_start: 0.9248 (mt0) cc_final: 0.9002 (mt0) REVERT: F 91 THR cc_start: 0.8937 (m) cc_final: 0.8481 (p) REVERT: F 92 ASN cc_start: 0.8826 (m-40) cc_final: 0.8192 (m110) REVERT: G 41 GLU cc_start: 0.7844 (tt0) cc_final: 0.7177 (tt0) REVERT: G 45 ARG cc_start: 0.7923 (mtm-85) cc_final: 0.7500 (mtm-85) REVERT: H 45 ARG cc_start: 0.7958 (mtt90) cc_final: 0.7464 (mtt90) REVERT: I 42 ASP cc_start: 0.9113 (m-30) cc_final: 0.8817 (m-30) REVERT: J 92 ASN cc_start: 0.9011 (m-40) cc_final: 0.8680 (m110) REVERT: K 88 PHE cc_start: 0.9166 (t80) cc_final: 0.8858 (t80) REVERT: L 92 ASN cc_start: 0.8785 (m-40) cc_final: 0.8206 (m-40) REVERT: N 33 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8390 (mm-30) REVERT: N 44 GLN cc_start: 0.9249 (mt0) cc_final: 0.8997 (mt0) REVERT: N 91 THR cc_start: 0.8938 (m) cc_final: 0.8479 (p) REVERT: N 92 ASN cc_start: 0.8823 (m-40) cc_final: 0.8187 (m110) REVERT: O 41 GLU cc_start: 0.7842 (tt0) cc_final: 0.7172 (tt0) REVERT: O 45 ARG cc_start: 0.7921 (mtm-85) cc_final: 0.7497 (mtm-85) REVERT: P 45 ARG cc_start: 0.7947 (mtt90) cc_final: 0.7541 (mtt90) outliers start: 21 outliers final: 16 residues processed: 331 average time/residue: 0.1356 time to fit residues: 61.3503 Evaluate side-chains 334 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 318 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain C residue 31 SER Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain H residue 23 ASP Chi-restraints excluded: chain J residue 31 SER Chi-restraints excluded: chain K residue 87 SER Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain M residue 31 SER Chi-restraints excluded: chain N residue 31 SER Chi-restraints excluded: chain N residue 84 MET Chi-restraints excluded: chain O residue 39 MET Chi-restraints excluded: chain P residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 0 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN A 92 ASN I 24 GLN I 92 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.093161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.082482 restraints weight = 17390.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.085159 restraints weight = 10497.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.087075 restraints weight = 6957.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.088407 restraints weight = 4939.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.089368 restraints weight = 3656.752| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12704 Z= 0.096 Angle : 0.415 4.784 17008 Z= 0.219 Chirality : 0.034 0.106 1888 Planarity : 0.003 0.021 2288 Dihedral : 3.081 17.715 1792 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.03 % Allowed : 18.24 % Favored : 80.74 % 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: 2.99 (0.22), residues: 1520 helix: 2.58 (0.15), residues: 1232 sheet: None (None), residues: 0 loop : -0.80 (0.34), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 93 PHE 0.004 0.001 PHE I 88 TRP 0.006 0.001 TRP N 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (12704) covalent geometry : angle 0.41526 / 0.22 (17008) hydrogen bonds : bond 0.03159 / 2.10 ( 756) hydrogen bonds : angle 2.81746 / 2.00 ( 2268) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2008.33 seconds wall clock time: 35 minutes 16.24 seconds (2116.24 seconds total)